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science.drug_combo_extraction_re
|
science.drug_combo_extraction_re.720
|
[
{
"role": "user",
"content": "You will be shown a paragraph from a biomedical research article. Your task is to extract all drug combinations appearing in a specific sentence within in the paragraph. Each drug combination should be assigned to one of the following three categories:\n\n- POS: Indicates a positive interaction between the drugs in the combination; for instance, drugs that have an additive or synergistic effect.\n- NEG: Indicates a negative interaction between the drugs in the combination; for instance, combining these drugs might result in adverse side effects, or might reduce their efficacy.\n- COMB: Indicates that the drugs are given in combination, but the type of interaction between the drugs cannot be determined based on the provided context.\n\nPlease format your answer as a json array. Each entry in the array should itself be an array formatted as [<drug_1>, <drug_2>, ..., <drug_n>, <category>] where <category> is one of the three categories listed above and <drug_1>, ..., <drug_n> are drug names copied verbatim from the input sentence. Different combinations may involve different numbers of drugs; in other words, the `n` in <drug_n> may vary.\n\nAs an example, the following output describes two extracted drug combinations; one between two drugs, and one between three drugs:\n\n[[\"artesunate\", \"artemether\", \"COMB\"], [\"Nifedipine\", \"Labetalol\", \"Prazosin\", \"POS\"]]\n\nThe paragraph and specific sentence are below. You should only extract relationships expressed in the specific sentence; the paragraph is provided for context.\n\nIn your output, return only the json array and no other text. If no drug combinations appear, return an empty array `[]`.\n\nparagraph: Combined therapy : what does acamprosate and naltrexone combination tell us ? Relapse prevention treatment with both acamprosate and naltrexone has been shown to be efficacious in the treatment of alcoholism. Whereas both compounds act pharmacologically differently, there is up to now only limited evidence as to whether combined treatment is efficacious and pharmacologically safe. It remains to be answered whether data justify the combination of both drugs in clinical practice. ### methods Review of the three pre-clinical and four clinical studies that have been published to date on either combined tolerability or efficacy. ### results Data available up to now show no occurrence of severe adverse events during combined treatment. Diarrhoea and nausea were shown to be the most significant side-effects. Whereas pre-clinical studies regarding efficacy of combined treatment are not yet conclusive, clinical data show the superiority of combined treatment compared with both placebo and acamprosate monotherapy. The synergistic effect of combined treatment remained after 12 weeks of drug-free follow-up. ### conclusions The combination of acamprosate with naltrexone in a clinical sample seems to be efficacious and safe. Numerous alcohol dependent patients could benefit, particularly those that responded insufficiently on monotherapeutic treatment with either acamprosate or naltrexone.\n\nsentence: Combined therapy : what does acamprosate and naltrexone combination tell us ?"
},
{
"role": "assistant",
"content": "[[\"acamprosate\", \"naltrexone\", \"POS\"]]"
}
] |
science.ncbi_ner
|
science.ncbi_ner.162
|
[
{
"role": "user",
"content": "You will be shown an abstract from a biomedical research paper. Given this abstract, your task is to extract all unique entities of the following types: [\"Disease\"].\n\nPlease return the output as a JSON object of the format: {\"Disease\" : [\"COVID-19\", ...]}. The keys should be entity types and values should be lists of extracted entities belonging to the corresponding type. If you cannot find entities belonging to a specific type, the value should be [].\n\nOnly output the JSON object and do not include any additional text.\n\nAbstract:\n\nInvestigation of thermoregulatory characteristics in patients with Prader-Willi syndrome. A survey instrument is used to assess temperature regulation characteristics in children with Prader-Willi syndrome (PWS) compared to 3 control groups sibs of PWS patients (SIB), neurodevelopmentally handicapped children (ND), and age and gender matched well children (WC). Significant differences were found between PWS patients, SIB controls, and WC controls in the prevalence of febrile convulsions, fever-associated symptoms, and temperature less than 94 degrees F. No differences were noted in any variable between the PWS patients and the ND controls, suggesting that these abnormalities are not unique to PWS, but can occur in any neurodevelopmentally handicapped individual, further suggesting these do not necessarily reflect syndrome-specific hypothalamic abnormalities.."
},
{
"role": "assistant",
"content": "{\"Disease\": [\"hypothalamic abnormalities\", \"neurodevelopmentally handicapped\", \"Prader-Willi syndrome\", \"PWS\"]}"
}
] |
science.scientific_papers_summarization_single_doc_pubmed
|
science.scientific_papers_summarization_single_doc_pubmed.88307
|
[
{
"role": "user",
"content": "You will be presented with the full text of a biomedical research paper. Please write an abstract for this paper. Your response should include the abstract and no additional text.\n\nPaper text:\ncarcinomas of accessory mammary tissue account for 0.3% of all breast cancers , 5% of which are within a supernumerary breast . due to its rarity and the low index of clinical suspicion ,\nthe following case report describes a case of ectopic breast carcinoma within a supernumerary breast below the inframammary fold .\nwe describe the mode of presentation , diagnosis and treatment with reference to the available literature .\na 48-year - old female presented with a 6-week history of a tender mass inferior to the right inframammary fold following trauma .\nantibiotics were initiated for presumed infection ; however , the mass persisted , prompting surgical referral .\nclinical examination demonstrated a 2 1 cm superficial mass , with adjacent accessory nipple .\nan ultrasound confirmed a 15-mm hypo - echoic mass consistent with a sebaceous cyst ; however , a core biopsy confirmed a grade 2 invasive ductal carcinoma ( idc ) , strongly positive for oestrogen and progesterone receptors ( allred scores of er 7 , pr7 ) .\nmagnetic resonance imaging ( mri ) confirmed a 22 12 mm spiculated ( fig . \n1 ) mass inferior to the right inframammary fold deep to the accessory nipple , compatible with a supernumerary breast .\nthere was evidence of overlying skin infiltration , with a clear margin of normal tissue between the tumour and costal fascia .\nshe proceeded to a wide local excision of the entire accessory breast , nipple - areolar complex and an additional ellipse of skin .\nthe deep margin was 2 mm , but the anterior subcutaneous margin was 0 mm .\nthe patient underwent a ct planning scan to assess the depth of tissue to be treated .\na 10 7 cm rectangular electron field was applied to the tumour bed incorporating the excision scar .\nthe patient was then treated with 9 megavoltage ( mev ) electrons to a dose of 40 gy in 15 fractions , over 21 days receiving 2.67 gy per fraction .\nthe dmax treatment depth was 12 mm , with the 90% isodose at 18 mm . the ipsilateral breast was not included in the treatment field as the tumour was in a separate accessory breast which had been fully excised .\ntwelve weeks post - radiotherapy , she was in remission and all acute radiotherapy reaction had subsided .\n95% of ectopic breast cancers occur in aberrant breast tissue ( islands of unorganized secretory systems without any relationship to the overlying skin ) compared with just 5% in a supernumerary breast ( an organized ductal system which is related to the overlying skin , via a separate nipple \nthey can present anywhere along the primitive milk ( galactic ) line , most commonly the axilla ( 6070% ) and infrequently on the thorax ( 510% in the inframammary region as described in our case ) and rarely the vulva [ 1 , 3 ] .\nthe most common histological type is idc , 5079% , with 9.5% medullary and lobular carcinomas [ 3 , 4 ] .\nectopic breast cancers are not detected at routine mammographic screening due to their location and may not present until signs and symptoms develop , including rapid growth of ectopic tissue , localized pain or inflammation and progressively growing nodules [ 1 , 7 ] .\nthe differential diagnosis of ectopic breast carcinoma is broad : lipoma , lymphadenopathy , follicular cysts , fibromas , tuberculosis , seborrheic keratosis and intra - dermal nevi .\nappropriate imaging ( including both breasts ) therefore needs to supplement clinical examination , with biopsy considered even if radiological findings are at variance with clinical presentation [ 1 , 4 ] .\nmri allows the evaluation of tumour extent and the relationship with normal breast issue prior to surgical intervention and is recommended to aid diagnosis and staging in patients presenting with a mass in the galactic line .\ntreatment regimes in the literature follow the standardized guidelines for breast cancer [ 2 , 3 , 7 , 9 ] .\ninitially , ipsilateral mastectomy of the adjacent breast was recommended ; however , this provides no additional benefit and is no longer advocated .\na review of the literature offers no formal guidance on radiotherapy dose , fractionation and treatment fields in this setting .\ntreatment fields have ranged from incorporating the tumour bed alone to inclusion of the ipsilateral uninvolved breast , axilla and supraclavicular fossa , even in the absence of nodal metastases [ 5 , 7 , 8 ] .\nour team made the decision to treat the tumour bed alone , as irradiation of the ipsilateral breast or axilla in the absence of disease was unlikely to improve local control further , and would contribute to increased toxicity , particularly cosmetic .\nelectron therapy allowed the treatment of the tumour bed effectively to the desired depth , without undue toxicity , although the superior margin of the field overlapped with the inferior part of the ipsilateral breast ( see fig . 2 ) .\ndoses used in the literature range from 50 to 66 gy in 2-gy fractions [ 7 , 8 ] .\nwe delivered a dose of 40 gy in 15 fractions : a standardized dose for breast radiotherapy in the uk following the results of the start b trial . . \n\nfigure 2:clinical photograph illustrating the acute radiation reaction on patient 's skin at completion of her electron beam therapy . clinical photograph illustrating the acute radiation reaction on patient 's skin at completion of her electron beam therapy .\nhowever , due to its late presentation , delay in diagnosis and difficulty in screening , both lymph node and distant metastasis are more prevalent at diagnosis which impacts on prognosis [ 5 , 10 ] . additionally , due to the small size of the gland early infiltration of the skin and chest wall is a feature .\nthis case describes a rare diagnosis of an inframammary ectopic breast carcinoma treated with wide local excision , adjuvant radiotherapy and hormone therapy .\nthis case highlights the importance of a high index of suspicion for investigating masses or ectopic breast tissue along the galactic line , and the importance of mri staging prior to considering surgical and oncological options .\nelectron therapy can be delivered safely , reducing treatment field size and subsequent late cosmetic effects .\nwritten informed consent was obtained from the patient for publication of this case report and case series and accompanying images .\na copy of the written consent is available for review by the editor - in - chief of this journal on request ."
},
{
"role": "assistant",
"content": "accessory mammary tissue occurs in 0.26% of women , and is under the same hormonal influences as breast tissue , potentially undergoing malignant transformation . \n carcinomas of accessory mammary tissue account for 0.3% of breast cancers , 5% of which are within a supernumerary breast . due to its rarity and the low index of clinical suspicion \n , it is often diagnosed at a later stage compared with breast cancer . \n reports of carcinoma developing in a supernumerary breast are rare . \n we describe a case of a 48-year - old woman , presenting with ectopic breast carcinoma within a supernumerary breast below the inframammary fold . \n we describe the mode of presentation , diagnosis and treatment with reference to the available literature . \n the radiotherapy treatment plan is discussed in detail to provide reference for future cases as the available literature offers no formal guidance on radiotherapy dose , fractionation or treatment field ."
}
] |
science.chia_ner
|
science.chia_ner.1589
|
[
{
"role": "user",
"content": "You will be shown inclusion or exclusion criteria for a clinical trial. Given these criteria, your task is to extract all unique entities of the following types: [\"Observation\", \"Condition\", \"Procedure\", \"Drug\", \"Temporal\", \"Multiplier\", \"Qualifier\", \"Negation\", \"ReferencePoint\", \"Scope\", \"Value\", \"Mood\", \"Device\", \"Visit\", \"Measurement\", \"Person\"].\n\nPlease return the output as a JSON object of the format: {\"Condition\" : [\"breast cancer\", ...], \"Device\" : [\"ports\", ...], \"Drug\" : [\"Atenolol\", ...], \"Measurement\" : [\"blood pressure\", ...], \"Mood\" : [\"suspected\", ...], \"Multiplier\" : [\"more than two\", ...], \"Negation\" : [\"no\", ...], \"Observation\" : [\"history\", ...], \"Person\" : [\"male\", ...], \"Procedure\" : [\"surgery\", ...], \"Qualifier\" : [\"severe\", ...], \"ReferencePoint\" : [\"enrollment\", ...], \"Scope\" : [\"infection\", ...], \"Temporal\" : [\"one day\", ...], \"Value\" : [\"50%\", ...], \"Visit\" : [\"ICU\", ...]}. The keys should be entity types and values should be lists of extracted entities belonging to the corresponding type. If you cannot find entities belonging to a specific type, the value should be [].\n\nOnly output the JSON object and do not include any additional text.\n\nAbstract:\n\nSystemically healthy adults.\nMinimum of 24 permanent teeth.\nNo gingivitis (Community Periodontal Index score = 0).\nNo periodontitis (Community Periodontal Index score = 0).\nAbsence of untreated caries."
},
{
"role": "assistant",
"content": "{\"Condition\": [\"caries\", \"gingivitis\", \"periodontitis\", \"healthy\"], \"Device\": [], \"Drug\": [], \"Measurement\": [\"Community Periodontal Index score\"], \"Mood\": [], \"Multiplier\": [\"Minimum of 24\"], \"Negation\": [\"Absence\", \"No\"], \"Observation\": [\"permanent teeth\"], \"Person\": [\"adults\"], \"Procedure\": [], \"Qualifier\": [\"Systemically\", \"untreated\"], \"ReferencePoint\": [], \"Scope\": [\"No gingivitis\", \"No periodontitis\", \"Community Periodontal Index score = 0\"], \"Temporal\": [], \"Value\": [\"= 0\"], \"Visit\": []}"
}
] |
science.qasper_extractive_qa
|
science.qasper_extractive_qa.384.1
|
[
{
"role": "user",
"content": "You will be shown sections from a scientific research paper, together with a question about the paper. Your task is to answer the question based on the contents of the paper. Your response should be a `json` object with two fields:\n\n\"answer\": An array of strings extracted directly from the paper which, collectively, answer the question.\n\"evidence\": An array of strings. Each should be an excerpt from the paper, in which one or more of the extracted answers can be found.\n\nFor instance, for the question \"What baselines did the authors compare against?\", a sample response might be:\n\n{\n \"answer\": [\"BERT\", \"RoBERTa\"],\n \"evidence\": [\"In our experiments, we compare the performance of our model against BERT and RoBERTa.\"]\n}\n\nDo not include any text in your response other than the json.\n\nIf the question is unanswerable given the provided excerpts, respond with the single word \"null\".\n\nPaper: Multimodal Differential Network for Visual Question Generation\n\nGenerating natural questions from an image is a semantic task that requires using visual and language modality to learn multimodal representations. Images can have multiple visual and language contexts that are relevant for generating questions namely places, captions, and tags. In this paper, we propose the use of exemplars for obtaining the relevant context. We obtain this by using a Multimodal Differential Network to produce natural and engaging questions. The generated questions show a remarkable similarity to the natural questions as validated by a human study. Further, we observe that the proposed approach substantially improves over state-of-the-art benchmarks on the quantitative metrics (BLEU, METEOR, ROUGE, and CIDEr).\n\nMethod\nThe task in visual question generation (VQG) is to generate a natural language question INLINEFORM0 , for an image INLINEFORM1 . We consider a set of pre-generated context INLINEFORM2 from image INLINEFORM3 . We maximize the conditional probability of generated question given image and context as follows: DISPLAYFORM0 \nwhere INLINEFORM0 is a vector for all possible parameters of our model. INLINEFORM1 is the ground truth question. The log probability for the question is calculated by using joint probability over INLINEFORM2 with the help of chain rule. For a particular question, the above term is obtained as: INLINEFORM3 \nwhere INLINEFORM0 is length of the sequence, and INLINEFORM1 is the INLINEFORM2 word of the question. We have removed INLINEFORM3 for simplicity.\nOur method is based on a sequence to sequence network BIBREF38 , BIBREF12 , BIBREF39 . The sequence to sequence network has a text sequence as input and output. In our method, we take an image as input and generate a natural question as output. The architecture for our model is shown in Figure FIGREF4 . Our model contains three main modules, (a) Representation Module that extracts multimodal features (b) Mixture Module that fuses the multimodal representation and (c) Decoder that generates question using an LSTM-based language model.\nDuring inference, we sample a question word INLINEFORM0 from the softmax distribution and continue sampling until the end token or maximum length for the question is reached. We experimented with both sampling and argmax and found out that argmax works better. This result is provided in the supplementary material.\n\nInference\nWe made use of the 1250 validation images to tune the hyperparameters and are providing the results on test set of VQG-COCO dataset. During inference, We use the Representation module to find the embeddings for the image and ground truth caption without using the supporting and contrasting exemplars. The mixture module provides the joint representation of the target image and ground truth caption. Finally, the decoder takes in the joint features and generates the question. We also experimented with the captions generated by an Image-Captioning network BIBREF13 for VQG-COCO dataset and the result for that and training details are present in the supplementary material.\n\nExperiments\nWe evaluate our proposed MDN method in the following ways: First, we evaluate it against other variants described in section SECREF19 and SECREF10 . Second, we further compare our network with state-of-the-art methods for VQA 1.0 and VQG-COCO dataset. We perform a user study to gauge human opinion on naturalness of the generated question and analyze the word statistics in Figure FIGREF22 . This is an important test as humans are the best deciders of naturalness. We further consider the statistical significance for the various ablations as well as the state-of-the-art models. The quantitative evaluation is conducted using standard metrics like BLEU BIBREF46 , METEOR BIBREF47 , ROUGE BIBREF48 , CIDEr BIBREF49 . Although these metrics have not been shown to correlate with `naturalness' of the question these still provide a reasonable quantitative measure for comparison. Here we only provide the BLEU1 scores, but the remaining BLEU-n metric scores are present in the supplementary. We observe that the proposed MDN provides improved embeddings to the decoder. We believe that these embeddings capture instance specific differential information that helps in guiding the question generation. Details regarding the metrics are given in the supplementary material.\n\nQuestion: How/where are the natural question generated?"
},
{
"role": "assistant",
"content": "{\"answer\": [\"Decoder that generates question using an LSTM-based language model\"], \"evidence\": [\"Our method is based on a sequence to sequence network BIBREF38 , BIBREF12 , BIBREF39 . The sequence to sequence network has a text sequence as input and output. In our method, we take an image as input and generate a natural question as output. The architecture for our model is shown in Figure FIGREF4 . Our model contains three main modules, (a) Representation Module that extracts multimodal features (b) Mixture Module that fuses the multimodal representation and (c) Decoder that generates question using an LSTM-based language model.\"]}"
}
] |
science.pico_ner
|
science.pico_ner.562
|
[
{
"role": "user",
"content": "You will be shown an abstract from a biomedical research paper. Given this abstract, your task is to extract all unique entities of the following types: [\"Outcome\", \"Participant\", \"Intervention\"].\n\nPlease return the output as a JSON object of the format: {\"Participant\" : [\"patients with COPD\", ...], \"Intervention\" : [\"Atenolol\", ...], \"Outcome\" : [\"blood pressure\", ...]}. The keys should be entity types and values should be lists of extracted entities belonging to the corresponding type. If you cannot find entities belonging to a specific type, the value should be [].\n\nOnly output the JSON object and do not include any additional text.\n\nAbstract:\n\nEffects of oral Lactobacillus GG on enteric microflora in low-birth-weight neonates . BACKGROUND Colonization patterns , especially by anaerobic flora , may play an important role in neonatal gut function . Probiotics could affect disease risk either directly through colonization or indirectly by promoting changes in gut microbial ecology . METHODS To study the ability of Lactobacillus GG ( LGG ) to colonize the neonatal gut and modify its microbial ecology , a prospective , randomized study was performed in 71 preterm infants of less than 2000 g birth weight . Infants less than 1500 g ( 24 treated , 15 control ) received 10 ( 9 ) LGG orally twice daily for 21 days . Those infants weighing 1500 to 1999 g ( 23 treated , 9 control ) were treated for 8 days . Stools were collected before treatment and on day 7 to 8 ( and day 14 and 21 , in the infants weighing less than 1500 g ) for quantitative aerobic and anaerobic cultures . RESULTS Colonization with LGG occurred in 5 of 24 ( 21 % ) infants who weighed less than 1500 g versus 11 of 23 ( 47 % ) in larger infants . Colonization was limited to infants who were not on antibiotics within 7 days of treatment with LGG . There was a paucity of bacterial species at baseline , although larger infants had more bacterial species ( 1.59 +/- 0.13 ( SEM ) vs 1.11 +/- 0.12 ; P < 0.03 ) and higher mean log colony forming units ( CFU ) ( 8.79 +/- 0.43 vs 7.22 +/- 0.63 ; P < 0.05 ) compared with infants weighing less than 1500 g LGG . Treatment in infants weighing less than 1500 g resulted in a significant increase in species number by day 7 , with further increases by day 21 . This increase was mainly the result of increased Gram ( + ) and anaerobic species . No difference in species number was noted in controls . Mean log CFU of Gram ( - ) bacteria did not change in treated infants weighing less than 1500 g. However , Gram ( + ) mean log CFU showed a significant increase on day 21 ( 6.1 +/- 0.9 ) compared with day 0 ( 3.5 +/- 0.9 ) ( P < 0.05 ) . No significant changes in species number or quantitative counts were noted after LGG treatment in the infants weighing 1500 to 1999 g LGG was well tolerated in all infants . CONCLUSION The neonatal response to a probiotic preparation is dependent on gestational and post-natal age and prior antibiotic exposure . Although LGG is a relatively poor colonizer in infants , especially those infants weighing less than 1500 g at birth , it does appear to affect neonatal intestinal colonization patterns ."
},
{
"role": "assistant",
"content": "{\"Intervention\": [\"oral Lactobacillus GG\", \"antibiotics\", \"LGG\", \"Lactobacillus GG ( LGG )\"], \"Outcome\": [\"Mean log CFU of Gram ( - ) bacteria\", \"neonatal response to a probiotic preparation\", \"mean log colony forming units ( CFU )\", \"enteric microflora\", \"increase in species number by day 7 , with further increases by day 21 .\", \"Gram ( + ) mean log CFU\", \"Colonization\", \"bacterial species\", \"species number\", \"Colonization with LGG occurred\", \"increased Gram ( + ) and anaerobic species\", \"LGG was well tolerated\", \"disease risk\", \"colonize the neonatal gut and modify its microbial ecology\", \"quantitative aerobic and anaerobic cultures\", \"species number or quantitative counts\", \"neonatal intestinal colonization patterns\"], \"Participant\": [\"infants weighing less than 1500 g\", \"enteric microflora in low-birth-weight neonates .\", \"Infants less than 1500 g\"]}"
}
] |
science.ddi_ner
|
science.ddi_ner.526
|
[
{
"role": "user",
"content": "You will be shown an abstract from a biomedical research paper. Given this abstract, your task is to extract all unique entities of the following types: [\"Brand\", \"UnapprovedDrug\", \"Drug\", \"DrugGroup\"].\n\nPlease return the output as a JSON object of the format: {\"Brand\" : [\"Aspirin\", ...], \"DrugGroup\": [\"Salicyclate\", ...], \"Drug\": [\"Phenobarbital\", ...], \"UnapprovedDrug\": [\"Heroin\", ...]}. The keys should be entity types and values should be lists of extracted entities belonging to the corresponding type. If you cannot find entities belonging to a specific type, the value should be [].\n\nOnly output the JSON object and do not include any additional text.\n\nAbstract:\n\nTetracycline, a bacteriostatic antibiotic, may antagonize the bactericidal effect of penicillin and concurrent use of these drugs should be avoided."
},
{
"role": "assistant",
"content": "{\"Brand\": [], \"Drug\": [\"penicillin\", \"Tetracycline\"], \"DrugGroup\": [\"bacteriostatic antibiotic\"], \"UnapprovedDrug\": []}"
}
] |
science.ddi_ner
|
science.ddi_ner.685
|
[
{
"role": "user",
"content": "You will be shown an abstract from a biomedical research paper. Given this abstract, your task is to extract all unique entities of the following types: [\"Brand\", \"UnapprovedDrug\", \"Drug\", \"DrugGroup\"].\n\nPlease return the output as a JSON object of the format: {\"Brand\" : [\"Aspirin\", ...], \"DrugGroup\": [\"Salicyclate\", ...], \"Drug\": [\"Phenobarbital\", ...], \"UnapprovedDrug\": [\"Heroin\", ...]}. The keys should be entity types and values should be lists of extracted entities belonging to the corresponding type. If you cannot find entities belonging to a specific type, the value should be [].\n\nOnly output the JSON object and do not include any additional text.\n\nAbstract:\n\nAltered responsiveness to alcohol after exposure to organic lead. Ethyl alcohol is known to effect the functional integrity of the limbic system, particularly the hippocampus, and to alter behaviors which are thought to be mediated through limbic function. Organometals also compromise the limbic system and result in deficits in learning and memory. Since both alcohol and organoleads are present in the environment and seem to influence limbic integration, the interaction of these two compounds was assessed in the present experiment. Thirty male rats of the Fischer-344 strain were divided into three equal groups and were given injections of trimethyl lead (TML) (8.0 or 17.0 mg/kg/ml SC) or the saline vehicle. Fourteen days later, all animals were challenged with a single hypnotic dose of ethanol (3.5 g/kg IP). The 20% v/v solution of alcohol was prepared in water from a stock solution of 95% ethanol. The latency to loss of the righting reflex and duration of sleep time were recorded while the rats were kept in sound-attenuating chambers. The rats treated with the highest dose of TML manifested significantly longer latencies to lose the righting reflex and shorter durations of sleep than did controls. These results suggest that exposure to environmental lead may alter the biological and behavioral responsiveness of an animal to alcohol."
},
{
"role": "assistant",
"content": "{\"Brand\": [], \"Drug\": [\"Ethyl alcohol\", \"alcohol\", \"ethanol\"], \"DrugGroup\": [], \"UnapprovedDrug\": [\"lead\", \"trimethyl lead\", \"TML\"]}"
}
] |
science.drug_combo_extraction_re
|
science.drug_combo_extraction_re.1242
|
[
{
"role": "user",
"content": "You will be shown a paragraph from a biomedical research article. Your task is to extract all drug combinations appearing in a specific sentence within in the paragraph. Each drug combination should be assigned to one of the following three categories:\n\n- POS: Indicates a positive interaction between the drugs in the combination; for instance, drugs that have an additive or synergistic effect.\n- NEG: Indicates a negative interaction between the drugs in the combination; for instance, combining these drugs might result in adverse side effects, or might reduce their efficacy.\n- COMB: Indicates that the drugs are given in combination, but the type of interaction between the drugs cannot be determined based on the provided context.\n\nPlease format your answer as a json array. Each entry in the array should itself be an array formatted as [<drug_1>, <drug_2>, ..., <drug_n>, <category>] where <category> is one of the three categories listed above and <drug_1>, ..., <drug_n> are drug names copied verbatim from the input sentence. Different combinations may involve different numbers of drugs; in other words, the `n` in <drug_n> may vary.\n\nAs an example, the following output describes two extracted drug combinations; one between two drugs, and one between three drugs:\n\n[[\"artesunate\", \"artemether\", \"COMB\"], [\"Nifedipine\", \"Labetalol\", \"Prazosin\", \"POS\"]]\n\nThe paragraph and specific sentence are below. You should only extract relationships expressed in the specific sentence; the paragraph is provided for context.\n\nIn your output, return only the json array and no other text. If no drug combinations appear, return an empty array `[]`.\n\nparagraph: Management of recurrent head and neck cancer: recent progress and future directions. The incidence of squamous cell carcinoma of the head and neck (SCCHN) is on the rise in the US despite a drop in cigarette smoking rates. Much of this rise is due to the increasing incidence of SCCHN attributable to human papillomavirus (HPV). HPV-related SCCHN has a high cure rate, which contributes to the stable death rates despite the increased incidence. Up to half of patients with SCCHN will develop recurrence. For these patients, the first clinical decision is whether the recurrence is potentially treatable for cure, or is incurable. For those deemed potentially curable, surgical or radiation-based therapies, or both, are undertaken. For those who have incurable recurrences, the goals are palliation and possibly prolongation of life - average survivals are in the range of 6-12 months depending on the type of recurrence and other factors. Several chemotherapy drugs are active in SCCHN , most notably the platinum compounds , taxanes , fluorouracil ( 5-FU ) , methotrexate and cetuximab . Approximately 10-25% of patients will respond to treatment with one of these drugs. The response rate is higher for combinations such as a platinum plus a taxane, a platinum plus 5-FU, a combination of the three, or one of more of these drugs plus cetuximab. Combination chemotherapy has not been shown to prolong survival over single-agent therapy, with the exception of the addition of cetuximab to a platinum and 5-FU combination. A number of orally bioavailable tyrosine kinase inhibitors have been tested or are undergoing trials in SCCHN. None of these has as yet been shown to be more effective than the currently available drugs. For patients with recurrences who are undergoing active therapy, and especially for those for whom further therapy is no longer appropriate or is declined, strict attention is necessary to palliation of pain, oral and airway issues, and to nutrition, speech, and social and psychological issues.\n\nsentence: Several chemotherapy drugs are active in SCCHN , most notably the platinum compounds , taxanes , fluorouracil ( 5-FU ) , methotrexate and cetuximab ."
},
{
"role": "assistant",
"content": "[]"
}
] |
science.mslr2022_cochrane_multidoc_summarization
|
science.mslr2022_cochrane_multidoc_summarization.2275
|
[
{
"role": "user",
"content": "You will be provided with the titles and abstracts of a collection of medical RCT reports studying a clinical question -- for instance, the efficacy of an intervention on some medical outcome. Please write a few sentences synthesizing the findings of these reports, which could serve as a conclusion section for a systematic review article. Your response should not include any other text. The RCT reports are below.\n\n\n\nTitle 1:\nRandomised, double-blind, placebo controlled pilot study assessing nitroglycerin as a tocolytic.\nAbstract 1:\nThirty-three women in preterm labour were randomised in a double-blind fashion to receive either transdermal nitroglycerin (n = 17) or placebo (n = 16). Both groups had significant (P < 0.001) change in the cervix prior to randomisation. The primary outcome measure was delivery within 48 hours of randomisation. Fewer women randomised to nitroglycerin treatment (6/17) were delivered within 48 hours, compared with the placebo treatment (10/16) (RR 0.56, 95% CI 0.27 to 1.19). This pilot study lends support to two case series published that suggest that transdermal nitroglycerin may be promising as a safe, effective means for tocolysis.\n\n\nTitle 2:\nRandomized comparison of intravenous nitroglycerin and magnesium sulfate for treatment of preterm labor.\nAbstract 2:\nTo compare the safety and efficacy of high-dose intravenous (IV) nitroglycerin with those of IV magnesium sulfate for acute tocolysis of preterm labor.\n Thirty-one women with preterm labor before 35 weeks' gestation were assigned randomly to IV magnesium sulfate or IV nitroglycerin for tocolysis. Preterm labor was defined as the occurrence of at least two contractions in 10 minutes, with cervical change or ruptured membranes. Acute tocolysis was defined as tocolysis for up to 48 hours. Magnesium sulfate was administered as a 4-g bolus, then at a rate of 2-4 g/h. Nitroglycerin was administered as a 100-microg bolus, then at a rate of 1- to 10-microg/kg/min. The primary outcome measure was achievement of at least 12 hours of successful tocolysis.\n Thirty patients were available for analysis. There were no significant differences in gestational age, cervical dilation, or incidence of ruptured membranes between groups at the initiation of tocolysis. Successful tocolysis was achieved in six of 16 patients receiving nitroglycerin, compared with 11 of 14 receiving magnesium sulfate (37.5 versus 78.6%, P = .033). Tocolytic failures (nitroglycerin versus magnesium sulfate) were due to persistent contractions with cervical change or rupture of previously intact membranes (five of 16 versus two of 14), persistent hypotension (four of 16 versus none of 14), and other severe side effects (one of 16 versus one of 14). Maternal hemodynamic alterations were more pronounced in patients who received nitroglycerin, and 25% of patients assigned to nitroglycerin treatment had hypotension requiring discontinuation of therapy.\n Tocolytic failures were more common with nitroglycerin than with magnesium sulfate. The hemodynamic alterations noted in patients receiving nitroglycerin, including a 25% incidence of persistent hypotension, might limit the usefulness of IV nitroglycerin for the acute tocolysis of preterm labor.\n\n\nTitle 3:\nGlyceryl trinitrate and ritodrine in tocolysis: an international multicenter randomized study. GTN Preterm Labour Investigation Group.\nAbstract 3:\nTo compare the efficacy of transdermal glyceryl trinitrate and intravenous (IV) ritodrine as tocolytics.\n Two hundred forty-five women with preterm labor and intact membranes between 24 and 36 weeks' gestation were randomized to transdermal glyceryl trinitrate or intravenous ritodrine. Treatment was continued until contractions stopped or a maximum of 7 days. Glyceryl trinitrate was administered as a 10- or 20-mg transdermal patch. Intravenous ritodrine was administered according to nationally available guidelines. The primary outcome was prolongation of gestation expressed as a percentage of the time from entry to 37 weeks. Secondary outcomes were proportion of women who delivered the same day, next day, or within 7 and 14 days of entry, and by 32, 34, and 37 weeks. Analysis was by intention to treat.\n Twelve women (5%) were lost to follow-up. Glyceryl trinitrate and ritodrine prolonged gestation by 74% of time to 37 weeks (difference glyceryl trinitrate-ritodrine 0%; 95% confidence interval (CI) -10%, +10%). There was no significant difference in the proportion of women receiving glyceryl trinitrate or ritodrine who delivered within the specified days from study entry or weeks of gestation; however, 42 women who received glyceryl trinitrate and 58 women who received ritodrine delivered by 37 weeks (difference -11%; 95% CI -24%, +2%). No serious maternal side effects were reported for ritodrine or glyceryl trinitrate.\n We found no overall difference between glyceryl trinitrate and ritodrine in the acute tocolysis of preterm labor but a suggested advantage of glyceryl trinitrate over ritodrine in reducing preterm delivery rate. The maternal side effect profile and treatment discontinuation rates were fewer for glyceryl trinitrate, suggesting it was a safer alternative to ritodrine.\n\n\nTitle 4:\nCorticotropin-releasing hormone: a biochemical predictor of preterm delivery in a pilot randomized trial of the treatment of preterm labor.\nAbstract 4:\nWe assessed the ability of maternal plasma corticotropin-releasing hormone measurements to predict preterm delivery in the setting of a pilot study comparing transdermal glyceryl trinitrate with standard beta-mimetic therapy for preterm labor and to determine the effect of these tocolytics on maternal plasma corticotropin-releasing hormone concentrations.\n Twenty-six consecutive patients with preterm labor were randomized to tocolytic treatment with transdermal glyceryl trinitrate (n=13) or intravenous albuterol (n=13).\n Plasma corticotropin-releasing hormone immunoreactivity levels were higher in women who were delivered within 7 days (41.4+/-13.5 pmol/L) than in those continuing to term (14.2+/-2.4 pmol/L, p=0.011) and were not altered by treatment. Two women in each of the treatment groups delivered within 7 days of the initiation of treatment, two women in the glyceryl trinitrate group were changed to albuterol because of persistence of contractions. Glyceryl trinitrate treatment was associated with significantly fewer maternal side effects. Neither treatment altered umbilical artery Doppler ultrasonographic findings.\n Transdermal glyceryl trinitrate is better tolerated than intravenous albuterol but may be no more efficacious than albuterol for the treatment of preterm labor. Biologic markers such as plasma corticotropin-releasing hormone levels may be an important method of identifying women at high risk of preterm delivery."
},
{
"role": "assistant",
"content": "There is currently insufficient evidence to support the routine administration of nitric oxide donors in the treatment of threatened preterm labour.\n[Note: The 26 citations in the awaiting classification section of the review may alter the conclusions of the review once assessed.]"
}
] |
science.bc7_litcovid_topic_classification
|
science.bc7_litcovid_topic_classification.11779
|
[
{
"role": "user",
"content": "You are presented with a paragraph from a COVID-19 literature. Classify the topics of this piece of text by choosing from the following categories:\n\n- Epidemic Forecasting: The content relates to predictions about the spread of COVID-19.\n- Treatment: The paragraph discusses therapeutic methods or medication for COVID-19.\n- Prevention: The content covers measures to prevent the spread of COVID-19.\n- Mechanism: The paragraph explains the biological mechanisms of the virus.\n- Case Report: The content is a report of a COVID-19 case.\n- Transmission: The paragraph discusses how COVID-19 is transmitted.\n- Diagnosis: The content is about diagnosing COVID-19 in individuals.\n\nYour classification should be provided as an element within a JSON array. The array should be formatted with topics enclosed in double quotes and separated by commas, following the JSON format, for example: [\"Topic1\", \"Topic2\", ...]. Include all applicable topics within the array. Your output should be a valid JSON array, and no additional text should be included in your response.\n\nArticle:\n\nBackground Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) utilizes the angiotensin-converting enzyme-2 (ACE-2) receptor to enter human cells. Angiotensin-converting enzyme inhibitors (ACEI) and angiotensin II receptor antagonists (ARB) are associated with ACE-2 upregulation. We hypothesized that antecedent use of ACEI/ARB may be associated with mortality in coronavirus disease 2019 (COVID-19). Methods and Results We used the Coracle registry, which contains data of patients hospitalized with COVID-19 in 4 regions of Italy, and restricted analyses to those >/=50 years of age. The primary outcome was in-hospital mortality. Among these 781 patients, 133 (17.0%) used an ARB and 171 (21.9%) used an ACEI. While neither sex nor smoking status differed by user groups, patients on ACEI/ARB were older and more likely to have hypertension, diabetes mellitus, and congestive heart failure. The overall mortality rate was 15.1% (118/781) and increased with age (PTrend<0.0001). The crude odds ratios (ORs) for death for ACEI users and ARB users were 0.98, 95% CI, 0.60-1.60, P=0.9333, and 1.13, 95% CI, 0.67-1.91, P=0.6385, respectively. After adjusting for age, hypertension, diabetes mellitus, and congestive heart failure, antecedent ACEI administration was associated with reduced mortality (OR, 0.55; 95% CI, 0.31-0.98, P=0.0436); a similar, but weaker trend was observed for ARB administration (OR, 0.58; 95% CI, 0.32-1.07, P=0.0796). Conclusions In those aged >/=50 years hospitalized with COVID-19, antecedent use of ACEI was independently associated with reduced risk of inpatient death. Our findings suggest a protective role of renin-angiotensin-aldosterone system inhibition in patients with high cardiovascular risk affected by COVID-19."
},
{
"role": "assistant",
"content": "[\"Treatment\", \"Mechanism\"]"
}
] |
science.mslr2022_ms2_multidoc_summarization
|
science.mslr2022_ms2_multidoc_summarization.6239
|
[
{
"role": "user",
"content": "You will be presented with a collection of medical randomized controlled trial (RCT) reports addressing a shared clinical question -- for instance, the efficacy of a medical intervention on a disease or condition. Given the titles and abstracts of these reports, your task is to generate the conclusion of the systematic review article synthesizing the key findings. Your conclusion should be a few sentences long. In your response, include only the conclusion and no other text. The RCT reports are below.\n\n\n\nTitle 1:\nCytoplasmic expression of estrogen receptor beta (ERβ) predicts poor clinical outcome in advanced serous ovarian cancer.\nAbstract 1:\nOBJECTIVE In this study we investigated the prognostic value of estrogen receptor α ( ERα ) , ERβ and progesterone receptor ( PR ) expression in 58 untreated advanced serous ovarian cancer patients . The study also included 12 macroscopically and histopathologically normal ovaries . MATERIAL S AND METHODS Protein expression was evaluated by immunohistochemistry , and antibody staining detected in both the nuclear and cytoplasmic compartments was taken into account . Immunopositivity was analyzed in relation to tumor clinicopathological variables , disease-free survival ( DFS ) , and overall survival ( OS ) . RESULTS Epithelial cells in ovarian cancer tissue showed significantly lower levels of nuclear ERβ and PR , but not ERα , than in normal ovarian tissue . In the case of ERβ , however , while normal ovarian epithelium exhibited almost exclusively strong nuclear staining , ovarian cancer tissue mostly showed cytoplasmic immunopositivity . Nuclear ERα and ERβ expression were not associated with clinical outcome . Conversely , any cytoplasmic ERβ expression was an independent unfavorable prognostic factor for DFS , a finding approaching statistical significance also for OS . These data suggest that , in advanced serous ovarian cancer , cytoplasmic ERβ signaling may be more important for patient survival than its nuclear signaling . In the case of PR , positivity was an independent favorable prognostic factor for DFS . CONCLUSIONS These novel findings , that need to be confirmed in a large prospect i ve trial , suggest that additional prognostic , and possibly therapeutic opportunities may be available in advanced serous ovarian cancer\n\n\nTitle 2:\nHER2 Status in Ovarian Carcinomas: A Multicenter GINECO Study of 320 Patients\nAbstract 2:\nBackground Despite a typically good response to first-line combination chemotherapy , the prognosis for patients with advanced ovarian cancer remains poor because of acquired chemoresistance . The use of targeted therapies such as trastuzumab may potentially improve outcomes for patients with ovarian cancer . HER2 overexpression/amplification has been reported in ovarian cancer , but the exact percentage of HER2-positive tumors varies widely in the literature . In this study , HER2 gene status was evaluated in a large , multicentric series of 320 patients with advanced ovarian cancer , including 243 patients enrolled in a multicenter prospect i ve clinical trial of paclitaxel/carboplatin-based chemotherapy . Methodology /Principal Findings The HER2 status of primary tumors and metastases was evaluated by both immunohistochemistry ( IHC ) and fluorescence in situ hybridization ( FISH ) analysis of paraffin-embedded tissue on conventional slides . The prognostic impact of HER2 expression was analyzed . HER2 gene was overexpressed and amplified in 6.6 % of analyzed tumors . Despite frequent intratumoral heterogeneity , no statistically significant difference was detected between primary tumors and corresponding metastases . Conclusions / Significance Our results show that the decision algorithm usually used in breast cancer ( IHC as a screening test , with equivocal results confirmed by FISH ) is appropriate in ovarian cancer . In contrast to previous series , HER2-positive status did not influence outcome in the present study , possibly due to the fact that patients in our study received paclitaxel/carboplatin-based chemotherapy . This raises the question of whether HER2 status and paclitaxel sensitively are linked"
},
{
"role": "assistant",
"content": "In patients with ovarian cancer , elevated level of PR predicted favorable survival , and elevated level of HER2 was associated with worse survival"
}
] |
science.healthver_entailment
|
science.healthver_entailment.4252
|
[
{
"role": "user",
"content": "You will be shown a claim about public health, and the abstract of a biomedical research paper. Each sentence from the abstract will be on a separate line. Your task is to return a JSON object with two fields:\n\n- \"verdict\": The fact-checking verdict. If the information in the abstract supports the claim, write \"SUPPORT\". If the abstract contradicts the claim, write \"CONTRADICT\". If the abstract does not provide enough information to arrive at a verdict, write \"NEI\" (for \"not enough information\").\n- \"evidence\": An array of sentences providing evidence for the verdict. Please copy all relevant sentences verbatim from the abstract. If the verdict was \"NEI\", then return an empty array.\n\nFor instance, if the model were given the claim \"wearing masks can prevent the spread of COVID\", the output might be\n{\n \"verdict\": \"SUPPORT\",\n \"evidence\": [\"Our findings indicate that mass mask-wearing reduces the transmission rate for COVID-19.\"]\n}\n\nClaim: dexamethasone is not a treatment for covid-19.\n\nAbstract:\nRecent announcements indicated, without sharing any distinct published set of results, that the corticosteroid dexamethasone may reduce mortality of severe COVID-19 patients only.\nThe recent Coronavirus [severe acute respiratory syndrome (SARS)-CoV-2]-associated multiorgan disease, called COVID-19, has high morbidity and mortality due to autoimmune destruction of the lungs stemming from the release of a storm of pro-inflammatory cytokines.\nDefense against this Corona virus requires activated T cells and specific antibodies.\nInstead, cytokines are responsible for the serious sequelae of COVID-19 that damage the lungs.\nDexamethasone is a synthetic corticosteroid approved by the FDA 1958 as a broad-spectrum immunosuppressor and it is about 30 times as active and with longer duration of action (2-3 days) than cortisone.\nDexamethasone would limit the production of and damaging effect of the cytokines, but will also inhibit the protective function of T cells and block B cells from making antibodies, potentially leading to increased plasma viral load that will persist after a patient survives SARS.\nMoreover, dexamethasone would block macrophages from clearing secondary, nosocomial, infections.\nHence, dexamethasone may be useful for the short-term in severe, intubated, COVID-19 patients, but could be outright dangerous during recovery since the virus will not only persist, but the body will be prevented from generating protective antibodies.\nInstead, a pulse of intravenous dexamethasone may be followed by administration of nebulized triamcinolone (6 times as active as cortisone) to concentrate in the lungs only.\nThese corticosteroids could be given together with the natural flavonoid luteolin because of its antiviral and anti-inflammatory properties, especially its ability to inhibit mast cells, which are the main source of cytokines in the lungs.\nAt the end, we should remember that \"The good physician treats the disease; the great physician treats the patient who has the disease\" [Sir William Osler's (1849-1919)]."
},
{
"role": "assistant",
"content": "{\"verdict\": \"SUPPORT\", \"evidence\": [\"Hence, dexamethasone may be useful for the short-term in severe, intubated, COVID-19 patients, but could be outright dangerous during recovery since the virus will not only persist, but the body will be prevented from generating protective antibodies.\"]}"
}
] |
science.covid_deepset_qa
|
science.covid_deepset_qa.1753
|
[
{
"role": "user",
"content": "You will be shown a paragraph from a biomedical research paper, followed by a question about the paper. Please extract text from the paragraph to answer the question. Do not include any text in your repsonse other than the answer.\n\nParagraph: Nevertheless, studies assessing the function of NEAT1 in viral infections are scarce. Here, the human umbilical vein endothelial cell (HUVEC) transcriptome was analyzed after HTNV infection by digital gene expression (DGE) profiling, and lncRNA NEAT1 was found to be remarkably upregulated by viral infection. Silencing NEAT1 in vitro or in vivo suppressed host immune responses and aggravated HTNV infection, whereas NEAT1 overexpression in vitro enhanced beta interferon (IFN-) production and inhibited HTNV replication. Further investigation showed that NEAT1 promoted RIG-I and DDX60 expression by relocating SFPQ and removing the transcriptional inhibitory effects of SFPQ, which are critical for IFN responses against HTNV infection. We also found that RIG-I signaling, rather than TLR3 and TLR4, accounted for the elevation of HTNV-induced NEAT1. Taken together, our findings provide novel insights into the lncRNA-mediated regulatory mechanism of host innate defense against HTNV infection. To explore the potential role of long noncoding RNAs in host innate immune responses, DGE analysis of HUVECs for whole-genome profiling was performed at 24 h post-HTNV infection. As shown in Fig. 1B , the NEAT1 level in the HTNV group was higher than that in the mock group (P ϭ 6.86 ϫ 10 Ϫ13 , false discovery rate [FDR] ϭ 9.75 ϫ 10 Ϫ12 ) or the 60 Co-inactivated HTNV group (P ϭ 1.75 ϫ 10 Ϫ14 , FDR ϭ 3.10 ϫ 10 Ϫ13 ); however, the difference between the 60 Co-inactivated HTNV group and the mock group was not significant (P ϭ 0.21034, FDR ϭ 0.58211). To confirm the profiling results, two primer pairs from the published literature (11) , one recognizing both NEAT1-1 and NEAT1-2 and the other specific for NEAT1-2 (Fig. 1A) , were applied to quantify NEAT1 RNA isoforms by quantitative real-time PCR (qRT-PCR). It has been reported that NEAT1-2 rather than NEAT1-1 plays a key regulatory role in paraspeckle formation (11) , and we also found that elevated NEAT1 levels depend on live HTNV infection rather than 60 Co-inactivated HTNV stimulation (Fig. 1C) . Fluorescence in situ hybridization (FISH) with probes specific for NEAT1-2 was performed with HUVECs, and the results confirmed increased NEAT1-2 expression and the aggregation of NEAT1-2 in the nucleus at 24 and 48 h postinfection (hpi) (Fig. 1D) . To further investigate whether NEAT1 expression was altered in other cell lines, HEK293, HeLa, and A549 cells were used. All these cells could be infected by HTNV ( Fig. 1E and F) and generated hantavirus progeny (Fig. 1G ). Similar to the data obtained from HUVECs, NEAT1 was indeed upregulated by HTNV at a multiplicity of infection (MOI) of 1 beginning at 24 hpi in HUVECs and A549, HEK293, and HeLa cells, and the increasing tendency occurred in a time-dependent manner (Fig. 1H ). Of note, the NEAT1 elevation at 2 hpi might have been unrelated to the virus but resulted in cellular stress responses. Besides, NEAT1 expression increased from an MOI of 0.1 to 1, indicating that the elevation occurred in a viral dose-dependent manner (Fig. 1I) . NEAT1-2 and not NEAT1-1 suppresses HTNV replication in HUVECs. The abovedescribed data showed that HTNV infection increased NEAT1, and we wondered how NEAT1 could reciprocally influence HTNV replication. The small interfering RNA (siRNA) transfection efficiency in HUVECs was confirmed by flow cytometry, and NEAT1 expression was significantly decreased, as assessed by qRT-PCR after RNA interference (RNAi) ( Fig. 2A) . Of note, si-NEAT1 targets both NEAT1-1 and NEAT1-2, whereas the stealth siRNA NEAT1-2 (st-NEAT1-2) is specific for NEAT1-2. Compared with the cells transfected with control siRNA (negative control [NC]), HUVECs with si-NEAT1 could dramatically promote HTNV NP production, and NP expression seemed to be related to the amount of applied si-NEAT1 (Fig. 2B) . Intriguingly, depletion of NEAT1-2 alone could mimic the antiviral effects of simultaneous NEAT1-1 and NEAT1-2 silencing (Fig. 2C) , indicating that NEAT1-2 was critical for the antiviral responses. Consistent with those data, the expressions of HTNV mRNA of S segment (Fig. 2D ) and HTNV titers (Fig. 2E ) were increased after NEAT1 silencing. On the other hand, plasmids, of which pCMV-NEAT1-1 is transcribed into the 3.7-kb NEAT1-1 (MEN) and pCMV-NEAT1-2 is transcribed into the 2-to 3-kb NEAT1-2 (MEN), were applied to directly investigate the role of NEAT1 in HTNV infection (Fig. 2F) . Surprisingly, we found NEAT1-1 overexpression restricted NEAT1-2 transcription (Fig. 2F ). Overexpression of NEAT1 with both pCMV-NEAT1-1 and pCMV-NEAT1-2 could conspicuously repress HTNV NP expression, and NP expression seemed to be associated with the transfected plasmids (Fig. 2G) . Furthermore, overexpression of NEAT1-2 instead of NEAT1-1 could efficiently suppress HTNV replication (Fig. 2H ). NEAT1-1 upregulation even aggravated HTNV infection (Fig. 2H ), which may be the result of downregulation of NEAT1-2. Consistently, through analysis of viral load detected by qRT-PCR and the 50% tissue culture infective dose (TCID 50 ) test by ELISA, we found that expression of HTNV-specific mRNA (Fig. 2I ) and HTNV titers (Fig. 2J ) were limited in HUVECs in which NEAT1-2 was ectopically expressed in comparison to those transfected with control vector or pCMV-NEAT1-1. These data further showed that NEAT1-2 and not NEAT1-1 suppresses HTNV replication in HUVECs. Alteration of NEAT1-2 affects HTNV-induced IFN expression in HUVECs. IFN- production or pretreatment at an early infection stage plays an important role in limiting HTNV infection, while IFN- treatment after 24 hpi exerts little antiviral effect (12, 13) . It has been reported that the GnT of hantaviruses suppressed IFN- expression of host cells at an early stage of infection (14) . Here, we also found that HUVECs could not efficiently produce IFN- until 12 hpi at an MOI of 0.1 or until 24 hpi at an MOI of 1 (Fig. 3A) , which indicated that high doses of HTNV could hamper prompt IFN responses. Notably, enhanced NEAT1-2 transcription appeared at 8 hpi at an MOI of 0.1 or at 20 hpi at an MOI of 1 (Fig. 3B) , suggesting that NEAT1-2 expression increased just before IFN production. We found that expression of endogenous IFN- mRNA was much lower in cells transfected with si-NEAT1-2 at MOIs of both 0.1 (Fig. 3C ) and 1 (Fig. 3D ) than in those transfected with control siRNA (NC). In contrast, overexpression of NEAT1 in HUVECs increased IFN- expression after HTNV infection (MOI ϭ 1) at 24 and 48 hpi (Fig. 3E ). More importantly, HUVECs transfected with pCMV-NEAT1-2 conspicuously increased IFN- gene expression compared with those cells with vector plasmids at 12 hpi (MOI ϭ 1), demonstrating that NEAT1-2 overexpression accelerated robust IFN responses in host cells against HTNV infection. With a dual luciferase reporter system Twenty-four hours after transfection, the cells expressing FAM were calculated by flow cytometry. Right, HUVECs in six-well plates were transfected with NC sequences, si-NEAT1, or the stealth siRNA NEAT1-2 (st-NEAT1-2) (3 g). Twenty-four hours after transfection, the cells were infected with HTNV at an MOI of 1. At 48 hpi, the NEAT1 expression levels were measured by qRT-PCR. Values are means Ϯ SD (n ϭ 3; *, P Ͻ 0.01; **, P Ͻ 0.001; ***, P Ͻ 0.0001; Student's t test, compared with the NC group). NS, nonsignificant. (B) HUVECs in six-well plates were transfected with NC sequences (the amount of Si-NEAT1-2 is considered 0 g) or increasing amounts of si-NEAT1 (0.1, 0.5, 1, and 3 g). Twenty-four hours after transfection, the cells were infected with HTNV at an MOI of 0.1 for 48 h. The expression of HTNV NP was measured by Western blotting. (C) HUVECs were treated as described for panel A, right, but at an MOI of 0.1. In-cell Western (ICW) analysis for HTNV NP was performed at 48 hpi. The ICW for HTNV NP staining is shown on the left, while the relative intensity of fluorescence (NP/-actin) was analyzed using Student's t test. (n ϭ 4; *, P Ͻ 0.01; **, P Ͻ 0.001; Student's t test, compared with the NC group). (D) HUVECs were treated as described for panel A, right, but at an MOI of 0.1. The expression of HTNV S segment was measured by qRT-PCR. Values are means Ϯ SD (n ϭ 3; *, P Ͻ 0.01; Student's t test, compared with the NC group). (E) HUVECs were treated as described for panel A, right, but at an MOI of 0.1. The propagated HTNV was acquired at 72 hpi, and viral titers were detected by TCID 50 with ELISA in Vero E6 cells. Values are means Ϯ SD (n ϭ 3; *, P Ͻ 0.01; Student's t test, compared with the NC group). (F) Left, HUVECs in six-well plates were transfected with vectors or pGFP (3 g). Twenty-four hours after transfection, the cells expressing green fluorescent protein (GFP) were calculated by flow cytometry. Right, HUVECs in six-well plates were transfected with control plasmids (vector), pCMV-NEAT1-1, or pCMV-NEAT1-2 (3 g). Twenty-four hours after transfection, the cells were infected with HTNV at an MOI of 1. At (Continued on next page) NEAT1 Promotes Innate Antiviral Responses Journal of Virology maintaining IFN- promoters, we found NEAT1-2 silencing or overexpression could inhibit or increase the promoter activity of the IFN- gene after HTNV infection, respectively, whereas silencing NEAT1-2 or ectopically expressing NEAT1-2 without HTNV infection could not inhibit or enhance IFN- expression (Fig. 3F) . These results showed that NEAT1-2 regulated HTNV-induced IFN- expression. To explore whether the antihantavirus effects of NEAT1 were caused by IFN- alteration, a series of compensatory experiments was designed. In NEAT1-2 knockdown HUVECs, the addition of IFN- at 12 hpi could efficiently block HTNV NP production (MOI ϭ 0.1), and such phenomena were also determined by the amount of applied IFN- (Fig. 3G ). In addition, in cells with high NEAT1-2 expression, treatment with neutralizing antibodies (NAbs) of IFN-␣ and IFN- could counteract the antiviral effects of NEAT1-2 (MOI ϭ 1), and the compensatory effects were dependent on the magnitude of the NAbs. Together these results demonstrated that NEAT1-2 especially enhanced the host antihantaviral innate immune responses by regulating IFN- signaling. RIG-I and DDX60 regulated by NEAT1-2 facilitate HTNV-induced IFN- production. PRRs maintain a vital role in the promotion of IFN responses, and we conjectured that NEAT1 might amplify IFN responses by modulating these molecules. TLR3, TLR4, and RIG-I have been shown to recognize HTNV infection (5, 15, 16) . DDX60 was recently reported as an important activator of RIG-I, but the antiviral effects of DDX60 remain a subject of debate (17, 18) , Here, we found that multiple Toll-like receptors like TLR1, TLR2, TLR3, and TLR4, as well as MDA5, were increased after HTNV infection, but none of them were influenced by silencing NEAT1-2 ( Fig. 4A ). The upregulated RIG-I and DDX60 were blocked in the cells with low NEAT1-2 expression after HTNV infection (Fig. 4A ). HUVECs with declining NEAT1-2 expression showed gradually decreasing expression of RIG-I and DDX60 (Fig. 4B) , and increasing NEAT1-2 transcription was found to activate RIG-I and DDX60 production accordingly (Fig. 4C ). These data indicated that NEAT1-2 could positively modulate RIG-I and DDX60 expression, while the role of RIG-I and DDX60 upon HTNV infection is obscure. We then found that RIG-I and DDX60 colocalized after HTNV infection\n\nQuestion: What evidence suggests that RIG-I and DDX60 collaborate to exert antiviral effects?"
},
{
"role": "assistant",
"content": "colocalized after HTNV infection"
}
] |
science.data_reco_mcq_sc
|
science.data_reco_mcq_sc.788
|
[
{
"role": "user",
"content": "Given a short query with keyphrases about a research idea in 2018 in the domain of artificial intelligence, recommend the relevant datasets to validate the research idea from options provided. A short description of the datasets is also provided to help you.\n\nQuery: I want to build a model for multimodal image generation.\n\nKeyphrases: multimodal image generation images\n\nDataset description:\nUAVA: The UAVA,<i>UAV-Assistant</i>, dataset is specifically designed for fostering applications which consider UAVs and humans as cooperative agents. We employ a real-world 3D scanned dataset (<a href=\"https://niessner.github.io/Matterport/\">Matterport3D</a>), physically-based rendering, a gamified simulator for realistic drone navigation trajectory collection, to generate realistic multimodal data both from the user’s exocentric view of the drone, as well as the drone’s egocentric view.\nRecipeQA: RecipeQA is a dataset for multimodal comprehension of cooking recipes. It consists of over 36K question-answer pairs automatically generated from approximately 20K unique recipes with step-by-step instructions and images.\nCIFAR-10: The CIFAR-10 dataset (Canadian Institute for Advanced Research, 10 classes) is a subset of the Tiny Images dataset and consists of 60000 32x32 color images. The images are labelled with one of 10 mutually exclusive classes: airplane, automobile (but not truck or pickup truck), bird, cat, deer, dog, frog, horse, ship, and truck (but not pickup truck).\nConvAI2: The ConvAI2 NeurIPS competition aimed at finding approaches to creating high-quality dialogue agents capable of meaningful open domain conversation. The ConvAI2 dataset for training models is based on the PERSONA-CHAT dataset.\n\nOptions:- A: UAVA B: RecipeQA C: CIFAR-10 D: ConvAI2"
},
{
"role": "assistant",
"content": "CIFAR-10"
}
] |
science.medmentions_ner
|
science.medmentions_ner.2451
|
[
{
"role": "user",
"content": "You will be shown an abstract from a biomedical research paper. Given this abstract, your task is to extract all unique entities of the following types: [\"HealthCareActivity\", \"InjuryOrPoisoning\", \"BodySubstance\", \"IntellectualProduct\", \"AnatomicalStructure\", \"SpatialConcept\", \"Chemical\", \"Bacterium\", \"MedicalDevice\", \"Organization\", \"BiomedicalOccupationOrDiscipline\", \"Finding\", \"BiologicFunction\", \"Virus\", \"ResearchActivity\", \"ClinicalAttribute\", \"PopulationGroup\", \"Eukaryote\", \"BodySystem\", \"Food\", \"ProfessionalOrOccupationalGroup\"].\n\nPlease return the output as a JSON object of the format: {\"Virus\": [\"HIV\", ...], \"Bacterium\": [\"MRSA\", ...], \"AnatomicalStructure\": [\"Lung\", ...], \"BodySystem\": [\"CNS\", ...], \"BodySubstance\": [\"Serum\", ...], \"Finding\": [\"Headache\", ...], \"InjuryOrPoisoning\": [\"Fracture\", ...], \"BiologicFunction\": [\"Death\", ...], \"HealthCareActivity\": [\"Biopsy\", ...], \"ResearchActivity\": [\"Clinical trial\", ...], \"MedicalDevice\": [\"Lenses\", ...], \"SpatialConcept\": [\"Camps\", ...], \"BiomedicalOccupationOrDiscipline\": [\"Forensic medicine\", ...], \"Organization\": [\"WHO\", ...], \"ProfessionalOrOccupationalGroup\": [\"Provider\", ...], \"PopulationGroup\": [\"Swimmers\", ...], \"Chemical\": [\"Gold\", ...], \"Food\": [\"Rice\", ...], \"IntellectualProduct\": [\"RPAM\", ...], \"ClinicalAttribute\": [\"Biomarker\", ...], \"Eukaryote\": [\"Dogs\", ...]}. The keys should be entity types and values should be lists of extracted entities belonging to the corresponding type. If you cannot find entities belonging to a specific type, the value should be [].\n\nOnly output the JSON object and do not include any additional text.\n\nAbstract:\n\nAnalyzing the clinical profile of swine flu / influenza A H1N1 infection in central India: a retrospective study Recently, India reported an increase in swine flu (influenza A H1N1) activity. There are limited studies on epidemiology of swine flu in Indian context. This study aims to analyze clinical and epidemiological profile of suspected swine flu cases in central India. 171 cases were included in a hospital based, observational, descriptive study conducted from December 2014 to April 2015. Demographics, clinical presentation and outcome of positive and negative cases were compared. Data was analyzed using STATA software. Distribution by age, sex and residence was found similar (p > 0.05) in positive and negative cases. Cough (89%), fever (85%) and throat irritation (51%) were chief complaints (avg. duration = 4.9 days). History of travel, history of contact with swine flu cases (p = 0.002) and history of visiting crowded places (p = 0.098) was reported considerably in higher proportion in positive cases as compared to negative cases. There were 14 deaths and they occurred significantly in younger age among positive cases as compared to negatives (Mean ± SD: 34 ± 2.8 vs 47 ± 8.4 years). Case fatality ratio (CFR) in positive cases showing history of travel, contact with swine flu cases, requiring invasive ventilator support and >3 X-ray zones involvement were significantly higher. Outbreak in later part of winter, high case fatality and younger population is more affected. In this study, swine flu infection and outbreaks started later in the year Hospital stay and CFR were increased. Understanding the swine flu infection, changing clinical presentation of swine flu and formulate new strategies for its prevention and management."
},
{
"role": "assistant",
"content": "{\"AnatomicalStructure\": [], \"Bacterium\": [], \"BiologicFunction\": [\"swine flu\", \"influenza A H1N1 infection\", \"deaths\", \"influenza A H1N1\", \"swine flu infection\"], \"BiomedicalOccupationOrDiscipline\": [\"epidemiology\"], \"BodySubstance\": [], \"BodySystem\": [], \"Chemical\": [], \"ClinicalAttribute\": [], \"Eukaryote\": [], \"Finding\": [\"positive cases\", \"Cough\", \"fever\", \"history of travel\", \"positive\", \"throat irritation\", \"negatives\", \"History of travel\", \"history\", \"negative cases\", \"chief complaints\"], \"Food\": [], \"HealthCareActivity\": [\"studies\", \"study\", \"management\", \"profile\"], \"InjuryOrPoisoning\": [], \"IntellectualProduct\": [\"descriptive\", \"STATA software\"], \"MedicalDevice\": [\"invasive ventilator support\"], \"Organization\": [\"Hospital\", \"hospital\"], \"PopulationGroup\": [\"younger population\"], \"ProfessionalOrOccupationalGroup\": [], \"ResearchActivity\": [\"Analyzing\", \"epidemiological profile\", \"retrospective study\", \"analyze\", \"analyzed\", \"observational\"], \"SpatialConcept\": [\"residence\", \"zones\", \"crowded places\", \"central India\", \"India\"], \"Virus\": []}"
}
] |
science.healthver_entailment
|
science.healthver_entailment.3387
|
[
{
"role": "user",
"content": "You will be shown a claim about public health, and the abstract of a biomedical research paper. Each sentence from the abstract will be on a separate line. Your task is to return a JSON object with two fields:\n\n- \"verdict\": The fact-checking verdict. If the information in the abstract supports the claim, write \"SUPPORT\". If the abstract contradicts the claim, write \"CONTRADICT\". If the abstract does not provide enough information to arrive at a verdict, write \"NEI\" (for \"not enough information\").\n- \"evidence\": An array of sentences providing evidence for the verdict. Please copy all relevant sentences verbatim from the abstract. If the verdict was \"NEI\", then return an empty array.\n\nFor instance, if the model were given the claim \"wearing masks can prevent the spread of COVID\", the output might be\n{\n \"verdict\": \"SUPPORT\",\n \"evidence\": [\"Our findings indicate that mass mask-wearing reduces the transmission rate for COVID-19.\"]\n}\n\nClaim: There is a significant correlation between low vitamin D levels and death from COVID-19\n\nAbstract:\nThe outbreak of COVID-19 has created a global public health crisis.\nLittle is known about the protective factors of this infection.\nTherefore, preventive health measures that can reduce the risk of infection, progression and severity are desperately needed.\nThis review discussed the possible roles of vitamin D in reducing the risk of COVID-19 and other acute respiratory tract infections and severity.\nMoreover, this study determined the correlation of vitamin D levels with COVID-19 cases and deaths in 20 European countries as of 20 May 2020.\nA significant negative correlation (p=0.033) has been observed between mean vitamin D levels and COVID-19 cases per one million population in European countries.\nHowever, the correlation of vitamin D with COVID-19 deaths of these countries was not significant.\nSome retrospective studies demonstrated a correlation between vitamin D status and COVID-19 severity and mortality, while other studies did not find the correlation when confounding variables are adjusted.\nSeveral studies demonstrated the role of vitamin D in reducing the risk of acute viral respiratory tract infections and pneumonia.\nThese include direct inhibition with viral replication or with anti-inflammatory or immunomodulatory ways.\nIn the meta-analysis, vitamin D supplementation has been shown as safe and effective against acute respiratory tract infections.\nThus, people who are at higher risk of vitamin D deficiency during this global pandemic should consider taking vitamin D supplements to maintain the circulating 25(OH)D in the optimal levels (75-125nmol/L).\nIn conclusion, there is not enough evidence on the association between vitamin D levels and COVID-19 severity and mortality.\nTherefore, randomized control trials and cohort studies are necessary to test this hypothesis."
},
{
"role": "assistant",
"content": "{\"verdict\": \"SUPPORT\", \"evidence\": [\"A significant negative correlation (p=0.033) has been observed between mean vitamin D levels and COVID-19 cases per one million population in European countries.\", \"Several studies demonstrated the role of vitamin D in reducing the risk of acute viral respiratory tract infections and pneumonia.\", \"These include direct inhibition with viral replication or with anti-inflammatory or immunomodulatory ways.\", \"In the meta-analysis, vitamin D supplementation has been shown as safe and effective against acute respiratory tract infections.\", \"Thus, people who are at higher risk of vitamin D deficiency during this global pandemic should consider taking vitamin D supplements to maintain the circulating 25(OH)D in the optimal levels (75-125nmol/L).\"]}"
}
] |
science.chemsum_single_document_summarization
|
science.chemsum_single_document_summarization.52520
|
[
{
"role": "user",
"content": "You will be shown the title of a chemistry paper, together with sections excerpted from the body of the paper. The paper sections may include HTML tags like `<p>` and `</p>`; please ignore these. Your task is to write an abstract for the paper. Your response should include the abstract and no other text.\n\nTitle:\nFacile Assembly/Disassembly of DNA Nanostructures Anchored on Cell-Mimicking Giant Vesicles\n\nPaper sections:\n\n<p>Oligonucleotides have emerged as programmable building blocks to create dynamic molecular devices1 from built-in DNA nanostructures.24 These dynamic DNA functional units exhibit good performance and have been used in the construction of DNA walkers,5 tweezers,6 logic circuits,7–9 gene regulators10–12 and smart therapeutics.13,14 Most recently, bioengineering has focused on DNA nanostructures on the cell surface, resulting in the design of many nanostructures and devices interacting with the cell membrane.15 Hence, most such DNA nanostructures built on synthetic lipid membranes have served as biomimetic membrane proteins, such as ion channels,16,17 membrane-sculpting protein18 and \"SNAP (Soluble NSF Attachment Protein) REceptor\" (SNARE) protein.19 To further manipulate DNA nanostructures at the mesoscale, strategies combining dynamic DNA nanotechnologies have been developed to study the complexities of cell membranes, such as cell-surface recognition20,21 and membrane receptor studies.22 However, such studies with DNA nano-structures are often confounded by dynamic cell behavior, observed, for example, in internalization and \"flip-flop\" leaflet movements.23 To solve this problem, researchers have turned to fluid soft lipid bilayers as materials to build an ideal model for cell-surface studies of DNA nanostructures.</p><p>To date, different studies have reported the dynamic behavior of tethered DNA nanostructures on various lipid membranes.24,25 However, all of these strategies have overlooked an obvious, but powerful, obstacle to the cell-mimicking membrane environment. As we know, membrane physico-chemical properties have a significant impact in dynamic behavior of DNA nanostructures and their assemblies.26–29 This means that DNA nanostructures on these synthetic model membranes would be remarkably different from their dynamic behavior on the natural membrane.30 Thus, it is necessary to study the dynamic behavior of DNA nanostructures on cell-mimicking giant vesicles model which would further advance our understanding on behavior of DNA nanostructures on biological interfaces.</p><p>Recently, giant membrane vesciles derived from live cells was proved to be an idea cell/membrane model. Because of their highly similarity to cell membrane structure, these membrane vesicles possess the unique superiority on a broad spectrum of studies such as biomembrane physics and biomimetic chemistry, such as phase separation and functional lipid raft domains, as well as membrane protein interactions.31–33 However, the assembly of DNA nanostructures in such cell-mimicking giant membrane vesicles has not been carried out, even though they have been proved to be an idea platform as cell membrane model.</p><p>Herein, as a proof-of-concept, we report manipulating the assembly/disassembly of 3D DNA nanostructures on the cell-mimicking surfaces of micrometer-scale giant membrane vesicles (MVs). DNA triangular prisms (TPs) were selected as a feasible and efficient 3D DNA nanostructural model to study their dynamic behavior on lipid membrane.34 Utilizing DNA hybridization and DNA strand displacement reaction, the dynamic assembly/disassembly processes of TPs on the MVs surface were studied, followed the monitoring by Förster resonance energy transfer (FRET) between the fluorophore pairs, and results also indicated the heterogeneity of DNA assembly on MVs.</p><p>As a starting point, a box-like nanoprism scaffold was initially fabricated by three long single-stranded DNAs (ssDNA) after annealing.34,35 Because of 3D DNA nanostructures consists of at least three DNA strands, DNA TPs scaffolds can be created with the minimum number of DNA strands to meet the requirement of economy in the use of DNA materials. One ssDNA segment elongates from its top face, farthest from the vesicle surface, and serves as an arm (arm strand), whereas a cholesterol-labeled ssDNA segment elongates from its bottom face, as an anchor (anchor strand) (Figure 1B) in order to immoblize the DNA nanoprism onto the surface of MVs. This nanoprism binds to the surface via hydrophobic cholesterol anchorage to the lipid bilayer of MVs, thus facilitating DNA-mediated dynamic regulation of the functional nanoprisms on the cell-mimicking membrane. Initially, we employed the native polyacrylamide gel electrophoresis (N-PAGE) to confirm the formation of the nanoprism scaffold in buffer solution (see Supporting Information (SI), Figure S1). Then the 3D DNA scaffold was transformed into a functional unit by loading an arm and an anchor strand (Figure 1B and SI, Figure S2).</p><p>After successfully demonstrating the feasibility of constructing these 3D DNA nanostructures, we investigated their plasticity in terms of ready assembly and disassembly. To accomplish this, The assembly/disassembly process of DNA nanoprisms was studied in buffer solution to verify their capacity for dynamic reversible manipulation (Figure 1A). Two different DNA nanostructures, TP-A and TP-B, were first constructed by loading alternative Arm A and Arm B strands on the top face, respectively. Assembly of TP-A and TP-B was achieved by hybridizing with a DNA linker. The optimized experiment also showed the high assembly efficiency of DNA nanoprisms (SI, Figure S3A,C). Then, to disassemble the dimeric DNA nanoprism, a toehold-mediated DNA strand displacement reaction was induced by a displacement strand, the disassembly efficiency was also optimozed (SI, Figure S3B,D). Next, N-PAGE results verified the dynamic assembly/disassembly process of TP-A and TP-B achieved by DNA hybridization and DNA strand displacement reaction (Figure 1C). Fluorescence spectral and kinetics results also demonstrated this efficient reversible manipulation, which in agreement with the gel electrophoresis results (SI, Figure S4).</p><p>Different from DNA nanoprisms assembled in buffer solution, where DNA strands are able to diffuse freely, the kinetics of DNA nanostructures on the surface of cell-mimicking giant vesicles was expected to be much more complex because they were derived from living cells and contain cell membrane constituents, such as proteins and glycocalyx,30 likely impacting the kinetics of assembly and disassembly.</p><p>Previously, we developed a facile strategy to prepare micrometer-scale giant membrane vesicles.36 They showed excellent cell-mimicking properties, thus providing an ideal dynamic soft platform at the mesoscale to study the behavior and kinetics of DNA nanostructures. Herein, cell-mimicking MVs detached from HeLa cells were initially obtained with good quality and high yields. To confirm the successful insertion of DNA nanostructures on the biological surface, multicolor fluorescence colocalization of nanoprisms was observed. First, three different DNA-fluorophore sequences were assembled with two nanoprism scaffolds in the test tube, in which a cholesterol-DNA-Alexa Fluor 488 sequence (AF 488-labeled anchor strand) was loaded on the bottom face of all nanoprisms. Afterward, fluorophore-modified nanoprisms TP-Cy3 and TP-Cy5 were created, in which Cy3- and Cy5-labeled arm strands were loaded on each respective top face.</p><p>To anchor nanoprisms on MVs, 22.2 μL mixtures of 9 μM cholesterol-labeled TP-Cy3 and TP-Cy5 were added to 400 μL MVs with 1640 medium containing 5 mM Mg2+. The divalent cation contributes to the binding of DNA nanostructures to the negatively charged lipid bilayers,37 and it also maintains the stability and integrity of DNA nanostructures.15 After incubation with MVs at 37 °C for 30 min, laser confocal scanning microscopy (LCSM) was employed to verify that the modified nanoprisms were readily localized on the cell-mimicking membrane of MVs in Group 1 (Figure 2A, the first panel), followed by quantification of fluorescence colocalization (SI, Figure S5). In the absence of DNA scaffolds, the anchor strand could immobilize onto the membrane via cholesterol insertion (Group 2), while the arm strands without cholesterol mainly distributed outside of the giant vesicles (Group 3). This result demonstrated that DNA TPs could bind to the lipid bilayer though cholesterol insertion, thus providing a facile strategy for anchoring DNA nanostructures to our cell-mimicking giant vesicles (SI, Figure S6). Moreover, the fluorescence intensity of the overlay images (488+Cy3+Cy5, Figure 2A, last line) was measured (Figure 2B) and also demonstrated that these DNA nanostructures could successfully anchor onto the membrane of MVs. Although the preference of DNA nanoprisms localized on the surface of MVs promised their reversible assembly and disassembly, synthetic giant vesicles made from phospholipid was not an idea platform for the surface manipulation, since nanoprisms are easily enriched in the chamber of MVs (SI, Figure S7). It indicate the behavior of DNA nanostructures on synthetic model membranes would be remarkably different from theirs on cell-mimicking surface.</p><p>To characterize the assembly/disassembly of cholesterol-labeled nanoprisms on the cell-mimicking membrane of MVs, we used a FRET configuration composed of TP-Cy3 and TP-Cy5. Thus, the dynamic assembly/disassembly of nanoprisms on the MVs could be visualized via the changes of FRET efficiency between Cy3 and Cy5 fluorescent dyes (Figure 3A). Initially, these nanoprisms (TP-Cy3: TP-Cy5 = 1:1.2) were mixed with MVs in solution and incubated at 37 °C for 10 min (panel 1). The assembly of TP-Cy3 and TP-Cy5 was performed by adding 1.5-fold excess DNA linker and incubating for 50 min at 4 °C (panel 2). Interestingly, we found that low temperature favored the assembly of TP-Cy3 and TP-Cy5 compared to 37 °C (SI, Figure S8), possibly due to the formation of a liquid-order phase in the lipid membrane.38 We speculated that the cholesterol component of anchor strands prefers to exist in this phase, which may increase the opportunity for molecular collision and thus facilitate the assembly of nanoprisms. To monitor the disassembly, 2-fold excess displacement strand was added into solution of MVs and the mixture was incubated for another 1 h. As shown in panel 3, decreased FRET efficiency can be observed by separation of the Cy3- and Cy5-labeled nanoprisms on the cell-mimicking membrane driven by toehold-mediated DNA strand displacement. When a random strand was added to assemble TP-Cy3 with TP-Cy5 on the MVs surface, little effect could be detected, demonstrating that the assembly process was not driven by temperature, but rather by strand hybridization based on specific Watson–Crick DNA base pairing (Figure 3A, panel 4). Furthermore, quantitative assay of FRET efficiency between heteronanoprisms demonstrated the feasibility of nanoprism assembly/disassembly on the MVs surface (Figure 3B). More interestingly, DNA assembly on the MVs surface revealed heterogeneous FRET efficacy. The calculated ratiometric fluorescence from a randomly selected giant vesicle via acceptor photobleaching showed the heterogeneous FRET efficiency of dimeric nanoprism assembly on the surface of our giant vesicles (Figure 3C). Normally, lipid structure in a biomembrane (e.g., plasma membrane and organelle membrane) exists in the form of separated microdomains, indicating the heterogeneity of the biomembrane.38 The membrane of MVs derived from mammalian cells represents one such biomembrane. Thus, we speculated that our giant vesicles would also exhibit membrane heterogeneity and that the observed heterogeneous FRET efficiency was likely caused by localization of cholesterol-labeled nanoprisms in microdomains.</p><p>Along with developing nanotechnology, oligonucleotides not only play an important biological role in living systems but also have emerged as building blocks for self-assembly nano-fabrication. Here, the DNA nanoprism served as the simplest 3D DNA nanostructure model and was thought to find a wide applications in logic computation,9 bioanalysis and biomimetics.16 Besides this nanostructural aspect, the method is also generally applicable to other DNA nanostructures37,39 based on Watson–Crick base pairing and the anchorage of hydrophobic components to membrane. Combining with cell-mimicking surface, manipution of these DNA nanofabrications provide a method to functionalize cell surface, which have to overcome dynamic cell surface movements, and suggest the long-term feasiblitity to regulate the membrane structures.</p><p>In summary, using DNA strand hybridization and toehold-mediated strand displacement, we have engineered the respective assembly and disassembly of DNA nanostructures on cell-mimicking membranes of MVs. The status of a single nanoprism and its dimeric assembly were monitored by FRET, and heterogeneous DNA assembly on MVs was observed. On the basis of the reported dynamic programmability, predictability and addressability of DNA nanostructures, the manipulation of membrane-anchored DNA nanostructures can serve as a new strategy for engineering artificial cells and combining DNA nanotechnology with biomimetics.</p>"
},
{
"role": "assistant",
"content": "DNA nanostructures assembled on living cell membranes have become powerful research tools. Synthetic lipid membranes have been used as a membrane model to study the dynamic behavior of DNA nanostructures on fluid soft lipid bilayers, but without the inherent complexity of natural membranes. Herein, we report the assembly and disassembly of DNA nanoprisms on cell-mimicking micrometer-scale giant membrane vesicles derived from living mammalian cells. Three-dimensional DNA nanoprisms with a DNA arm and a cholesterol anchor were efficiently localized on the membrane surface. The assembly and disassembly of DNA nanoprisms were dynamically manipulated by DNA strand hybridization and toehold-mediated strand displacement. Furthermore, the heterogeneity of reversible assembly/disassembly of DNA nanoprisms was monitored by F\\xc3\\xb6rster resonance energy transfer. This study suggests the feasibility of DNA-mediated functional biomolecular assembly on cell membranes for biomimetics studies and delivery systems."
}
] |
science.anat_em_ner
|
science.anat_em_ner.532
|
[
{
"role": "user",
"content": "You will be shown an abstract from a biomedical research paper. Given this abstract, your task is to extract all unique entities of the following types: [\"AnatomicalEntity\"].\n\nPlease return the output as a JSON object of the format: {\"AnatomicalEntity\": [\"tumor cells\", ...]}. The keys should be entity types and values should be lists of extracted entities belonging to the corresponding type. If you cannot find entities belonging to a specific type, the value should be [].\n\nOnly output the JSON object and do not include any additional text.\n\nAbstract:\n\n[In vitro studies of the thyroid gland regulation principles and their evaluation].\nThe free fractions of the thyroid hormone further the metabolism of the body cells and regulate the synthesis of the thyroid hormone. Once the level of FT3 and FT4 decreases. With the help of a liberation of the hormone stimulating the thyroid gland from the anterior lobe of the pituitary gland the lack of thyroid hormone is corrected. The synthesis and secretion of the thyroid gland stimulating hormone is induced by the thyreotropin releasing hormone which is given by the hypothalamus. Moreover, the organism is able as needed to carry out the monodiodation of LT4 to biologically active LT3 or biologically inactive so-called revers T3 (RT3). The estimation of thyroid gland stimulating hormone before and 30 minutes after intravenous application of thyreotropin releasing hormone has its main importance for the early recognition of a disturbance of the regulating circle hypophysis-thyroid gland, above all in the diagnosis of clinically not yet manifest clinical pictures, such as the latent hypothyreosis and the latent hyperthyreosis, respectively (Basedow hyperthyreosis and thyroidal autonomy). According to the questioning the estimations of the levels of the thyroid hormones and of the thyroid gland stimulating hormone should be used stepwise."
},
{
"role": "assistant",
"content": "{\"AnatomicalEntity\": [\"anterior lobe\", \"thyroid gland\", \"body cells\", \"hypothalamus\", \"pituitary gland\", \"intravenous\"]}"
}
] |
science.drug_combo_extraction_re
|
science.drug_combo_extraction_re.6
|
[
{
"role": "user",
"content": "You will be shown a paragraph from a biomedical research article. Your task is to extract all drug combinations appearing in a specific sentence within in the paragraph. Each drug combination should be assigned to one of the following three categories:\n\n- POS: Indicates a positive interaction between the drugs in the combination; for instance, drugs that have an additive or synergistic effect.\n- NEG: Indicates a negative interaction between the drugs in the combination; for instance, combining these drugs might result in adverse side effects, or might reduce their efficacy.\n- COMB: Indicates that the drugs are given in combination, but the type of interaction between the drugs cannot be determined based on the provided context.\n\nPlease format your answer as a json array. Each entry in the array should itself be an array formatted as [<drug_1>, <drug_2>, ..., <drug_n>, <category>] where <category> is one of the three categories listed above and <drug_1>, ..., <drug_n> are drug names copied verbatim from the input sentence. Different combinations may involve different numbers of drugs; in other words, the `n` in <drug_n> may vary.\n\nAs an example, the following output describes two extracted drug combinations; one between two drugs, and one between three drugs:\n\n[[\"artesunate\", \"artemether\", \"COMB\"], [\"Nifedipine\", \"Labetalol\", \"Prazosin\", \"POS\"]]\n\nThe paragraph and specific sentence are below. You should only extract relationships expressed in the specific sentence; the paragraph is provided for context.\n\nIn your output, return only the json array and no other text. If no drug combinations appear, return an empty array `[]`.\n\nparagraph: A case of Stenotrophomonas maltophilia keratitis effectively treated with moxifloxacin. A 70-year-old man with a long history of diabetes mellitus presented to our hospital (Department of Ophthalmology, Sahm Yook Medical Center, Seoul, Korea) complaining of severe ocular pain and visual disturbance in his left eye that had started three days prior to admission. A round 3.7 × 5.0 mm dense central stromal infiltrate with an overlying epithelial defect was noted on slit-lamp examination. Following corneal scrapings and culture , topical 0.5 % moxifloxacin and 0.5 % tobramycin were administered hourly . A few days later, Stenotrophomonas maltophilia was isolated in a bacterial culture from a corneal specimen. According to the results of susceptibility tests, topical 0.5% moxifloxacin was given every hour and 0.5% tobramycin was stopped. The patient's clinical features improved steadily with treatment. The corneal epithelium healed rapidly, and the infiltrate resolved within four weeks of the initiation of treatment. The patient's best corrected visual acuity improved from hand motion to 20 / 25.\n\nsentence: Following corneal scrapings and culture , topical 0.5 % moxifloxacin and 0.5 % tobramycin were administered hourly ."
},
{
"role": "assistant",
"content": "[[\"moxifloxacin\", \"tobramycin\", \"COMB\"]]"
}
] |
science.ddi_ner
|
science.ddi_ner.78
|
[
{
"role": "user",
"content": "You will be shown an abstract from a biomedical research paper. Given this abstract, your task is to extract all unique entities of the following types: [\"Brand\", \"UnapprovedDrug\", \"Drug\", \"DrugGroup\"].\n\nPlease return the output as a JSON object of the format: {\"Brand\" : [\"Aspirin\", ...], \"DrugGroup\": [\"Salicyclate\", ...], \"Drug\": [\"Phenobarbital\", ...], \"UnapprovedDrug\": [\"Heroin\", ...]}. The keys should be entity types and values should be lists of extracted entities belonging to the corresponding type. If you cannot find entities belonging to a specific type, the value should be [].\n\nOnly output the JSON object and do not include any additional text.\n\nAbstract:\n\nCo-administration of nelfinavir at steady-state with a single dose of azithromycin. Co-administration of nelfinavir at steady-state with a single dose of azithromycin (2 x 600 mg tablets) results in increased azithromycin serum concentrations. Although a dose adjustment of azithromycin is not recommended when administered in combination with nelfinavir, close monitoring for known side effects of azithromycin, such as liver enzyme abnormalities and hearing impairment, is warranted. Azithromycin did not affect the prothrombin time response to a single dose of warfarin. However, prudent medical practice dictates careful monitoring of prothrombin time in all patients treated with azithromycin and warfarin concomitantly. Concurrent use of macrolides and warfarin in clinical practice has been associated with increased anticoagulant effects. Drug interaction studies were performed with azithromycin and other drugs likely to be co-administered. When used in therapeutic doses, azithromycin had a modest effect on the pharmacokinetics of atorvastatin, carbamazepine, cetirizine, didanosine, efavirenz, fluconazole, indinavir, midazolam, rifabutin, sildenafil, theophylline (intravenous and oral), triazolam, trimethoprim/sulfamethoxazole or zidovudine. Co-administration with efavirenz or fluconazole had a modest effect on the pharmacokinetics of azithromycin. No dosage adjustment of either drug is recommended when azithromycin is co administered with any of the above agents. Interactions with the drugs listed below have not been reported in clinical trials with azithromycin; however, no specific drug interaction studies have been performed to evaluate potential drug-drug interaction. Nonetheless, they have been observed with macrolide products. Until further data are developed regarding drug interactions when azithromycin and these drugs are used concomitantly, careful monitoring of patients is advised: Digoxin elevated digoxin concentrations. Ergotamine or dihydroergotamine acute ergot toxicity characterized by severe peripheral vasospasm and dysesthesia. Cyclosporine, hexobarbital and phenytoin concentrations. Laboratory Test Interactions There are no reported laboratory test interactions. Repeat Treatment Studies evaluating the use of repeated courses of Zmax have not been conducted."
},
{
"role": "assistant",
"content": "{\"Brand\": [\"Zmax\"], \"Drug\": [\"Ergotamine\", \"triazolam\", \"Azithromycin\", \"cetirizine\", \"fluconazole\", \"azithromycin\", \"didanosine\", \"zidovudine\", \"midazolam\", \"Digoxin\", \"Cyclosporine\", \"carbamazepine\", \"trimethoprim\", \"hexobarbital\", \"phenytoin\", \"dihydroergotamine\", \"sulfamethoxazole\", \"efavirenz\", \"warfarin\", \"indinavir\", \"theophylline\", \"atorvastatin\", \"digoxin\", \"rifabutin\", \"sildenafil\", \"nelfinavir\"], \"DrugGroup\": [\"macrolide products\", \"macrolides\"], \"UnapprovedDrug\": []}"
}
] |
science.pico_ner
|
science.pico_ner.124
|
[
{
"role": "user",
"content": "You will be shown an abstract from a biomedical research paper. Given this abstract, your task is to extract all unique entities of the following types: [\"Outcome\", \"Participant\", \"Intervention\"].\n\nPlease return the output as a JSON object of the format: {\"Participant\" : [\"patients with COPD\", ...], \"Intervention\" : [\"Atenolol\", ...], \"Outcome\" : [\"blood pressure\", ...]}. The keys should be entity types and values should be lists of extracted entities belonging to the corresponding type. If you cannot find entities belonging to a specific type, the value should be [].\n\nOnly output the JSON object and do not include any additional text.\n\nAbstract:\n\nEfficacy of primaquine regimens for primaquine-resistant Plasmodium vivax malaria in Thailand . To define the current efficacy of Fansidar ( F. Hoffmann-La Roche Ltd. , Basel Switzerland ) ( pyrimethamine and sulfadoxine ) , primaquine in a high dose , and artesunate for treating acute Plasmodium vivax malaria , we conducted a comparative clinical trial of these 3 drugs in an open-label study . Patients ( 15-65 years old ) were assigned to 1 of 4 treatments regimens in a serial order . Ninety percent of the patients were infected at Thailand-Myanmar border . Patients in group I ( n = 23 ) received Fansidar ( 3 tablets , 75 mg of pyrimethamine and 1,500 mg of sulfadoxine , a single dose on the first day ) , group II ( n = 23 ) received Fansidar ( 3 tablets , 75 mg of pyrimethamine and 1,500 mg of sulfadoxine , a single dose on the first day ) and then received primaquine ( 30 mg a day for 14 days ) , group III ( n = 23 ) received primaquine ( 30 mg a day for 14 days ) , and group IV ( n = 23 ) received artesunate ( 200 mg once a day for 3 days ) and then primaquine ( 30 mg a day for 14 days ) . Cure rates on day 28 of follow-up were 40 % , 100 % , 100 % , and 100 % in groups I , II , II , and IV , respectively . There were 4 and 5 patients in group I showing post-treatment reappearance of parasitemia at < or = 16 days and between 17 and 28 days , respectively . Patients in the other 3 groups showed negative parasitemias within 7 days after treatment . Artesunate plus primaquine ( group IV ) cleared parasitemia faster than the other 3 regimens . There is a high proportion of ineffectiveness of Fansidar for treatment of P. vivax malaria and it should be no longer used for treatment of P. vivax malaria acquired at the Thailand-Myanmar border . A high dose of primaquine is safe and effective in the treatment of P. vivax malaria during the 28-day follow-up period ."
},
{
"role": "assistant",
"content": "{\"Intervention\": [\"sulfadoxine\", \"pyrimethamine\", \"artesunate\", \"primaquine ( 30 mg a day for 14 days )\", \"primaquine\", \"received primaquine ( 30 mg a day for 14 days )\", \"Hoffmann-La Roche Ltd.\", \"primaquine regimens\", \"Fansidar\", \"Basel Switzerland )\", \"1,500 mg of sulfadoxine\"], \"Outcome\": [\"ineffectiveness\", \"negative parasitemias\", \"parasitemia\", \"Cure rates\", \"post-treatment reappearance of parasitemia\", \"safe and effective\"], \"Participant\": [\"Thailand .\"]}"
}
] |
science.chemprot_ner
|
science.chemprot_ner.788
|
[
{
"role": "user",
"content": "You will be shown an abstract from a biomedical research paper. Given this abstract, your task is to extract all unique entities of the following types: [\"Protein\", \"Chemical\"].\n\nPlease return the output as a JSON object of the format: {\"Chemical\" : [\"Dexamethasone\", ...], \"Protein\" : [\"BRCA-1\", ...]}. The keys should be entity types and values should be lists of extracted entities belonging to the corresponding type. If you cannot find entities belonging to a specific type, the value should be [].\n\nOnly output the JSON object and do not include any additional text.\n\nAbstract:\n\n[Effect of mifepristone on the expression of progesterone receptor messenger RNA and protein in uterine leiomyomata].\nOBJECTIVE: To determine the expression of progesterone receptor (PR) mRNA and PR protein levels in the myometrium and leiomyomata from untreated and mifepristone pretreated women with leiomyoma and to examine the mechanism of mifepristone treatment on uterine leiomyomata. METHODS: Expression of PR mRNA and PR protein were determined by Northern blot and HAP of single-dose saturated analysis in myometrium and leiomyomata (center and marginal area) from 27 untreated and 6 mifepristone pretreated women with leiomyomata. RESULTS: PR mRNA abundance and PR protein levels in both myomatous center and marginal area were significantly greater than those in corporal myometrium (P < 0.01) in both follicular and luteal phases, but similar between myomatous center and marginal area (P > 0.05). 6 cases pretreated with mifepristone 25 mg/day for 3 months were operated, all but one patient displayed a decrease in leiomyomata volume. PR mRNA abundance in both myometruim and leiomyomata (center and marginal area) was significantly decreased in 4 patients continuing mifepristone treatment before the operation but not in the other 2 patients stopping RU486 1 month before operation. PR protein levels in these tissues showed significant decrease in all 6 cases. CONCLUSION: There are overexpression of PRmRNA and PR protein in leiomyomata. One of the mechanism of mifepristone action on decreasing leiomyomata volume may be related to suppression on expression of PR gene. It seems that suppression on transcription of PR gene is reversible, but on translation of PR gene may maintain in a relatively longer period."
},
{
"role": "assistant",
"content": "{\"Chemical\": [\"mifepristone\", \"RU486\", \"progesterone\"], \"Protein\": [\"PR mRNA\", \"PR\", \"progesterone receptor\", \"PR gene\", \"PRmRNA\", \"PR protein\"]}"
}
] |
science.chemdner_ner
|
science.chemdner_ner.3486
|
[
{
"role": "user",
"content": "You will be shown an abstract from a biomedical research paper. Given this abstract, your task is to extract all unique entities of the following types: [\"Chemical\"].\n\nPlease return the output as a JSON object of the format: {\"Chemical\": [\"Arsenic\", ...]}. The keys should be entity types and values should be lists of extracted entities belonging to the corresponding type. If you cannot find entities belonging to a specific type, the value should be [].\n\nOnly output the JSON object and do not include any additional text.\n\nAbstract:\n\nActivator or Inhibitor? GSK-3 as a new drug target. Glycogen synthase kinase-3 (GSK-3) is a cytoplasmic serine/threonine protein kinase that phosphorylates and inhibits glycogen synthase, thereby inhibiting glycogen synthesis from glucose. However, this serine/threonine kinase is now known to regulate numerous cellular processes through a number of signaling pathways important for cell proliferation, stem cell renewal, apoptosis and development. Because of these diverse roles, malfunction of this kinase is also known to be involved in the pathogenesis of human diseases, such as nervous system disorders, diabetes, bone formation, inflammation, cancer and heart failure. Therefore, GSK-3 is recognized as an attractive target for the development of new drugs. The present review summarizes the roles of GSK-3 in the insulin, Wnt/β-catenin and hedgehog signaling pathways including the regulation of their activities. The roles of GSK-3 in the development of human diseases within the context of its participation in various signaling pathways are also summarized. Finally, the possibility of new drug development targeting this kinase is discussed with recent information about inhibitors and activators of GSK-3."
},
{
"role": "assistant",
"content": "{\"Chemical\": [\"threonine\", \"glucose\", \"serine\"]}"
}
] |
science.drug_combo_extraction_re
|
science.drug_combo_extraction_re.808
|
[
{
"role": "user",
"content": "You will be shown a paragraph from a biomedical research article. Your task is to extract all drug combinations appearing in a specific sentence within in the paragraph. Each drug combination should be assigned to one of the following three categories:\n\n- POS: Indicates a positive interaction between the drugs in the combination; for instance, drugs that have an additive or synergistic effect.\n- NEG: Indicates a negative interaction between the drugs in the combination; for instance, combining these drugs might result in adverse side effects, or might reduce their efficacy.\n- COMB: Indicates that the drugs are given in combination, but the type of interaction between the drugs cannot be determined based on the provided context.\n\nPlease format your answer as a json array. Each entry in the array should itself be an array formatted as [<drug_1>, <drug_2>, ..., <drug_n>, <category>] where <category> is one of the three categories listed above and <drug_1>, ..., <drug_n> are drug names copied verbatim from the input sentence. Different combinations may involve different numbers of drugs; in other words, the `n` in <drug_n> may vary.\n\nAs an example, the following output describes two extracted drug combinations; one between two drugs, and one between three drugs:\n\n[[\"artesunate\", \"artemether\", \"COMB\"], [\"Nifedipine\", \"Labetalol\", \"Prazosin\", \"POS\"]]\n\nThe paragraph and specific sentence are below. You should only extract relationships expressed in the specific sentence; the paragraph is provided for context.\n\nIn your output, return only the json array and no other text. If no drug combinations appear, return an empty array `[]`.\n\nparagraph: [Therapy of severe fungal infections]. Severe fungal infections increase in numbers in the Western world. This is due to more intensive therapies against cancers leading to severe and prolonged immunosuppression. For many years treatment of severe fungal infections had to be done solely with amphothericin B desoxycholate and 5-fluorocytosine. With the advent of triazoles such as fluconazole, lipid formulations of amphotericin B and the development of echinocandines such as caspofungin also severe candidiasis and invasive aspergillosis has become treatable. In particular , caspofungin for invasive candidiasis and voriconazole for invasive aspergillosis seem at least equivalent to amphotericin B. A clear advantage is the advent of lipid formulations of amphotericin B. This regards especially side effects which are reduced with these newer formulations, i.e. nephrotoxicity. Due to the fact that prospective trials are difficult to conduct because patient populations may vary considerably (especially the underlying disease) many comparisons were not yet performed. Nevertheless, promising results indicate that certain combinations of antifungals may enhance prognosis of refractory fungal infections with a so far very serious prognosis.\n\nsentence: In particular , caspofungin for invasive candidiasis and voriconazole for invasive aspergillosis seem at least equivalent to amphotericin B. A clear advantage is the advent of lipid formulations of amphotericin B."
},
{
"role": "assistant",
"content": "[]"
}
] |
science.pubmedqa_qa
|
science.pubmedqa_qa.71
|
[
{
"role": "user",
"content": "You will be shown an abstract from a research paper, and a corresponding research question. Determine the answer to the research question based on the context provided. Your answer should be one of: \"YES\", \"NO\", or \"MAYBE\".\n\nContext:\n(OBJECTIVE) Digital tomosynthesis (DT) is a new X-ray-based imaging technique that allows image enhancement with minimal increase in radiation exposure. The purpose of this study was to compare DT with noncontrast computed tomography (NCCT) and to evaluate its potential role for the follow-up of patients with nephrolithiasis in a nonemergent setting.\n(METHODS) A retrospective review of patients with nephrolithiasis at our institution that underwent NCCT and DT from July 2012 to September 2013 was performed. Renal units (RUs) that did not undergo treatment or stone passage were randomly assigned to two blinded readers, who recorded stone count, size area (mm(2)), maximum stone length (mm), and location, for both DT and NCCT. Mean differences per RU were compared. Potential variables affecting stone detection rate, including stone size and body mass index (BMI), were evaluated. Interobserver agreement was determined using the intraclass correlation coefficient to measure the consistency of measurements made by the readers.\n(RESULTS) DT and NCCT demonstrated similar stone detection rates in terms of stone counts and stone area mm(2). Of the 79 RUs assessed, 41 RUs showed exact stone counts on DT and NCCT. The mean difference in stone area was 16.5 mm(2) (-4.6 to 38.5), p = 0.121. The mean size of the largest stone on NCCT and DT was 9.27 and 8.87 mm, respectively. Stone size and BMI did not cause a significant difference in stone detection rates. Interobserver agreement showed a strong correlation between readers and adequate reproducibility.\n\nQuestion:\nDigital Tomosynthesis: A Viable Alternative to Noncontrast Computed Tomography for the Follow-Up of Nephrolithiasis?\n\nAnswer:"
},
{
"role": "assistant",
"content": "YES"
}
] |
science.acl_arc_intent_classification
|
science.acl_arc_intent_classification.1076
|
[
{
"role": "user",
"content": "You will be presented with a citation segment from the section of an NLP research paper, as well as the context surrounding that citation. Classify the intent behind this citation by choosing from one of the following categories:\n- Background: provides context or foundational information related to the topic.\n- Extends: builds upon the cited work.\n- Uses: applies the methods or findings of the cited work.\n- Motivation: cites the work as inspiration or rationale for the research.\n- CompareOrContrast: compares or contrasts the cited work with others.\n- FutureWork: cites the work as a direction for future research.\n\nYour answer should be a single word from the following list of options: [\"Background\", \"Extends\", \"Uses\", \"Motivation\", \"CompareOrContrast\", \"FutureWork\"]. Do not include any other text in your response.\n\nSection Title:\nintroduction\n\nContext before the citation:\nMEDLINE, the authoritative repository of abstracts from the medical and biomedical primary literature maintained by the National Library of Medicine, provides the clinically relevant sources for answering physiciansâ questions, and is commonly used in that capacity (Cogdill and Moore 1997; De Groote and Dorsch 2003). Furthermore, the need to answer questions related to patient care at the point of service has been well studied and documented (Covell, Uman, and Manning 1985; Gorman, Ash, and Wykoff 1994; Ely et al. 1999, 2005). The confluence of these many factors makes clinical question answering a very exciting area of research.\n\nCitation Sentence:\nMEDLINE , the authoritative repository of abstracts from the medical and biomedical primary literature maintained by the National Library of Medicine , provides the clinically relevant sources for answering physicians ' questions , and is commonly used in that capacity ( Cogdill and Moore 1997 ; De Groote and Dorsch 2003 ) .\n\nContext after the citation:\nHowever, studies have shown that existing systems for searching MEDLINE (such as PubMed, the search service provided by the National Library of Medicine) are often inadequate and unable to supply clinically relevant answers in a timely manner (Gorman, Ash, and Wykoff 1994; Chambliss and Conley 1996). Furthermore, it is clear that traditional document retrieval technology applied to MEDLINE abstracts is insufficient for satisfactory information access; research and experience point to the need for systems that automatically analyze text and return only the relevant information, appropriately summarizing and fusing segments from multiple texts. Not only is clinical question answering interesting from a research perspective, it also represents a potentially high-impact, real-world application of language processing and information retrieval technologyâbetter information systems to provide decision support for physicians have the potential to improve the quality of health care. Our question-answering system supports the practice of evidence-based medicine (EBM), a widely accepted paradigm for medical practice that stresses the importance of evidence from patient-centered clinical research in the health care process."
},
{
"role": "assistant",
"content": "Background"
}
] |
science.bc7_litcovid_topic_classification
|
science.bc7_litcovid_topic_classification.4668
|
[
{
"role": "user",
"content": "You are presented with a paragraph from a COVID-19 literature. Classify the topics of this piece of text by choosing from the following categories:\n\n- Epidemic Forecasting: The content relates to predictions about the spread of COVID-19.\n- Treatment: The paragraph discusses therapeutic methods or medication for COVID-19.\n- Prevention: The content covers measures to prevent the spread of COVID-19.\n- Mechanism: The paragraph explains the biological mechanisms of the virus.\n- Case Report: The content is a report of a COVID-19 case.\n- Transmission: The paragraph discusses how COVID-19 is transmitted.\n- Diagnosis: The content is about diagnosing COVID-19 in individuals.\n\nYour classification should be provided as an element within a JSON array. The array should be formatted with topics enclosed in double quotes and separated by commas, following the JSON format, for example: [\"Topic1\", \"Topic2\", ...]. Include all applicable topics within the array. Your output should be a valid JSON array, and no additional text should be included in your response.\n\nArticle:\n\nBACKGROUND: The availability of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) serologic testing has rapidly increased. Current assays use a variety of technologies, measure different classes of immunoglobulin or immunoglobulin combinations and detect antibodies directed against different portions of the virus. The overall accuracy of these tests, however, has not been well-defined. The Infectious Diseases Society of America (IDSA) convened an expert panel to perform a systematic review of the coronavirus disease 2019 (COVID-19) serology literature and construct best practice guidance related to SARS-CoV-2 serologic testing. This guideline is the fourth in a series of rapid, frequently updated COVID-19 guidelines developed by IDSA. OBJECTIVE: IDSA's goal was to develop evidence-based recommendations that assist clinicians, clinical laboratories, patients and policymakers in decisions related to the optimal use of SARS-CoV-2 serologic tests in a variety of settings. We also highlight important unmet research needs pertaining to the use of anti-SARS-CoV-2 antibody tests for diagnosis, public health surveillance, vaccine development and the selection of convalescent plasma donors. METHODS: A multidisciplinary panel of infectious diseases clinicians, clinical microbiologists and experts in systematic literature review identified and prioritized clinical questions related to the use of SARS-CoV-2 serologic tests. Grading of Recommendations Assessment, Development and Evaluation (GRADE) methodology was used to assess the certainty of evidence and make testing recommendations. RESULTS: The panel agreed on eight diagnostic recommendations. CONCLUSIONS: Information on the clinical performance and utility of SARS-CoV-2 serologic tests are rapidly emerging. Based on available evidence, detection of anti-SARS-CoV-2 antibodies may be useful for confirming the presence of current or past infection in selected situations. The panel identified three potential indications for serologic testing including: 1) evaluation of patients with a high clinical suspicion for COVID-19 when molecular diagnostic testing is negative and at least two weeks have passed since symptom onset; 2) assessment of multisystem inflammatory syndrome in children; and 3) for conducting serosurveillance studies. The certainty of available evidence supporting the use of serology for either diagnosis or epidemiology was, however, graded as very low to moderate."
},
{
"role": "assistant",
"content": "[\"Diagnosis\"]"
}
] |
science.chemprot_re
|
science.chemprot_re.25
|
[
{
"role": "user",
"content": "Given an abstract from a research paper, your task is to identify and label relationships between chemical compounds and genes mentioned in the abstract.\n\nThe relationship type must be one of ['DOWNREGULATOR', 'SUBSTRATE', 'INDIRECT-REGULATOR', 'PART-OF', 'MODULATOR-ACTIVATOR', 'REGULATOR', 'INHIBITOR', 'COFACTOR', 'UPREGULATOR', 'ACTIVATOR', 'ANTAGONIST', 'NOT', 'INDIRECT-DOWNREGULATOR', 'SUBSTRATE_PRODUCT-OF', 'INDIRECT-UPREGULATOR', 'AGONIST', 'PRODUCT-OF', 'MODULATOR', 'DIRECT-REGULATOR', 'UNDEFINED', 'AGONIST-INHIBITOR', 'AGONIST-ACTIVATOR', 'MODULATOR-INHIBITOR'].\n\nPlease format your output as a JSON array. Each entry in the array should express a single relation, formatted as [\"<Entity_A>\", \"<RELATION_A_B>\", \"<Entity_B>\"]. If no relations can be found, please output an empty JSON array [].\n\nAbstract:\n\nWater extract of licorice had anti-viral activity against human respiratory syncytial virus in human respiratory tract cell lines. ETHNOPHARMACOLOGICAL RELEVANCE: Licorice (Glycyrrhiza uralensis Fisch., Leguminosae) has been used in herbal medicine and food supplement worldwide for centuries. Licorice is a common ingredient of several prescriptions of traditional Chinese medicine which have been proved to inhibit infection of human respiratory syncytial virus (HRSV). There are two preparations of licorice, Radix Glycyrrhizae and Radix Glycyrrhizae Preparata. However, it is unknown whether licorice or which preparation of licorice is effective against HRSV, nor is its active constituent. AIM OF THE STUDY: We tested the hypothesis that Radix Glycyrrhizae can effectively decrease HRSV-induced plaque formation in respiratory mucosal cell lines. We also tried to find out the active constituent. MATERIALS AND METHODS: Anti-HRSV activities of hot water extracts of preparations of licorice, glycyrrhizin and 18β-glycyrrhetinic acid (18β-GA), the active constituents of licorice, were examined by plaque reduction assay in both human upper (HEp-2) and low (A549) respiratory tract cell lines. Abilities of crude licorice to inhibit viral replication and to stimulate IFN-β were evaluated by reverse transcription polymerase chain reaction (RT-PCR) and enzyme-linked immunosorbent assay (ELISA), respectively. RESULTS: Radix Glycyrrhizae and Radix Glycyrrhizae Preparata dose-dependently inhibited HRSV-induced plaque formation in both HEp-2 and A549 cell lines (p<0.0001). The effect of Radix Glycyrrhizae was better than that of Radix Glycyrrhizae Preparata on HEp-2 cells. However, there was no difference of their anti-HRSV effects on A549 cells. Besides, glycyrrhizin was ineffective at all. Nevertheless, 18β-GA showed a potent anti-HRSV activity. Radix Glycyrrhizae was more effective when given before viral inoculation (p<0.0001) which may be due to its inhibition of viral attachment on (p<0.0001) and penetration (p<0.0001) into the host cells. The anti-HRSV activity of Radix Glycyrrhizae was further confirmed by RT-PCR and qRT-PCR. 300μg/ml Radix Glycyrrhizae markedly decreased the viral amounts within the cells and in the suspension. Radix Glycyrrhizae might further stimulate mucosal cells to secrete IFN-β to counteract viral infection. CONCLUSIONS: Both Radix Glycyrrhizae and Radix Glycyrrhizae Preparata are effective against HRSV infection on airway epithelial cells. Radix Glycyrrhizae inhibited HRSV mainly by preventing viral attachment, internalization, and by stimulating IFN secretion. 18β-GA may be one of its active constituents."
},
{
"role": "assistant",
"content": "[]"
}
] |
science.anat_em_ner
|
science.anat_em_ner.335
|
[
{
"role": "user",
"content": "You will be shown an abstract from a biomedical research paper. Given this abstract, your task is to extract all unique entities of the following types: [\"AnatomicalEntity\"].\n\nPlease return the output as a JSON object of the format: {\"AnatomicalEntity\": [\"tumor cells\", ...]}. The keys should be entity types and values should be lists of extracted entities belonging to the corresponding type. If you cannot find entities belonging to a specific type, the value should be [].\n\nOnly output the JSON object and do not include any additional text.\n\nAbstract:\n\nInhibition of Dll4-mediated signaling induces proliferation of immature vessels and results in poor tissue perfusion.\nVascular development is dependent on various growth factors and certain modifiers critical for providing arterial or venous identity, interaction with the surrounding stroma and tissues, hierarchic network formation, and recruitment of pericytes. Notch receptors and ligands (Jagged and Delta-like) play a critical role in this process in addition to VEGF. Dll4 is one of the Notch ligands that regulates arterial specification and maturation events. In the current study, we have shown that loss of function by either targeted allele deletion or use of a soluble form of Dll4 extracellular domain leads to inhibition of Notch signaling, resulting in increased vascular proliferation but defective maturation. Newly forming vessels have thin caliber, a markedly reduced vessel lumen, markedly reduced pericyte recruitment, and deficient vascular perfusion. sDll4 similarly induced defective vascular response in tumor implants leading to reduced tumor growth. Interference with Dll4-Notch signaling may be particularly desirable in tumors that have highly induced Dll4-Notch pathway."
},
{
"role": "assistant",
"content": "{\"AnatomicalEntity\": [\"stroma\", \"Vascular\", \"tumors\", \"tissues\", \"vascular\", \"venous\", \"tissue\", \"vessel lumen\", \"tumor\", \"pericyte\", \"pericytes\", \"arterial\", \"vessels\", \"hierarchic network\", \"caliber\", \"extracellular\"]}"
}
] |
science.anat_em_ner
|
science.anat_em_ner.23
|
[
{
"role": "user",
"content": "You will be shown an abstract from a biomedical research paper. Given this abstract, your task is to extract all unique entities of the following types: [\"AnatomicalEntity\"].\n\nPlease return the output as a JSON object of the format: {\"AnatomicalEntity\": [\"tumor cells\", ...]}. The keys should be entity types and values should be lists of extracted entities belonging to the corresponding type. If you cannot find entities belonging to a specific type, the value should be [].\n\nOnly output the JSON object and do not include any additional text.\n\nAbstract:\n\nImmunocytochemistry\nC2C12 cells grown in 8-chamber slides (Nunc) were fixed in 4% PFA/PBS for 10 min and permeabilized in 0.1% Triton X-100 for 20 min. In some cases, they were fixed and permeabilized in methanol at -20degreesC for 2 min. The fixed and permeabilized cells were blocked in PBS containing 3% BSA (Jackson ImmunoResearch Laboratories) and incubated overnight at 4degreesC with primary antibodies in blocking solution. Immunoreactivity was detected with either Alexa-conjugated secondary antibody (Molecular Probes) or a combination of biotin-conjugated secondary antibody (Vector Laboratories) and Alexa-conjugated streptavidin (Molecular Probes)."
},
{
"role": "assistant",
"content": "{\"AnatomicalEntity\": [\"C2C12 cells\", \"cells\"]}"
}
] |
science.scientific_papers_summarization_single_doc_arxiv
|
science.scientific_papers_summarization_single_doc_arxiv.60502
|
[
{
"role": "user",
"content": "You will be presented with the full text of a science research paper. Please write an abstract for this paper. Your response should include the abstract and no additional text.\n\nPaper text:\nthere has been much recent progress in detecting and modeling high energy ( @xmath1ev ) magnetospheric emission from spin powered pulsars .\ni will not discuss the coherent radio pulsations which provide the primary channel for pulsar discovery and dynamics / evolutionary studies ( as our three honorees and their colleagues continue to teach us ) .\nthe mechanism producing the radio has been very difficult to reconstruct ( however see gupta , jenet , melrose , these proceedings ) , but a well established phenomenology suggests that this is relatively low altitude emission above the magnetic polar cap .\ni will also only briefly describe the soft x - ray thermal emission from neutron star surfaces ( for a recent review , see pavlov , zavlin & sanwal 2002 ) .\nthus we focus here on the incoherent , non - thermal radiation , which is the product of magnetosphere gaps .\nthis radiation is highly pulsed and , hence , highly beamed . with pulse profiles having characteristic component widths @xmath2 in phase and the cusp of the crab optical pulse extending over no more than @xmath3 we must have radiation dominated by @xmath4 with @xmath5 .\nwe also must have relatively narrow radiating zones in the magnetosphere , where again the component widths restrict us to a few percent of the open field line volume .\nto set the stage i plot a compilation of light curves from many sources , updated from romani ( 2000 ) .\ni have placed the closest approach of the radio pole at phase 0 and 1.5 pulse periods are shown for clarity . for geminga the phase is set by the predicted outer magnetosphere pulses matched to the @xmath0-ray . for psr b1055 - 52 ,\nthe radio polarization indicates that the pulse at @xmath6 passes closest to the line of sight ; the interpulse is apparently stronger . in several cases\nthe source has only an unpulsed detection ; these are shown as flat lines . in the outer magnetosphere picture ( morini 1983\n; cheng , ho & ruderman 1986 ) the light curves displayed in this way make a fairly coherent set .\nthe gev pulses have double peaks which come from the pole at @xmath7 and are beamed toward the spin equator ( @xmath8 ) .\naberration shifts the peaks forward in phase and pulsars viewed at smaller @xmath9 have a smaller gev peak separation ; the model provides a quantitative match to the observed profiles ( romani & yadigaroglu 1995 ) .\nthe non - thermal optical and hard x - ray emissions lie largely within the @xmath0-ray peaks and arise at lower altitudes , close to the null charge surface that serves as the inner boundary of the acceleration gap .\nthe interpretation of the soft x - ray emission is complicated by the presence of thermal surface flux , which itself may be pulsed if the surface temperature is non - uniform .\nthe radio emission , being more tightly beamed , shows narrow pulses covering a small portion of the sky . the exception to this picture is the crab , whose strong non - thermal accelerators seem to keep pair production rates and particle densities so high that all emissions ( radio-@xmath0-ray ) are dominated by the outer gap zone .\nthis interpretation has encouraging successes , but is not unique .\nin particular , harding and colleagues ( _ e.g. _ daugherty and harding 1996 ) have described an aligned rotator polar cap model that can produce high energy hollow cone emission .\nlight curves locate the position of the radiation zones , but spectral energy distributions ( seds ) are the key to identifying the radiation processes . thompson ( 1998 )\nhas compiled a useful set of broad - band seds for the young pulsars .\nthe most striking feature of these @xmath10 plots is the power peak at @xmath11mev , with a rollover at several gev .\nthis component clearly arises from the radiation - reaction limit process for the primary magnetosphere @xmath4 .\nmost recent models ( _ e.g. _ daugherty & harding 1996 , romani 1996 , zhang & cheng 1997 , hirotani & shibata 1999 ) conclude that the particles are curvature radiation limited . at present ,\nouter magnetosphere spectral computations are more complex and less complete than near - surface polar cap models .\nthe key difference is that at the polar cap @xmath12 provides an efficient source of pair plasma to limit the gap potentials and provide the radiating plasma .\nmoreover , in modern polar cap models ( harding , muslimov & zhang 2002 ) the acceleration field is set by general relativistic frame dragging , providing some insulation from the details of gap electrodynamics .\nin contrast , outer gap models produce pairs via @xmath13 , and rely on the charge gaps themselves to provide the acceleration field .\nin fact in some pulsars the soft target photons are provided by the gap as well . in this way\ngap luminosity and spectrum computations are ( at least ) doubly recursive ( figure 2 ) . in effect , outer magnetosphere gaps are self - limiting : to provide the relatively large gev efficiencies observed for some pulsars from curvature radiation of @xmath14 @xmath4 primaries the gaps must _ by definition _ be barely closed .\nthus computations are difficult and to get the details right will likely require dynamic 3-d gap models , well beyond the state of the art today . in brief , acceleration of the primary electrons\nis limited by curvature radiation reaction ( cr ) .\nthese curvature photons convert on soft thermal ( kt ) or synchrotron ( sy ) photons to make the pairs which limit the growth of the acceleration gap .\nthe thermal emission produced by the general star surface and the pair - heated polar cap zone may dominate the target soft photons for vela - like pulsars , but for younger pulsars and for msp the synchrotron component should control the gaps .\nthis synchrotron emission comes from cooling of the initial pitch angle of the @xmath13 pairs . aside from the uv / soft x - ray band it dominates the spectrum in the mev - ev range . for crab - like pulsars\nthis emission may be self - absorbed at sub - ev energies .\nthere may also be ir - uv spectral features related to the local cyclotron energy ; in general we expect a peak in the photon number flux in the optical / ir range .\ninterestingly , it seems likely that this radiation represents an unusual low pitch angle @xmath15 regime of synchrotron emission ( cruzius - wtzel , kunzl & lesch 2001 ) .\nthe presence of these soft photons guarantees some inverse compton scattering emission at multi - tev energies , however the ir spectral break of the synchrotron component and the substantial beaming of this low energy flux greatly reduce the ics optical depth and make computation of the ics flux difficult .\nphase - resolved measurements of the spectral breaks provide the best test of these models .\nfor example , while polar cap models predict a very abrupt gev turnover from @xmath16 absorption , in the outer magnetosphere the gev cutoff is the more gradual rollover of the primary curvature spectrum for @xmath17 @xmath4 .\nexisting egret data suggest mild ( exponential ) cut - offs for vela and geminga , but a definitive answer requires glast .\nthe peak of the synchrotron spectrum is at @xmath18mev for @xmath19 near the null - charge surface , where @xmath20 induced by aberration .\nmeasurement of this component and its variation with pulse phase thus probes both the birth - site of the @xmath13 pairs and the field in the emission zone .\nsimilarly measurement of the optical / ir spectral breaks ( and polarization behavior ) can probe the cooled population of @xmath4 .\nhowever , except for crab - like pulsars , this will be a challenge , as the emission is faint , typically @xmath21 even for the nearest young objects .\nof course , the gap emissions described above are highly beamed , so the observed sed of a young , @xmath0-ray active pulsar will depend on the magnetic inclinations @xmath22 and earth viewing angle @xmath9 . to illustrate how viewing geometry affects the source appearance , i present a ` unified model ' , in the spirit of the agn unified model .\nthere are four main cases , illustrated in figure 3 .\nfirst , with large @xmath23 , the object is visible as a radio pulsar and the active gaps dominate the high energy flux . a nearly isotropic thermal component ( possibly with pulsations from a hot polar cap )\nis also visible .\nthe bulk of the _ known _\n@xmath0-ray pulsars fall in this class , as the sample is highly biased to objects amenable to radio discovery . the other class of\neasily discovered , radio bright young pulsars has small @xmath24 . for these objects the strong outer gap cr component will miss earth .\ngev emission may be present , but it will represent ` off - pulse ' emission with fluxes a small @xmath25% fraction of that for the vela - like objects .\nevidence for such weak , more widely beamed flux comes from the low level gap emission seen for crab and vela through all pulse phases .\none picture for such ` off - beam ' emission in the polar cap scenario has been described by harding & zhang ( 2001 ) . for small @xmath26 ( e.g. psr b0565 + 14 )\nsources , the mev synchrotron flux from the newly produced @xmath4 with relatively large @xmath27 may still be visible .\nnot also that for this geometry , we _ expect _ to see @xmath0-ray emission from near surface polar cap gaps , presumably with low flux\n. for @xmath28 neither the radio nor gap beams will be visible , although the neutron star can still be discovered via the nearly isotropic thermal emission .\nrx j1856 - 3754 provides a likely example of this geometry ( braje & romani 2002 ) .\nfinally when @xmath9 is appreciably larger than @xmath22 , radio emission is not visible , but the non - thermal gap emission will be strong .\ngeminga is the archetype of this case .\nsince they lack radio pulses , we expect that the handful of such objects known today is much smaller than their true population .\nthus to understand individual seds , we need robust estimates of @xmath22 and @xmath9 .\nthe recent discoveries of equatorial tori in pulsar wind nebula ( pwn ) provide such estimates for the crab and vela pulsars .\nwe have shown that even for fainter pwn useful constraints on @xmath9 can be obtained ( romani & ng 2002 ) .\nthese measurements provide predictions of which pulsars will show bright non - thermal high energy emission and can also probe the relationship between neutron star linear and angular momenta ( lai , these proceedings ) .\nwhile geometry offers a uniform interpretation of the phase - averaged seds of young neutron stars , as observation sensitivities increase , finer details in the pulse profiles and phase - resolved spectra provide continued challenges .\nfor example crab ( moffett & hankins 1996 ) and vela ( harding et al .\n2002 ) multiwavelength profile compilations show at least four components each\n. clearly multiple regions are active in the pulsar magnetosphere . of course\n, even if the bulk of the high energy emission is produced in the outer magnetosphere , some pairs and faint @xmath0-rays associated with the radio - generating polar cap gaps _ must _ be present .\n[ mutual gap poisoning may prevent both being visible from the same pole ; note that for outer gaps we automatically see the opposite pole in the radio . ]\nit seems plausible that with the @xmath29 dynamic range available in the glast era , we may be able to identify @xmath0 activity from both gaps .\none further radio - high energy connection deserves comment .\nthe crab giant radio pulses must , of course , be a high altitude phenomenon .\nthe discovery of similar pulses in millisecond pulsars , apparently aligned with strong narrow x - ray components , suggests a more general connection between such pulses and high energy emission ( romani & johnston 2001 , johnston , these proceedings ) . with this zoo of behaviors ,\nclearly the high - energy / radio connection will keep observers and theorists busy for some time to come .\nbraje , t.m . &\nromani , r.w .\n2002 , in press .\ncheng , k.s , ho , c. & ruderman , m. 1986 , , 300 , 522 cruzius - wtzel , a.r .\n, kunzl , t. & lesch , h. 2001 , , 546 , 401 daugherty , j.k . & harding , a.k .\n1996 , , 458 , 278 harding , a.k . ,\nmusslimov , a.g . &\nzhang , b. 2002 , , 576 , 366 harding , a.k . & zhang , b. 2001 , , 548 , l37 harding , a.k .\n2002 , , 576 , 376 hirotani , k. & shibata , s. 1999 , , 308 , 54 moffett , d.a & hankins , t.h .\n1996 , 468 , 779 morini , m. 1983 , , 202 , 495 pavlov , g.g . , zavlin , v.e . & sanwal , d. 2002 , astro - ph/0206024 romani , r.w . 1996 , , 470 , 469 romani , r.w . &\nng , c .- y .\n2002 , , submitted .\nromani , r.w . &\nyadigaroglu , i .- a .\n1995 , , 438 , 314 romani , r.w . &\njohnston 2001 , , 557 , l93 thompson , d.j .\n1998 , in neutron stars and pulsars , ed .\nn. shibazaki , n. kawai , s. shibata & t. kifune ( tokyo : universal academy ) 273 .\nzhang , l. & cheng , k.s .\n1997 , , 487 , 370"
},
{
"role": "assistant",
"content": "recent observations have detected a number of young pulsars from the power peak in the @xmath0-ray band to the incoherent photon peak in the optical / ir . \n we have made progress on the multiwavelength phenomenology of pulsar emission and beaming , but a wide variation of light curves between different objects and different energy bands makes the full story complex . \n i sketch here a ` unified model ' of pulsar beaming and summarize the radiation mechanisms and their interplay in outer magnetosphere models of pulsar high energy emission . \n # 1_#1 _ # 1_#1 _ = # 1 1.25 in .125 in .25 in"
}
] |
science.bioasq_yesno_qa
|
science.bioasq_yesno_qa.412
|
[
{
"role": "user",
"content": "You have to answer a biomedical question in binary format, i.e. only yes and no are the only acceptable answer formats. A list of paragraphs is provided as context to help you answer the question.\n\nQuestion: Is it possible to visualize subtahalamic nucleus by using transcranial ultrasound?\n\nContext: After measuring thermal effects of TCS and imaging artefact sizes of DBS lead using a skull phantom, we prospectively enrolled 34 patients with DBS of globus pallidus internus, ventro-intermediate thalamic or subthalamic nucleus. TCS had no influence on lead temperature, electrical parameters of DBS device or clinical state of patients. TCS measures of lead coordinates agreed with MRI measures in anterior-posterior and medial-lateral axis. Lead dislocation requiring reinsertion was reliably detected.\nTCS may therefore become a first-choice modality to monitor lead location.\nTwo pilot studies have demonstrated that the intraoperative visualization with TCS and the TCS-assisted insertion of deep-brain stimulation (DBS) electrodes into the subthalamic nucleus and the globus pallidus interna are feasible and safe provided there is exact knowledge on the extent of electrode TCS imaging artifacts.\nPeroperative transcranial sonography for electrode placement into the targeted subthalamic nucleus of patients with Parkinson disease: technical note\nThe correct anatomic position of the electrode tip could be indirectly assessed thanks to the topographic relationship of the STN with the hyperechogenic substantia nigra and the nucleus ruber.\nCONCLUSIONS: Transcranial sonography is easily feasible during stereotactic surgery. In combination with the clinical effects of electrostimulation on the symptoms of Parkinson's disease and with stereotactic x-ray images, it enables the assessment and the documentation of the correct position of implanted STN electrodes in real time.\nAfter measuring thermal effects of TCS and imaging artefact sizes of DBS lead using a skull phantom, we prospectively enrolled 34 patients with DBS of globus pallidus internus, ventro-intermediate thalamic or subthalamic nucleus\nTwo pilot studies have demonstrated that the intraoperative visualization with TCS and the TCS-assisted insertion of deep-brain stimulation (DBS) electrodes into the subthalamic nucleus and the globus pallidus interna are feasible and safe provided there is exact knowledge on the extent of electrode TCS imaging artifacts"
},
{
"role": "assistant",
"content": "yes"
}
] |
science.chia_ner
|
science.chia_ner.1459
|
[
{
"role": "user",
"content": "You will be shown inclusion or exclusion criteria for a clinical trial. Given these criteria, your task is to extract all unique entities of the following types: [\"Observation\", \"Condition\", \"Procedure\", \"Drug\", \"Temporal\", \"Multiplier\", \"Qualifier\", \"Negation\", \"ReferencePoint\", \"Scope\", \"Value\", \"Mood\", \"Device\", \"Visit\", \"Measurement\", \"Person\"].\n\nPlease return the output as a JSON object of the format: {\"Condition\" : [\"breast cancer\", ...], \"Device\" : [\"ports\", ...], \"Drug\" : [\"Atenolol\", ...], \"Measurement\" : [\"blood pressure\", ...], \"Mood\" : [\"suspected\", ...], \"Multiplier\" : [\"more than two\", ...], \"Negation\" : [\"no\", ...], \"Observation\" : [\"history\", ...], \"Person\" : [\"male\", ...], \"Procedure\" : [\"surgery\", ...], \"Qualifier\" : [\"severe\", ...], \"ReferencePoint\" : [\"enrollment\", ...], \"Scope\" : [\"infection\", ...], \"Temporal\" : [\"one day\", ...], \"Value\" : [\"50%\", ...], \"Visit\" : [\"ICU\", ...]}. The keys should be entity types and values should be lists of extracted entities belonging to the corresponding type. If you cannot find entities belonging to a specific type, the value should be [].\n\nOnly output the JSON object and do not include any additional text.\n\nAbstract:\n\nPatient harboring a GRE or CRE bacteria\nColonization confirmed by our microbiology department, including at least 3 positives swabs in the last month"
},
{
"role": "assistant",
"content": "{\"Condition\": [\"CRE bacteria\", \"Colonization\", \"GRE bacteria\"], \"Device\": [], \"Drug\": [], \"Measurement\": [], \"Mood\": [], \"Multiplier\": [\"at least 3\"], \"Negation\": [], \"Observation\": [], \"Person\": [], \"Procedure\": [\"swabs\"], \"Qualifier\": [\"confirmed by our microbiology department\"], \"ReferencePoint\": [], \"Scope\": [], \"Temporal\": [\"in the last mont\"], \"Value\": [\"positives\"], \"Visit\": []}"
}
] |
science.data_reco_mcq_mc
|
science.data_reco_mcq_mc.854
|
[
{
"role": "user",
"content": "You are provided with a research question, keyphrases about the question, a description of candidate datasets and dataset options. Read the description of popular datasets provided below and select the ones that can be used to validate the following research question. Use your knowledge of machine learning datasets to make the best judgement.\nYour response should be formatted as a `json` array. For instance, for the query \"Semi supervised image classification\", a sample response might be: [\"CIFAR-10\", \"CIFAR-100\"]. Do not include any extra text in the response other than the answer array.\n\nQuery: I want to train a video completion model for filling holes in a video.\n\nKeyphrases: video completion\n\nDataset description:\nMovieFIB: A quantitative benchmark for developing and understanding video of fill-in-the-blank question-answering dataset with over 300,000 examples, based on descriptive video annotations for the visually impaired.\nDAVIS: The Densely Annotation Video Segmentation dataset (DAVIS) is a high quality and high resolution densely annotated video segmentation dataset under two resolutions, 480p and 1080p. There are 50 video sequences with 3455 densely annotated frames in pixel level.\nTVQA: The TVQA dataset is a large-scale vido dataset for video question answering. It is based on 6 popular TV shows (Friends, The Big Bang Theory, How I Met Your Mother, House M.D., Grey's Anatomy, Castle).\nPlaces: The Places dataset is proposed for scene recognition and contains more than 2.5 million images covering more than 205 scene categories with more than 5,000 images per category.\nViolin: Video-and-Language Inference is the task of joint multimodal understanding of video and text. Given a video clip with aligned subtitles as premise, paired with a natural language hypothesis based on the video content, a model needs to infer whether the hypothesis is entailed or contradicted by the given video clip.\n\nOptions:- A: MovieFIB B: DAVIS C: TVQA D: Places E: Violin"
},
{
"role": "assistant",
"content": "[\"DAVIS\", \"Places\"]"
}
] |
science.scierc_re
|
science.scierc_re.110
|
[
{
"role": "user",
"content": "Below is an abstract from a computer science research paper. Given this abstract, your task is to extract all unique relationships between entities of the following types:\n\n- \"USED-FOR\": For instance, \"Our method models user proficiency\" -> [\"method\", \"user proficiency\", \"USED-FOR\"].\n- \"EVALUATE-FOR\": For instance, \"We evaluate our method using F1-measure\" -> [\"F1-measure\", \"method\", \"EVALUATE-FOR\"].\n- \"FEATURE-OF\": For instance, \"prior knowledge of the model\" -> [\"prior knowledge\", \"model\", \"FEATURE-OF\"].\n- \"HYPONYM-OF\": For instance, \"TUIT is a software library\" -> [\"TUIT\", \"software library\", \"HYPONYM-OF\"].\n- \"PART-OF\": For instance, \"We incorporate NLU module into the system.\" -> [\"NLU module\", \"system\", \"PART-OF\"].\n- \"COMPARE\": For instance, \"Unlike the quantitative prior, the qualitative prior is often ignored\" -> [\"quantitative prior\", \"qualitative prior\", \"COMPARE\"].\n- \"CONJUNCTION\": For instance: \"obtained from human expert or knowledge base\" -> [\"human expert\", \"knowledge base\", \"CONJUNCTION\"].\n\nFormat your output as a json array. Each entry in the array should express a single relation, formatted as [\"<Entity_A>\", \"<Entity_B>\", \"<RELATION_A_B>\"]. An example output might look like:\n\n[[\"neural networks\", \"classification\", \"USED-FOR\"], [\"neuron\", \"neural network\", \"PART-OF\"]].\n\nIf no relations are found, please return an empty array [].\n\nAbstract:\n\nWe present an efficient algorithm for chart-based phrase structure parsing of natural language that is tailored to the problem of extracting specific information from unrestricted texts where many of the words are unknown and much of the text is irrelevant to the task. The parser gains algorithmic efficiency through a reduction of its search space. As each new edge is added to the chart, the algorithm checks only the topmost of the edges adjacent to it, rather than all such edges as in conventional treatments. The resulting spanning edges are insured to be the correct ones by carefully controlling the order in which edges are introduced so that every final constituent covers the longest possible span. This is facilitated through the use of phrase boundary heuristics based on the placement of function words, and by heuristic rules that permit certain kinds of phrases to be deduced despite the presence of unknown words. A further reduction in the search space is achieved by using semantic rather than syntactic categories on the terminal and non-terminal edges, thereby reducing the amount of ambiguity and thus the number of edges, since only edges with a valid semantic interpretation are ever introduced."
},
{
"role": "assistant",
"content": "[[\"natural language\", \"chart-based phrase structure parsing\", \"USED-FOR\"], [\"semantic\", \"syntactic categories\", \"COMPARE\"], [\"algorithm\", \"chart-based phrase structure parsing\", \"USED-FOR\"], [\"semantic\", \"terminal and non-terminal edges\", \"FEATURE-OF\"], [\"syntactic categories\", \"terminal and non-terminal edges\", \"FEATURE-OF\"], [\"function words\", \"phrase boundary heuristics\", \"USED-FOR\"], [\"semantic\", \"reduction in the search space\", \"USED-FOR\"]]"
}
] |
science.scireviewgen_multidoc_summarization
|
science.scireviewgen_multidoc_summarization.17843
|
[
{
"role": "user",
"content": "You are presented with multiple paper abstracts, alongside the associated literature review and chapter titles. Given the provided information, you are going to do a literature review. Please generate a coherent literature review that synthesizes the content, draws connections between different works, highlights major findings, and identifies any gaps in the existing research.\n\nLiterature Review Title: A Survey of Medium Access Mechanisms for Providing Robust Audio Video Streaming in IEEE 802.11aa Standard \nChapter Title: 1) THE FRAME AGGREGATION SCHEME (FAS) \n1. Abstract of Cited Paper (BIB001): Abstract Based on the IoT Communication Reference Model, the poster proposes a substantial amendment to its layers through adding an extra layer called “Security Layer”. This proposed layer can be considered as a step forward to a centralized management of all security mechanisms into a single and powerful layer. The Security Layer aims to confirm the identity of the sender/receiver, and to help to block connections to potentially vulnerable services. Furthermore, this centralization would leave other IoT's Communication Reference Model Layers to perform their specified functions without paying attention to any security problems, thus supporting the creation of future troubleshooting processes for such problems. \n2. Abstract of Cited Paper (BIB002): The reduction of the energy footprint of large and mid-sized IEEE 802.11 access networks is gaining momentum. When operating at the network management level, the availability of an accurate power model of the APs becomes of paramount importance, because different detail levels have a non-negligible impact on the performance of the optimisation algorithms. The literature is plentiful of AP power models, and choosing the right one is not an easy task. In this paper we report the outcome of a thorough study on the impact that various inflections of the AP power model have when minimising the energy consumption of the infrastructure side of an enterprise wireless LAN. Our study, performed on several network scenarios and for various device energy profiles, reveals that simple one- and two-component models can provide excellent results in practically all cases. Conversely, employing accurate and detailed power models rarely offers substantial advantages in terms of power reduction, but, on the other hand, makes the solving algorithms much slower to execute.\n\nLiterature Review:"
},
{
"role": "assistant",
"content": "The aim of the FAS scheme is to reduce the overhead of transmission time as well as decrease the back-off time during successive frame transmissions by transmitting several frames as one aggregated frame. Two aggregation frame schemes are introduced. The first is A-MSDU. This scheme allows the aggregation of several MSDUs into the one MAC Protocol Data Unit (MPDU). The Destination Address (DA) and Source Address (SA) of each aggregated MSDU must match the Receiver Address (RA) and Transmitter Address (TA) of the MPDU MAC header. All MSDUs within an A-MSDU should belong to the same TID. The maximum length of an A-MSDU is 7935 bytes. The A-MSDU aggregation reduces the transmission overhead since only one MAC header is generated for all aggregated MSDUs. However, it becomes inefficient in noisy channels: if even one MSDU is corrupted, VOLUME 6, 2018 the entire A-MSDU is rejected, and all aggregated MSDUs are lost. The second is A-MPDU. The A-MPDU scheme allows the aggregation of several MPDUs into the same PHY protocol data unit frame (PPDU). The maximum supported length for an A-MPDU is 65535 bytes. Each MPDU is encapsulated with its MAC header and Cyclic Redundancy Check (CRC). Hence, the corruption of an MPDU is separately detected and does not affect the entire A-MPDU. However, the A-MPDU aggregation requires more overhead than A-MSDU, which becomes heavy for small MSDUs . 2) BLOCK ACKNOWLEDGMENT (BA) SCHEME The scheme consists of grouping the frame and sharing the access time in the channel between several frames possessing the same destination. All the sent frames are acknowledged by a unique BA instead of an Ack frame for each frame transmitted as in Fig. 6 [30] , BIB002 . The BA mechanism improves channel efficiency by aggregating several acknowledgements into one frame. There are two types of BA mechanisms: immediate and delayed. Immediate BA is suitable for high-bandwidth, low-latency traffic, whereas delayed BA is suitable for applications that tolerate moderate latency. If all recipients are requesting BA, long transmission delays may occur that are not appropriate for specific applications (e.g., real-time multimedia streaming) due to strict QoS requirements, especially when the number of group cast recipients is large , BIB003 . Using the BA scheme, the originator and the recipient are referred to the QSTA with data to send and receive, respectively. The originator and the recipient initiate the exchange of ADD Block Acknowledgment (ADDBA) RR frames. Blocks of QoS data frames can only be sent from the originator to the recipient after initialization and winning the channel, either by EDCA contention or a polled TXOP. The block has a limited number of both frames and the number of states to be retained by the recipient. When a BA frame requests the MPDUs, the BA response frame is acknowledged by a BA control frame. If the immediate BA policy is used, the recipient responds to a BA Request frame with a BA frame. If the recipient sends the BA frame, the originator updates its record and retries any frames that were not acknowledged in the BA frame, either in another block or individually. The immediate BA with RIFS mode can be used instead of BA Short Inter-Frame Space (SIFS) mode. This mode is similar to immediate BA SIFS mode, but the frames are separated with RIFS, which is less less time-consuming than SIFS BIB001 . In Fig. 7 , a typical BA frame exchange sequence using the immediate BA for a single TID is illustrated. When HC is the originator in the delayed BA policy, the HC may respond with a +CF Ack frame when the BA frame is the last frame of the TXOPs frame exchange. If the delayed BA policy is used, the recipient responds to a BA Request frame with an Ack frame. The recipient then sends its BA response in a subsequently obtained TXOP. Once the contents of the BA frame have been prepared, the recipient submits this frame in the earliest possible TXOP using the highest-priority AC. The originator responds with an Ack frame upon receipt of the BA frame. In Fig. 8 , a typical BA sequence using the delayed BA is illustrated."
}
] |
science.drug_combo_extraction_re
|
science.drug_combo_extraction_re.621
|
[
{
"role": "user",
"content": "You will be shown a paragraph from a biomedical research article. Your task is to extract all drug combinations appearing in a specific sentence within in the paragraph. Each drug combination should be assigned to one of the following three categories:\n\n- POS: Indicates a positive interaction between the drugs in the combination; for instance, drugs that have an additive or synergistic effect.\n- NEG: Indicates a negative interaction between the drugs in the combination; for instance, combining these drugs might result in adverse side effects, or might reduce their efficacy.\n- COMB: Indicates that the drugs are given in combination, but the type of interaction between the drugs cannot be determined based on the provided context.\n\nPlease format your answer as a json array. Each entry in the array should itself be an array formatted as [<drug_1>, <drug_2>, ..., <drug_n>, <category>] where <category> is one of the three categories listed above and <drug_1>, ..., <drug_n> are drug names copied verbatim from the input sentence. Different combinations may involve different numbers of drugs; in other words, the `n` in <drug_n> may vary.\n\nAs an example, the following output describes two extracted drug combinations; one between two drugs, and one between three drugs:\n\n[[\"artesunate\", \"artemether\", \"COMB\"], [\"Nifedipine\", \"Labetalol\", \"Prazosin\", \"POS\"]]\n\nThe paragraph and specific sentence are below. You should only extract relationships expressed in the specific sentence; the paragraph is provided for context.\n\nIn your output, return only the json array and no other text. If no drug combinations appear, return an empty array `[]`.\n\nparagraph: Nitrendipine facilitates recovery of cerebral blood flow, EEG and metabolites following cerebral ischemia in anesthetized rabbits. The effect of nitrendipine, an antihypertensive calcium antagonist, on the impairment of cerebral blood flow and EEG observed after 10-min complete cerebral ischemia in anesthetized rabbits was compared with those of nicardipine. The ischemia was produced by neck tourniquet in combination with hypotension (50-60 mmHg). Blood flow was measured by hydrogen-clearance method. Transient reactive hyperemia was observed immediately after the cessation of ischemic procedure, and was followed by a decrease in blood flow in the range of 58-73% of corresponding basal values in the total brain, cortex and thalamus. The postischemic decrease in blood flow was suppressed when nitrendipine (0.3-1 mg/kg) or nicardipine (3-10 mg/kg) was given intraduodenally before ischemia. The postischemic decrease in total intensity and frequency index in EEG recovered rapidly when nitrendipine was pretreated , whereas the recovery of EEG parameters was not obtained by the nicardipine pretreatment . These results suggest that the effect of nitrendipine and nicardipine on the postischemic cerebral blood flow may be due to the inhibition of calcium-induced contraction in cerebral vessels, whereas the discrepancy between the effects of these agents on EEG may not be due solely to the improvement in cerebral circulation. Furthermore, the improvement in postischemic cerebral energy metabolism was confirmed by nitrendipine pretreatment (0.3 mg/kg).\n\nsentence: The postischemic decrease in total intensity and frequency index in EEG recovered rapidly when nitrendipine was pretreated , whereas the recovery of EEG parameters was not obtained by the nicardipine pretreatment ."
},
{
"role": "assistant",
"content": "[]"
}
] |
science.scierc_re
|
science.scierc_re.347
|
[
{
"role": "user",
"content": "Below is an abstract from a computer science research paper. Given this abstract, your task is to extract all unique relationships between entities of the following types:\n\n- \"USED-FOR\": For instance, \"Our method models user proficiency\" -> [\"method\", \"user proficiency\", \"USED-FOR\"].\n- \"EVALUATE-FOR\": For instance, \"We evaluate our method using F1-measure\" -> [\"F1-measure\", \"method\", \"EVALUATE-FOR\"].\n- \"FEATURE-OF\": For instance, \"prior knowledge of the model\" -> [\"prior knowledge\", \"model\", \"FEATURE-OF\"].\n- \"HYPONYM-OF\": For instance, \"TUIT is a software library\" -> [\"TUIT\", \"software library\", \"HYPONYM-OF\"].\n- \"PART-OF\": For instance, \"We incorporate NLU module into the system.\" -> [\"NLU module\", \"system\", \"PART-OF\"].\n- \"COMPARE\": For instance, \"Unlike the quantitative prior, the qualitative prior is often ignored\" -> [\"quantitative prior\", \"qualitative prior\", \"COMPARE\"].\n- \"CONJUNCTION\": For instance: \"obtained from human expert or knowledge base\" -> [\"human expert\", \"knowledge base\", \"CONJUNCTION\"].\n\nFormat your output as a json array. Each entry in the array should express a single relation, formatted as [\"<Entity_A>\", \"<Entity_B>\", \"<RELATION_A_B>\"]. An example output might look like:\n\n[[\"neural networks\", \"classification\", \"USED-FOR\"], [\"neuron\", \"neural network\", \"PART-OF\"]].\n\nIf no relations are found, please return an empty array [].\n\nAbstract:\n\nIn this paper, we want to show how the morphological component of an existing NLP-system for Dutch (Dutch Medical Language Processor-DMLP) has been extended in order to produce output that is compatible with the language independent modules of the LSP-MLP system (Linguistic String Project-Medical Language Processor) of the New York University. The former can take advantage of the language independent developments of the latter, while focusing on idiosyncrasies for Dutch. This general strategy will be illustrated by a practical application, namely the highlighting of relevant information in a patient discharge summary (PDS) by means of modern HyperText Mark-Up Language (HTML) technology. Such an application can be of use for medical administrative purposes in a hospital environment."
},
{
"role": "assistant",
"content": "[[\"language independent modules\", \"LSP-MLP system (Linguistic String Project-Medical Language Processor)\", \"PART-OF\"], [\"HyperText Mark-Up Language (HTML) technology\", \"application\", \"USED-FOR\"], [\"Dutch\", \"idiosyncrasies\", \"USED-FOR\"], [\"relevant information\", \"patient discharge summary (PDS)\", \"PART-OF\"], [\"language independent modules\", \"morphological component\", \"USED-FOR\"], [\"application\", \"medical administrative purposes\", \"USED-FOR\"], [\"morphological component\", \"NLP-system for Dutch (Dutch Medical Language Processor-DMLP)\", \"PART-OF\"]]"
}
] |
science.bc7_litcovid_topic_classification
|
science.bc7_litcovid_topic_classification.17457
|
[
{
"role": "user",
"content": "You are presented with a paragraph from a COVID-19 literature. Classify the topics of this piece of text by choosing from the following categories:\n\n- Epidemic Forecasting: The content relates to predictions about the spread of COVID-19.\n- Treatment: The paragraph discusses therapeutic methods or medication for COVID-19.\n- Prevention: The content covers measures to prevent the spread of COVID-19.\n- Mechanism: The paragraph explains the biological mechanisms of the virus.\n- Case Report: The content is a report of a COVID-19 case.\n- Transmission: The paragraph discusses how COVID-19 is transmitted.\n- Diagnosis: The content is about diagnosing COVID-19 in individuals.\n\nYour classification should be provided as an element within a JSON array. The array should be formatted with topics enclosed in double quotes and separated by commas, following the JSON format, for example: [\"Topic1\", \"Topic2\", ...]. Include all applicable topics within the array. Your output should be a valid JSON array, and no additional text should be included in your response.\n\nArticle:\n\nObjective: To understand the treatment status and effects on colorectal cancer (CRC) patients in China during the COVID-19 pandemic, and provide evidence for decision-making for health-care workers. Methods: The method of cross-sectional study was applied. A questionnaire survey of CRC patients in China was carried out. Their basic and treatment information during the COVID-19 were collected and associated effects on treatment, nursing, state of psychology and needs of social support were analyzed. Results: Of the 1147 participants in the study, 635 (55.4%) were male and 512 (44.6%) were female with mean age of (52.8+/-12.8) years. The treatment or follow up of 896 (78.1%) CRC patients were affected during the COVID-19 outbreak. A total of 253 patients (22.1%) had their treatment regiments changed, of whom 141 (12.3%) had their chemotherapy regiments postponed or changed, and 83 patients (7.2%) had their surgical treatment affected. Among the above 83 patients, 39 patients (3.4%) underwent emergency surgery. A total of 277 patients (24.1%) had their out-of-hospital care needs affected, mainly due to maintenance of PICC (49.5%, 137/277). CRC patients had poorer sleep quality and increased levels of insomnia than before (P<0.001), and were more distressed, anxious, depressed, and angry than they were before. They presented the more requirements of help (P<0.001). In addition, 376 patients (32.8%) had received telemedicine services, but only 36.4% (137/376) of them were satisfied. Conclusions: The COVID-19 epidemic has effect on the integrated treatment of CRC patients include diagnosis, treatment, examination and prognosis. While protecting CRC patients from being infected with SARS-CoV-2, health-care workers should also actively help them to receive timely and correct treatment and pay attention to their nursing, nutritional, psychological and social support needs in the COVID-19 epidemic."
},
{
"role": "assistant",
"content": "[\"Prevention\"]"
}
] |
science.genia_ner
|
science.genia_ner.805
|
[
{
"role": "user",
"content": "You will be shown an abstract from a biomedical research paper. Given this abstract, your task is to extract all unique entities of the following types: [\"RNA\", \"CellLine\", \"Protein\", \"DNA\", \"CellType\"].\n\nPlease return the output as a JSON object of the format: {\"DNA\" : [\"TAL1\", ...], \"RNA\": [\"mRNAs\", ...], \"CellLine\": [\"T cells\", ...], \"CellType\": [\"monocytes\", ...], \"Protein\": [\"IL-2\", ...]}. The keys should be entity types and values should be lists of extracted entities belonging to the corresponding type. If you cannot find entities belonging to a specific type, the value should be [].\n\nOnly output the JSON object and do not include any additional text.\n\nAbstract:\n\nImmunosuppressant PG490 (triptolide) inhibits T-cell interleukin-2 expression at the level of purine-box / nuclear factor of activated T-cells and NF-kappaB transcriptional activation. PG490 (triptolide) is a diterpene triepoxide with potent immunosuppressive and antiinflammatory properties. PG490 inhibits interleukin (IL) -2 expression by normal human peripheral blood lymphocytes stimulated with phorbol 12-myristate 13-acetate (PMA) and antibody to CD3 (IC50 of 10 ng / ml), and with PMA and ionomycin (Iono, IC50 of 40 ng / ml). In Jurkat T-cells, PG490 inhibits PMA / Iono-stimulated IL-2 transcription. PG490 inhibits the induction of DNA binding activity at the purine-box / antigen receptor response element (ARRE) / nuclear factor of activated T-cells (NF-AT) target sequence but not at the NF-kappaB site. PG490 can completely inhibit transcriptional activation at the purine-box / ARRE / NF-AT and NF-kappaB target DNA sequences triggered by all stimuli examined (PMA, PMA / Iono, tumor necrosis factor-alpha). PG490 also inhibits PMA-stimulated activation of a chimeric transcription factor in which the C-terminal TA1 transactivation domain of NF-kappaB p65 is fused to the DNA binding domain of GAL4. In 16HBE human bronchial epithelial cells, IL-8 expression is regulated predominantly by NF-kappaB, and PG490 but not cyclosporin A can completely inhibit expression of IL-8. The mechanism of PG490 inhibition of cytokine gene expression differs from cyclosporin A and involves nuclear inhibition of transcriptional activation of NF-kappaB and the purine-box regulator operating at the ARRE / NF-AT site at a step after specific DNA binding."
},
{
"role": "assistant",
"content": "{\"CellLine\": [\"Jurkat T - cells\"], \"CellType\": [\"16HBE human bronchial epithelial cells\", \"normal human peripheral blood lymphocytes\", \"activated T - cells\"], \"DNA\": [\"purine - box / antigen receptor response element (ARRE) / nuclear factor of activated T - cells (NF - AT) target sequence\", \"ARRE / NF - AT site\", \"cytokine gene\", \"purine - box / ARRE / NF - AT and NF - kappaB target DNA sequences\", \"purine - box regulator\", \"NF - kappaB site\"], \"Protein\": [\"chimeric transcription factor\", \"T - cell interleukin - 2\", \"tumor necrosis factor - alpha\", \"NF - kappaB\", \"IL - 8\", \"C - terminal TA1 transactivation domain\", \"DNA binding domain\", \"purine - box / nuclear factor\", \"NF - kappaB p65\", \"CD3\", \"interleukin (IL) - 2\", \"IL - 2\", \"GAL4\"], \"RNA\": []}"
}
] |
science.scientific_papers_summarization_single_doc_arxiv
|
science.scientific_papers_summarization_single_doc_arxiv.157590
|
[
{
"role": "user",
"content": "You will be presented with the full text of a science research paper. Please write an abstract for this paper. Your response should include the abstract and no additional text.\n\nPaper text:\nstudy of @xmath0 and @xmath1 bosons at the turn - on of the large hadron collider provides a high - statistics probe of the atlas @xcite detector , in terms of characterizing tracking , lepton identification , lepton and missing energy scale and resolution , and trigger performance . theoretically , measurements at the new energy of @xmath8 probe the proton at low-@xmath9 , constraining parton density functions . the @xmath0 and @xmath1 cross - sections are known at nnlo , giving a test of perturbative calculations . also , these channels are important backgrounds for beyond sm processes .\nthe data for these analyses come from the first lhc runs at @xmath8 , between march and july 2010 .\nthe datasets for the @xmath10 and @xmath6 boson analyses are approximately @xmath11 and @xmath12 respectively , the luminosity being to known to @xmath13 .\nthe analyses operate upon events from a collision bunch and both detector and machine status are used to select run periods for analysis .\nthe data are compared to pythia @xcite samples processed with the atlas detector simulation software based on geant4 @xcite and fully reconstructed .\nthe trigger for the muon analysis uses hit patterns in dedicated chambers(@xmath14 ) .\nthe trigger efficiency is estimated at @xmath15 ( fully dominated by detector acceptance ) using orthogonal jet - based triggers .\nthe electron data are triggered in calorimetric towers that identify @xmath16 activity in a window of @xmath17 .\na threshold of five trigger counts ( @xmath18 ) is used .\nthe efficiency of this trigger is better than @xmath19 , with negligible uncertainty .\nboth @xmath20 and @xmath21 analyses require a reconstructed vertex ( @xmath22 three tracks ) consistent with the beam spot .\nin addition , to reject cosmic rays and beam halo events , the muon analyses require that the primary vertex be found within @xmath23 of the nominal position .\nelectron measurements come from the energy of calorimeter clusters found in using a sliding - window approach . for electron identification ,\ncalorimetric shower shapes , hadronic leakage , track - cluster matching and impact parameter criteria are used . for the @xmath10 analysis ,\npurity is enhanced by requiring @xmath24 compatibility between track and cluster , high - threshold transition radiation hits , and criteria to reject conversions .\nthe analysis uses electrons with @xmath25 in the region @xmath26 .\nthe barrel - endcap transition region @xmath27 is excluded .\nmuon reconstruction combines tracking information in the inner detector ( i d ) the muon spectrometer ( ms ) .\ndecays in flight are rejected with minimum @xmath28 requirements on the ms track , and by imposing @xmath28 compatibility between i d and ms track reconstructions .\nthe cosmic ray contamination is reduced by requiring that the muon come from within 1 cm of a reconstructed vertex .\nmuons with @xmath25 are used , with @xmath14 . to reduce qcd background ,\nthe summed @xmath29 of tracks in a cone ( @xmath30 ) around the muon must be @xmath31 of muon @xmath29 .\nmissing @xmath32 is found using em - scale calorimeter energy deposited in topological clusters , corrected for hadronic response , dead material and out - of - cluster losses . for muons ,\nthis is supplemented with the momentum , the muon s calorimeter deposition not being added to the calorimeter term .\na requirement of @xmath33 is imposed for the @xmath0 analysis .\nthe @xmath10 analysis requires that the transverse mass @xmath34 of the candidate @xmath35 - @xmath36 system , plotted in fig .\n[ fig : mtw ] , be @xmath37 .\nthere are @xmath38 ( @xmath39 ) @xmath40 ( @xmath41 ) candidates .\nelectroweak ( ew ) backgrounds for @xmath10 are obtained from monte carlo predictions . in the electron channel ,\nthe ew background is @xmath42 , coming chiefly from leptonic @xmath43 .\nthe muon channel background of @xmath44 , is dominated by @xmath43 and @xmath45 .\nthe qcd background in @xmath46 comes from hadrons misidentification , as well as electrons from conversion and heavy quark decay .\nit is estimated with a binned likelihood fit to data of monte carlo templates of calorimetric isolation , at @xmath47 events .\nthe muon channel qcd background , mainly from heavy quark decay , is estimated by extrapolating from control regions in the @xmath48 vs. isolation plane , at @xmath49 .\n@xmath6 boson candidates are formed using pairs of oppositely charged leptons , with the invariant mass of the lepton pair required to be between @xmath50 and @xmath51 .\n46 ( 79 ) candidates are observed in the @xmath52 ( @xmath53 ) channel , whose peak is shown in fig .\n[ fig : mll ] .\nthe background for @xmath54 is @xmath55 .\nthe background in the muon channel is @xmath56 .\nfor @xmath57 observed events and background estimate of @xmath58 in a luminosity of @xmath59 , we have : @xmath60 here , @xmath61 is the geometrical acceptance at generator level , while @xmath62 is the ratio between the number of selected reconstructed events and the number of generated events in the fiducial region .\nthe systematics on @xmath63 and @xmath64 are estimated at @xmath65 , from using different pdf sets and comparing mc@nlo and pythia values .\nthe uncertainty on @xmath62 in the electron channel is @xmath66 and @xmath67 for @xmath0 and @xmath1 , driven by the lepton identification .\nthe muon systematic comes from the trigger , muon reconstruction and resolution , and from missing energy for the @xmath0 .\nit is @xmath68 in both the @xmath0 and @xmath1 analyses .\nthe cross - section times leptonic branching fraction for @xmath0 is @xmath69\\,\\mathrm{nb}$ ] in the electronic channel and @xmath70\\,\\mathrm{nb}$ ] for the muonic channel .\nthe combined value is @xmath71\\,\\mathrm{nb}$ ] .\nthe @xmath72 and @xmath73 results are respectively @xmath74\\,\\mathrm{nb}$ ] and @xmath75\\,\\mathrm{nb}$ ] , for a combined result of @xmath76\\,\\mathrm{nb}$ ] .\nthese results are placed in historical context in fig .\n[ fig : vbxsec ] , and in agreement with theoretical expectations of @xmath77 , and @xmath78 , computed at nnlo with 4% uncertainty using fewz @xcite and mstw2008 @xcite . 9 atlas collaboration , `` the atlas experiment at the cern large hadron collider '' , jinst 3 ( 2008 ) 003 .\nt. sjostrand , s. mrenna , and p. skands , `` pythia 6.4 physics and manual '' , jhep 05 ( 2006 ) 026 .\ngeant4 collaboration , s. agostinelli et al .\n, `` geant4 : a simulation toolkit '' , nucl . instrum . meth .\na506 ( 2003 ) 250 .\natlas collaboration , `` measurement of the @xmath79 production cross - section and observation of @xmath80 production in proton - proton collisions at @xmath81 with the atlas detector '' , http://cdsweb.cern.ch/record/1281306[atlas-conf-2010-051 ] .\natlas collaboration , `` measurement of the @xmath80 production cross - section in proton - proton collisions at @xmath82 with the atlas detector '' , http://cdsweb.cern.ch/record/1281367[atlas-conf-2010-076 ] . c. anastasiou , l. dixon , k. melnikov , and f. petriello , `` high - precision qcd at hadron colliders : electroweak gauge boson rapidity distributions at nnlo '' , phys .\nd69 ( 2004 ) 094008 .\na. d. martin , w. j. stirling , r. s. thorne , and g. watt , `` parton distributions for the lhc '' , eur .\nj. c63 ( 2009 ) 189 - 285 ."
},
{
"role": "assistant",
"content": "measurements of @xmath0 and @xmath1 cross - sections in @xmath2 collisions at @xmath3 at the large hadron collider are reported from the atlas experiment . from an observation of @xmath4 leptonic @xmath0 candidates , the inclusive @xmath0 cross - section times leptonic branching fraction is measured as @xmath5\\mathrm{nb}$ ] . \n the result for the @xmath6 boson is @xmath7\\mathrm{nb}$ ] . \n these results agree with theoretical expectations from nnlo qcd ."
}
] |
science.covid_deepset_qa
|
science.covid_deepset_qa.1018
|
[
{
"role": "user",
"content": "You will be shown a paragraph from a biomedical research paper, followed by a question about the paper. Please extract text from the paragraph to answer the question. Do not include any text in your repsonse other than the answer.\n\nParagraph: However, the mechanism by which severe acute respiratory syndrome coronavirus (SARS-CoV) activates the NLRP3 inflammasome remains unknown. Here, we provide direct evidence that SARS-CoV 3a protein activates the NLRP3 inflammasome in lipopolysaccharide-primed macrophages. SARS-CoV 3a was sufficient to cause the NLRP3 inflammasome activation. The ion channel activity of the 3a protein was essential for 3a-mediated IL-1β secretion. While cells uninfected or infected with a lentivirus expressing a 3a protein defective in ion channel activity expressed NLRP3 uniformly throughout the cytoplasm, NLRP3 was redistributed to the perinuclear space in cells infected with a lentivirus expressing the 3a protein. K(+) efflux and mitochondrial reactive oxygen species were important for SARS-CoV 3a-induced NLRP3 inflammasome activation. These results highlight the importance of viroporins, transmembrane pore-forming viral proteins, in virus-induced NLRP3 inflammasome activation. Text: Severe acute respiratory syndrome coronavirus (SARS-CoV), a member of the genus Betacoronavirus within the family Coronaviridae, is an enveloped virus with a single-stranded positive-sense RNA genome of approximately 30 kb in length. The 5 two-thirds of the genome encodes large polyprotein precursors, open reading frame (ORF) 1 and ORF1b, which are proteolytically cleaved to generate 16 non-structural proteins (Tan et al., 2005) . The 3 one-third of the genome encodes four structural proteins, spike (S), envelope (E), matrix (M) and nucleocapsid (N), and non-structural proteins, along with a set of accessory proteins (3a, 3b, 6, 7a, 7b, 8a, 8b, and 9b) (Perlman and Dandekar, 2005; Tan et al., 2005) . SARS-CoV is the etiological agent of SARS (Drosten et al., 2003; Fouchier et al., 2003; Ksiazek et al., 2003; Kuiken et al., 2003; Peiris et al., 2003) . At least 8,098 laboratory-confirmed cases of human infection, with a fatality rate of 9.6%, were reported to the World Health Organization from November 2002 to July 2003. High levels of proinflammatory cytokines, including tumor necrosis factor (TNF)-α, interleukin (IL)-1β, and IL-6, were detected in autopsy tissues from SARS patients (He et al., 2006) . Although dysregulation of inflammatory cytokines may be involved in lung injury and the pathogenesis of SARS-CoV, the underlying molecular mechanisms are not fully understood. The innate immune systems utilizes pattern recognition receptors (PRRs) to detect pathogen-associated molecular patterns (Medzhitov, 2001; Kawai and Akira, 2010) . Recognition of virus infection plays an important role in limiting virus replication at the early stages of infection. Nod-like receptor family, pyrin domain-containing 3 (NLRP3) is activated by a wide variety of stimuli, including virus infection (Bauernfeind et al., 2011) . Four models describing activation of the NLRP3 inflammasome have been proposed thus far (Hornung and Latz, 2010; Schroder et al., 2010; Tschopp and Schroder, 2010) . First, the disturbances in intracellular ionic concentrations, including K + efflux and Ca 2+ influx, play an important role (Fernandes-Alnemri et al., 2007; Petrilli et al., 2007; Arlehamn et al., 2010; Ichinohe et al., 2010; Ito et al., 2012; Murakami et al., 2012; Munoz-Planillo et al., 2013) . Second, cathepsin B and L, which are specific lysosomal cysteine proteases, are though to play a role after phagocytosis of cholesterol crystals (Duewell et al., 2010) , fibrillar peptide amyloid-beta , silica crystals, and aluminum salts . Third is the release of reactive oxygen species (ROS) or mitochondrial DNA from damaged mitochondria (Zhou et al., , 2011 Nakahira et al., 2011; Shimada et al., 2012) . Finally, viral RNA or RNA cleavage products generated by RNase L activate the NLRP3 inflammasome via the DExD/H-box helicase, DHX33 (Allen et al., 2009; Mitoma et al., 2013; Chen et al., 2014; Chakrabarti et al., 2015) . Upon activation, the NLRP3 is recruited to the mitochondria via association with mitochondrial antiviral signaling (MAVS) or mitofusin 2 expressed on the outer mitochondrial membrane Subramanian et al., 2013) ; these molecules then recruit the apoptosis-associated speck-like protein containing a caspase recruitment domain (ASC) and pro-caspase-1 to form the NLRP3 inflammasome. This event activates the downstream molecule, caspase-1, which catalyzes the proteolytic processing of pro-IL-1β and pro-IL-18 into their active forms and stimulates their secretion (Kayagaki et al., 2015; Shi et al., 2015) . It is increasingly evident that NLRP3 detects RNA viruses by sensing the cellular damage or distress induced by viroporins (Ichinohe et al., 2010; Ito et al., 2012; Triantafilou et al., 2013; Nieto-Torres et al., 2015) , transmembrane pore-forming proteins, encoded by certain RNA viruses; these proteins alter membrane permeability to ions by forming membrane channels (Tan et al., 2005; Chen and Ichinohe, 2015) . A recent study shows that the SARS-CoV E protein, which comprise only 76 amino acids, forms Ca 2+ -permeable ion channels and activates the NLRP3 inflammasome (Nieto-Torres et al., 2015) . Although the E and 3a proteins of SARS-CoV, which comprise 274 amino acids and contain three transmembrane domains (Zeng et al., 2004; Lu et al., 2006) , are thought to act as Na + /K + and K + channels, respectively (Wilson et al., 2004; Lu et al., 2006; Torres et al., 2007; Parthasarathy et al., 2008; Pervushin et al., 2009; Wang et al., 2011) , the role of the 3a protein in activating the NLRP3 inflammasome remains unknown. Here, we examined the role of the 3a protein in activating the NLRP3 inflammasome. Six-week-old female C57BL/6 mice were purchased from The Jackson Laboratory. All animal experiments were approved by the Animal Committees of the Institute of Medical Science (The University of Tokyo). Bone marrow-derived macrophages (BMMs) were prepared as described previously (Ichinohe et al., 2009) . In brief, bone marrow was obtained from the tibia and femur by flushing with Dulbecco's modified Eagle's medium (DMEM; Nacalai Tesque). Bone marrow cells were cultured for 5 days in DMEM supplemented with 30% L929 cell supernatant containing macrophage colony-stimulating factor, 10% heat-inactivated fetal bovine serum (FBS), and L-glutamine (2 mM) at 37 • C/5% CO 2 . HEK293FT cells (a human embryonic kidney cell line) and HeLa cells (a human epithelial carcinoma cell line) were maintained in DMEM supplemented with 10% FBS, penicillin (100 units/ml), and streptomycin (100 µg/ml) (Nacalai Tesque). MDCK cells (Madin-Darby canine kidney cells) and HT-1080 cells (a human fibrosarcoma cell line) were grown in Eagle's minimal essential medium (E-MEM; Nacalai Tesque) supplemented with 10% FBS, penicillin (100 units/ml), and streptomycin (100 µg/ml) (Nacalai Tesque). Influenza A virus strain A/PR8 (H1N1) was grown at 35 • C for 2 days in the allantoic cavities of 10-day-old fertile chicken eggs (Ichinohe et al., 2009) . The viral titer was quantified in a standard plaque assay using MDCK cells (Pang et al., 2013) . Plasmids cDNAs encoding the E and M proteins of SARS-CoV Frankfurt 1 strain (Matsuyama et al., 2005) were obtained by reverse transcription and PCR of total RNA extracted from SARS-CoVinfected Vero cells, followed by PCR amplification using specific primers. pcDNA3.1D-3a-V5His was provided by Ming-Fu Chang (National Taiwan University College of Medicine, Taipei, Taiwan). To generate the plasmids pLenti6-E-V5His, pLenti6-3a-V5His, and pLenti-M-V5His, cDNA fragments of E, 3a, and M were amplified from pcDNA3.1D-E-V5His, pcDNA3.1D-3a-V5His, and pcDNA3.1D-M-V5His using specific primer sets and then ligated into pLenti6-TOPO vectors (Invitrogen). To generate plasmids pCA7-flag-E, pCA7-flag-3a, and pCA7flag-M, pCA7-HA-E, pCA7-HA-3a, and pCA7-HA-M, cDNA fragments of E, 3a, and M were amplified from pcDNA3.1D-E-V5His, pcDNA3.1D-3a-V5His, and pcDNA3.1D-M-V5His using specific primer sets, digested with EcoR I and Not I, and subcloned into the EcoR I-Not I sites of the pCA7-flag-ASC plasmid or pCA7-HA-M2 plasmid, respectively (Ito et al., 2012) . To construct plasmids expressing the E mutant V25F, the mutated E fragments were amplified by inverse PCR with wildtype E-containing plasmids and specific primer sets. The PCR products were cleaved by Dpn I, ligated in a ligase-and T4 kinase-containing reaction and then transformed into DH5α competent cells (TOYOBO). To construct plasmids expressing the 3a mutant 3a-CS, fragments were amplified from wildtype 3a-containing plasmids using 3a-specific primer sets and transformed as described above. HEK293FT cells were seeded in 24-well cluster plates and transfected with 1 µg pLenti6-E/3a/M-V5His, pLenti-GFP (green fluorescent protein), or pLenti-M2 using polyethylenimine (PEI) Max. At 24 h post-transfection, the cells were lysed with RIPA buffer (50 mM Tris-HCl, 1% NP-40, 0.05% sodium dodecyl sulfate (SDS), 150 mM NaCl and 1 mM EDTA). And the lysates were subjected to SDS-polyacrylamide gel electrophoresis (PAGE) followed by electroblotting onto polyvinylidene difluoride (PVDF) membranes. The membranes were incubated over night with mouse anti-V5-tag (R960-25, Invitrogen), mouse anti-influenza A virus M2 (14C2, Abcam), mouse anti-GFP (GF200, Nacalai Tesque), or rabbit antitubulin (DM1A, Santa Cruz) antibodies, followed by horseradish peroxide-conjugated anti-mouse IgG (Jackson Immuno Research Laboratories) or anti-rabbit IgG (Invitrogen). After washing 3 times with washing buffer (0.05% Tween-20/PBS), the membranes were exposed using Chemi-Lumi One Super (Nacalai Tesque), and the chemiluminescent signals were captured by an ImageQuant LAS-4000 mini apparatus (GE Healthcare). To generate lentiviruses expressing V5-tagged SARS-CoV E, 3a, and M proteins, the full-length cDNA encoding each viral protein was cloned into the pLenti6.3/V5-TOPO vector (Invitrogen) using the following primers: SARS-CoV E forward, 5 -caccatgtactcattcgtttcgga-3 , and reverse, 5 -gaccagaagatcaggaactc-3 ; SARS-CoV 3a forward, 5caccatggatttgtttatgagatt-3 , and reverse, 5 -caaaggcacgctagtagtcg-3 ; SARS-CoV M forward, 5 -caccatggcagacaacggtactat-3 , and reverse, 5 -ctgtactagcaaagcaatat-3 . Sub-confluent monolayers of HEK293FT cells seeded in a collagen-coated dish (10 cm in diameter) were transfected with 3 µg of pLenti6.3/V5-TOPO vector expressing each viral protein or EGFP together with ViraPower Packaging Mix (Invitrogen) using Lipofectamine 2000 (Invitrogen). The supernatants containing lentiviruses were harvested and filtered through a 0.45 µm filter (Millipore) at 72-96 h post-transfection (Ito et al., 2012) . The lentiviral titer was then quantified using HT-1080 cells as described previously .\n\nQuestion: How many laboratory-confirmed cases of SARS coronavirus infections were reported between November 2002 and July 2003?"
},
{
"role": "assistant",
"content": "At least 8,098"
}
] |
science.acl_arc_intent_classification
|
science.acl_arc_intent_classification.972
|
[
{
"role": "user",
"content": "You will be presented with a citation segment from the section of an NLP research paper, as well as the context surrounding that citation. Classify the intent behind this citation by choosing from one of the following categories:\n- Background: provides context or foundational information related to the topic.\n- Extends: builds upon the cited work.\n- Uses: applies the methods or findings of the cited work.\n- Motivation: cites the work as inspiration or rationale for the research.\n- CompareOrContrast: compares or contrasts the cited work with others.\n- FutureWork: cites the work as a direction for future research.\n\nYour answer should be a single word from the following list of options: [\"Background\", \"Extends\", \"Uses\", \"Motivation\", \"CompareOrContrast\", \"FutureWork\"]. Do not include any other text in your response.\n\nSection Title:\nmethod\n\nContext before the citation:\nIt is analogous to the step in other translation model induction algorithms that sets all probabilities below a certain threshold to negligible values (Brown et al., 1990; Dagan et al., 1993; Chen, 1996). This step significantly reduces the computational burden of the algorithm. Discard all likelihood scores for word types deemed unlikely to be mutual translations, i.e. all L(u, v) < 1.\n\nCitation Sentence:\nIt is analogous to the step in other translation model induction algorithms that sets all probabilities below a certain threshold to negligible values ( Brown et al. , 1990 ; Dagan et al. , 1993 ; Chen , 1996 ) .\n\nContext after the citation:\nTo retain word type pairs that are at least twice as likely to be mutual translations than not, the threshold can be raised to 2. Conversely, the threshold can be lowered to buy more coverage at the cost of a larger model that will converge more slowly. 2. Sort all remaining likelihood estimates L(u, v) from highest to lowest."
},
{
"role": "assistant",
"content": "Background"
}
] |
science.chemprot_re
|
science.chemprot_re.203
|
[
{
"role": "user",
"content": "Given an abstract from a research paper, your task is to identify and label relationships between chemical compounds and genes mentioned in the abstract.\n\nThe relationship type must be one of ['DOWNREGULATOR', 'SUBSTRATE', 'INDIRECT-REGULATOR', 'PART-OF', 'MODULATOR-ACTIVATOR', 'REGULATOR', 'INHIBITOR', 'COFACTOR', 'UPREGULATOR', 'ACTIVATOR', 'ANTAGONIST', 'NOT', 'INDIRECT-DOWNREGULATOR', 'SUBSTRATE_PRODUCT-OF', 'INDIRECT-UPREGULATOR', 'AGONIST', 'PRODUCT-OF', 'MODULATOR', 'DIRECT-REGULATOR', 'UNDEFINED', 'AGONIST-INHIBITOR', 'AGONIST-ACTIVATOR', 'MODULATOR-INHIBITOR'].\n\nPlease format your output as a JSON array. Each entry in the array should express a single relation, formatted as [\"<Entity_A>\", \"<RELATION_A_B>\", \"<Entity_B>\"]. If no relations can be found, please output an empty JSON array [].\n\nAbstract:\n\nThe in vivo antioxidant and antifibrotic properties of green tea (Camellia sinensis, Theaceae). The in vivo antioxidant and antifibrotic properties of green tea (Camellia sinensis, Theaceae) were investigated with a study of carbon tetrachloride (CCl (4))-induced oxidative stress and hepatic fibrosis in male ICR mice. Oral administration of green tea extract at doses of 125, 625 and 1250 mg/kg for 8 weeks significantly reduced (p<0.05) the levels of thiobarbituric acid-reactive substances (TBARS) and protein carbonyls in the liver by at least 28% compared with that was induced by CCl (4) (1 mL/kg) in mice. Moreover, green tea extract administration significantly increased (p<0.05) the activities of catalase, glutathione peroxidase (GSH-Px) and glutathione reductase (GSH-Rd) in the liver. Our study found that oral administration of green tea extract prevented CCl (4) -induced hepatic fibrosis, as evidenced by a decreased hydroxyproline level in the liver and a reduced incidence of hepatic fibrosis by histological observations. These results indicate that green tea exhibits potent protective effects against CCl (4) -induced oxidative stress and hepatic fibrosis in mice by inhibiting oxidative damage and increasing antioxidant enzyme activities."
},
{
"role": "assistant",
"content": "[]"
}
] |
science.craftchem_ner
|
science.craftchem_ner.7434
|
[
{
"role": "user",
"content": "You will be presented a sentence from biomedical research text. Extract all terms that correspond to chemical entities of biological interest (ChEBI).\nReturn your identified terms in a JSON array, formatted like this: [\"Entity1\", \"Entity2\", ...].\nIf no such entities are detected, respond by providing an empty JSON array [].\n\nBiomedical context:\nDiscussion"
},
{
"role": "assistant",
"content": "[]"
}
] |
science.covidfact_entailment
|
science.covidfact_entailment.621
|
[
{
"role": "user",
"content": "You will be shown a claim related to the COVID-19 pandemic, and the abstract of a biomedical research paper. Each sentence from the abstract will be on a separate line. Your task is to return a JSON object with two fields:\n\n- \"verdict\": The fact-checking verdict. If the information in the abstract supports the claim, write \"SUPPORT\". If the abstract contradicts the claim, write \"CONTRADICT\".\n- \"evidence\": An array of sentences providing evidence for the verdict. Please copy all relevant sentences verbatim from the abstract.\n\nFor instance, if the model were given the claim \"the COVID vaccine is safe for healthy adults\", the output might be\n{\n \"verdict\": \"SUPPORT\",\n \"evidence\": [\"Our findings indicate that the risks of severe COVID vaccine side effects are low for healthy adults.\"]\n}\n\nClaim: Repurposing of miglustat to inhibit the coronavirus severe acquired respiratory syndrome sars-cov-2\n\nAbstract:\nRepurposing clinically available drugs to treat the new coronavirus disease COVID-19 is an urgent need in these early stages of the SARS-CoV-2 pandemic, when very few treatment options are available.\nThe iminosugar Miglustat is a well-characterized drug for the treatment of rare genetic lysosome storage diseases such as Gaucher and Niemann-Pick type C, and has also been described to be active against a variety of enveloped viruses.\nThe activity of Miglustat is here demonstrated for SARS-CoV-2 at concentrations achievable in the plasma by current clinical regimens without cytotoxicity.\nThe drug acts at the post-entry level and leads to a marked decrease of viral proteins and release of infectious virus.\nThe mechanism resides in the inhibitory activity towards α-glucosidases that are involved in early stages of glycoprotein N-linked oligosaccharide processing in the endoplasmic reticulum, leading to a marked decrease of the viral Spike protein.\nThe wealth of available data on the clinical use of Miglustat for the treatment of lysosomal storage disorders and the antiviral properties against SARS-CoV-2 make it an ideal candidate for drug repurposing."
},
{
"role": "assistant",
"content": "{\"verdict\": \"SUPPORT\", \"evidence\": [\"The iminosugar Miglustat is a well-characterized drug for the treatment of rare genetic lysosome storage diseases such as Gaucher and Niemann-Pick type C, and has also been described to be active against a variety of enveloped viruses.\", \"The activity of Miglustat is here demonstrated for SARS-CoV-2 at concentrations achievable in the plasma by current clinical regimens without cytotoxicity.\", \"The wealth of available data on the clinical use of Miglustat for the treatment of lysosomal storage disorders and the antiviral properties against SARS-CoV-2 make it an ideal candidate for drug repurposing.\"]}"
}
] |
science.genia_ner
|
science.genia_ner.331
|
[
{
"role": "user",
"content": "You will be shown an abstract from a biomedical research paper. Given this abstract, your task is to extract all unique entities of the following types: [\"RNA\", \"CellLine\", \"Protein\", \"DNA\", \"CellType\"].\n\nPlease return the output as a JSON object of the format: {\"DNA\" : [\"TAL1\", ...], \"RNA\": [\"mRNAs\", ...], \"CellLine\": [\"T cells\", ...], \"CellType\": [\"monocytes\", ...], \"Protein\": [\"IL-2\", ...]}. The keys should be entity types and values should be lists of extracted entities belonging to the corresponding type. If you cannot find entities belonging to a specific type, the value should be [].\n\nOnly output the JSON object and do not include any additional text.\n\nAbstract:\n\n[ The value of the clinical test of glucocorticoid receptors of peripheral blood leukocytes in patients with chronic pulmonary heart disease ] In order to inquire into the functional state of adrenal cortex in patients with pulmonary heart disease, the number of glucocorticoid receptors (GCR) of peripheral blood leukocytes in patients with chronic pulmonary heart disease was determined with radioligand-binding assay and the corresponding plasma cortisol levels were assessed with radioimmune assays. The results showed that the number of GCR in the patients was significantly reduced (P < 0. 01) and it was increased when their health state was improved. However, it was still lower than that in healthy subjects (P < 0. 01). The number of GCR in the patients was greatly increased when these patients were treated with oxygen (P < 0. 01). No difference in plasma cortisol was found between the patients and the healthy subjects (P > 0. 05). These results indicate that the function of adrenal cortex may be improved by the compensation mechanism of the patients, but the lower GCR number was the result of lacking of oxygen in the patients. The number of GCR may be improved by inhalation of oxygen. Therefore oxygen therapy is helpful in raising the activity of glucocorticoid receptors and controlling the development of the disease."
},
{
"role": "assistant",
"content": "{\"CellLine\": [], \"CellType\": [\"peripheral blood leukocytes\"], \"DNA\": [], \"Protein\": [\"GCR\", \"glucocorticoid receptors\"], \"RNA\": []}"
}
] |
science.chia_ner
|
science.chia_ner.202
|
[
{
"role": "user",
"content": "You will be shown inclusion or exclusion criteria for a clinical trial. Given these criteria, your task is to extract all unique entities of the following types: [\"Observation\", \"Condition\", \"Procedure\", \"Drug\", \"Temporal\", \"Multiplier\", \"Qualifier\", \"Negation\", \"ReferencePoint\", \"Scope\", \"Value\", \"Mood\", \"Device\", \"Visit\", \"Measurement\", \"Person\"].\n\nPlease return the output as a JSON object of the format: {\"Condition\" : [\"breast cancer\", ...], \"Device\" : [\"ports\", ...], \"Drug\" : [\"Atenolol\", ...], \"Measurement\" : [\"blood pressure\", ...], \"Mood\" : [\"suspected\", ...], \"Multiplier\" : [\"more than two\", ...], \"Negation\" : [\"no\", ...], \"Observation\" : [\"history\", ...], \"Person\" : [\"male\", ...], \"Procedure\" : [\"surgery\", ...], \"Qualifier\" : [\"severe\", ...], \"ReferencePoint\" : [\"enrollment\", ...], \"Scope\" : [\"infection\", ...], \"Temporal\" : [\"one day\", ...], \"Value\" : [\"50%\", ...], \"Visit\" : [\"ICU\", ...]}. The keys should be entity types and values should be lists of extracted entities belonging to the corresponding type. If you cannot find entities belonging to a specific type, the value should be [].\n\nOnly output the JSON object and do not include any additional text.\n\nAbstract:\n\nSubjects with a supine BP >140 mm Hg systolic or >90 mm Hg diastolic or <100 mm Hg systolic or <60 mm Hg diastolic based on the average of the triplicate \nSerum potassium >=5.1 mmol/L or <3.5 mmol/L at screening, confirmed by a single repeat if deemed necessary. \nEstimated GFR <60 mL/min/1.73 m2 using the Cockcroft-Gault formula measurement of the individual parameters following at least 5 minutes of rest at Screening."
},
{
"role": "assistant",
"content": "{\"Condition\": [], \"Device\": [], \"Drug\": [], \"Measurement\": [\"supine BP\", \"Estimated GFR\", \"Serum potassium\"], \"Mood\": [], \"Multiplier\": [], \"Negation\": [], \"Observation\": [\"Cockcroft-Gault formula\"], \"Person\": [], \"Procedure\": [], \"Qualifier\": [], \"ReferencePoint\": [], \"Scope\": [\"\\u003e=5.1 mmol/L or \\u003c3.5 mmol/L\", \"\\u003e140 mm Hg systolic or \\u003e90 mm Hg diastolic or \\u003c100 mm Hg systolic or \\u003c60 mm Hg diastolic\"], \"Temporal\": [\"at screening\"], \"Value\": [\"\\u003e140 mm Hg systolic\", \"\\u003e=5.1 mmol/L\", \"\\u003c60 mL/min/1.73 m2\", \"\\u003c60 mm Hg diastolic\", \"\\u003c100 mm Hg systolic\", \"\\u003c3.5 mmol/L\", \"\\u003e90 mm Hg diastolic\"], \"Visit\": []}"
}
] |
science.bioasq_yesno_qa
|
science.bioasq_yesno_qa.845
|
[
{
"role": "user",
"content": "You have to answer a biomedical question in binary format, i.e. only yes and no are the only acceptable answer formats. A list of paragraphs is provided as context to help you answer the question.\n\nQuestion: Velocardial facial syndrome, otherwise known as Di George syndrome is caused by a deletion in chromosome 21, yes or no?\n\nContext: The deletion of chromosome 22q11.2 is involved in the majority of DiGeorge or velo-cardiofacial syndrome.\ndeletions of chromosome 7q11.23 (Williams syndrome), 15q11-q13 (Angelman syndrome, Prader-Willi syndrome) and 22q11 (Di George syndrome)\nSubmicroscopic deletions of chromosome 22q11 have been reported in a multiple anomaly syndrome variously labelled as velocardiofacial syndrome, conotruncal anomaly face syndrome, and Di George syndrome\nThe 22q11.2 deletion syndrome (di George syndrome) is one of the most prevalent genetic disorders.\nUNLABELLED Most of the children with Di George syndrome and 60% of patients with velocardiofacial syndrome exhibit a microdeletion within chromosome 22q11.\nSubmicroscopic deletions of chromosome 22q11 have been reported in a multiple anomaly syndrome variously labelled as velocardiofacial syndrome, conotruncal anomaly face syndrome, and Di George syndrome.\n22q11.2DS has several presentations including Di George's syndrome, velo-cardio-facial syndrome or Shprintzen's syndrome and it is the most frequent microdeletion syndrome in the general population (prevalence estimated at 1/4000 births, de novo: 90%).\nDi George syndrome due to mutation on 22q or 10q) and can also result from microdeletion or point mutation (in the Shprintzen syndrome 70% represent microdeletion and 30% point mutation at 22q11, in Rubinstein-Taybi syndrome 10% cases result from microdeletions and 90% from point mutations); 7) Population incidence of microdeletions is high (1:4000 to 1:30,000) because their etiologic mechanism is related to the common unequal crossing over; 8) Imprinting plays a role in some cases, e.g.\n[Microdeletion of the chromosome 22q11 in children: apropos of a series of 49 patients].<AbstractText Label=\"UNLABELLED\">Most of the children with Di George syndrome and 60% of patients with velocardiofacial syndrome exhibit a microdeletion within chromosome 22q11.\n22q11.2DS has several presentations including Di George's syndrome, velo-cardio-facial syndrome or Shprintzen's syndrome and it is the most frequent microdeletion syndrome in the general population (prevalence estimated at 1/4000 births, de novo: 90%).\n<b>UNLABELLED</b>: Most of the children with Di George syndrome and 60% of patients with velocardiofacial syndrome exhibit a microdeletion within chromosome 22q11.\nMost of the children with Di George syndrome and 60% of patients with velocardiofacial syndrome exhibit a microdeletion within chromosome 22q11."
},
{
"role": "assistant",
"content": "no"
}
] |
science.anat_em_ner
|
science.anat_em_ner.530
|
[
{
"role": "user",
"content": "You will be shown an abstract from a biomedical research paper. Given this abstract, your task is to extract all unique entities of the following types: [\"AnatomicalEntity\"].\n\nPlease return the output as a JSON object of the format: {\"AnatomicalEntity\": [\"tumor cells\", ...]}. The keys should be entity types and values should be lists of extracted entities belonging to the corresponding type. If you cannot find entities belonging to a specific type, the value should be [].\n\nOnly output the JSON object and do not include any additional text.\n\nAbstract:\n\nPurification and characterization of various esterases from rat liver.\nThe major rat liver microsomal esterases acting on o-nitrophenylacetate with isoelectric points 5.0, 5.5, 6.1 and 6.4 were resolved by isoelectric focusing. Molecular weights were determined by sedimentation analysis in isokinetic gradients of sucrose and, after purification, in sodium dodecyl sulphate/polyacrylamide gel electrophoresis. Their subunit molecular weights were between 57 000 and 60 000. They behaved as monomers except the pI-6.1 enzyme which behaved as a trimer. Esterases of pI 5.0, pI 6.1 and pI 6.4 behaved like glycoproteins of the polymannose type in the presence of 125I-labelled concanavalin A. Preparations of the pI-5.0 enzyme contained two esterases of highly homologous structure. Antibodies directed against this preparation did not inhibit but precipitated pI-5.0 esterase activity quantitatively. They did not react with the pI-6.1 and pI-6.4 esterases but precipitated several nonimmunologically related esterases. Two of these enzymes were inducible by phenobarbital. Total activity was very low in 3-day-old animals. Individual esterase activities rose at different rates during development; the enzyme focusing near pI 5.0 was about three times more active in adult females than in males. All microsomal esterases are located on the luminal side of the endoplasmic reticulum."
},
{
"role": "assistant",
"content": "{\"AnatomicalEntity\": [\"luminal\", \"endoplasmic reticulum\", \"liver microsomal\", \"liver\"]}"
}
] |
science.bioasq_yesno_qa
|
science.bioasq_yesno_qa.720
|
[
{
"role": "user",
"content": "You have to answer a biomedical question in binary format, i.e. only yes and no are the only acceptable answer formats. A list of paragraphs is provided as context to help you answer the question.\n\nQuestion: Is there a disease or condition called Exploding Head Syndrome?\n\nContext: This case report describes the first-ever diagnosis of exploding head syndrome in a patient with longstanding epilepsy and novel nocturnal events.\nExploding head syndrome (EHS) is characterized by loud noises or a sense of explosion in the head during sleep transitions.\nExploding head syndrome is characterized by the perception of loud noises during sleep-wake or wake-sleep transitions.\nExploding head syndrome (EHS) is characterized by attacks of a sudden noise or explosive feeling experienced in the head occurring during the transition from wake to sleep or from sleep to wake.\nExploding head syndrome is characterized by the perception of abrupt, loud noises when going to sleep or waking up.\nxploding head syndrome (EHS) is a rare parasomnia in which affected individuals awaken from sleep with the sensation of a loud bang.\nContrary to some earlier theorizing, exploding head syndrome was found to be a relatively common experience in younger individuals.\nExploding head syndrome is characterized by the perception of loud noises during sleep-wake or wake-sleep transitions.\nFifty patients suffering from the \"exploding head syndrome\" are described.\nIn spite of the fact that its characteristic symptomatology was first described approximately 150 y ago, exploding head syndrome has received relatively little empirical and clinical attention.\nAfter first discussing the history, prevalence, and associated features, the available polysomnography data and five main etiological theories for exploding head syndrome are summarized.\nExploding head syndrome: six new cases and review of the literature.\nExploding Head Syndrome in the Epilepsy Monitoring Unit: Case Report and Literature Review.\nExploding head syndrome: a case report.\nExploding head syndrome is common in college students.\nExploding head syndrome episodes were accompanied by clinically significant levels of fear, and a minority (2.80%) experienced it to such a degree that it was associated with clinically significant distress and/or impairment.\nAttention has recently been drawn to a condition termed the exploding head syndrome, which is characterized by unpleasant, even terrifying sensations of flashing lights and/or sounds during reported sleep.\nExploding head syndrome is a rare phenomenon but can be a significant disruption to quality of life.\nThe rare headache disorder hypnic headache and the exploding head syndrome are also discussed.\nThis case report describes the first-ever diagnosis of exploding head syndrome in a patient with longstanding epilepsy and novel nocturnal events.\nBACKGROUND Exploding head syndrome (EHS) is characterized by attacks of a sudden noise or explosive feeling experienced in the head occurring during the transition from wake to sleep or from sleep to wake.\nINTRODUCTION Exploding head syndrome (EHS) is a rare parasomnia in which affected individuals awaken from sleep with the sensation of a loud bang.\nContrary to some earlier theorizing, exploding head syndrome was found to be a relatively common experience in younger individuals.\nThis hitherto unreported syndrome is characterised by a sense of an explosive noise in the head usually in the twilight stage of sleep.\nEHS is a well-defined disease entity with a benign nature.\nExploding head syndrome: a case report.\nClinical features of the exploding head syndrome.\nExploding head syndrome is common in college students.\nThe exploding head syndrome: polysomnographic recordings and therapeutic suggestions.\nThis article reviews the features of an uncommon malady termed \"the exploding head syndrome.\" Sufferers describe terrorizing attacks of a painless explosion within their head\nThe case is reported of a 47-year old female suffering from the exploding head syndrome. This syndrome consists of a sudden awakening due to a loud noise shortly after falling asleep, sometimes accompanied by a flash of light."
},
{
"role": "assistant",
"content": "yes"
}
] |
science.pico_ner
|
science.pico_ner.769
|
[
{
"role": "user",
"content": "You will be shown an abstract from a biomedical research paper. Given this abstract, your task is to extract all unique entities of the following types: [\"Outcome\", \"Participant\", \"Intervention\"].\n\nPlease return the output as a JSON object of the format: {\"Participant\" : [\"patients with COPD\", ...], \"Intervention\" : [\"Atenolol\", ...], \"Outcome\" : [\"blood pressure\", ...]}. The keys should be entity types and values should be lists of extracted entities belonging to the corresponding type. If you cannot find entities belonging to a specific type, the value should be [].\n\nOnly output the JSON object and do not include any additional text.\n\nAbstract:\n\nMetoprolol CR/XL improves systolic and diastolic left ventricular function in patients with chronic heart failure . AIMS To investigate whether metoprolol controlled release/extended release ( CR/XL ) once daily would improve diastolic and systolic left ventricular function in patients with chronic heart failure and decreased ejection fraction . METHODS In an echocardiographic substudy to the Metoprolol CR/XL Randomized Intervention Trial in Heart Failure ( MERIT-HF ) , 66 patients were examined three times during a 12-month period blinded to treatment group , assessing left ventricular dimensions and ejection fraction , and Doppler mitral inflow parameters , all measured in a core laboratory . RESULTS In the metoprolol CR/XL group left ventricular ejection fraction increased from 0.26 to 0.31 ( P = 0.009 ) after a mean observation period of 10.6 months , and deceleration time of the early mitral filling wave ( E ) increased from 189 to 246 ms ( P = 0.0012 ) , time velocity integral of E-wave increased from 8.7 to 11.2 cm ( P = 0.018 ) , and the duration of the late mitral filling wave ( A ) increased from 122 to 145 ms ( P = 0.014 ) . No significant changes were seen in the placebo group regarding any of these variables . CONCLUSION Metoprolol CR/XL once daily in addition to standard therapy improved both diastolic and systolic function in patients with chronic heart failure and decreased ejection fraction ."
},
{
"role": "assistant",
"content": "{\"Intervention\": [\"metoprolol controlled release/extended release ( CR/XL )\", \"Metoprolol CR/XL\", \"metoprolol CR/XL\", \"placebo\"], \"Outcome\": [\"systolic and diastolic left ventricular function\", \"left ventricular ejection fraction\", \"duration of the late mitral filling wave\", \"time velocity integral of E-wave\", \"left ventricular dimensions and ejection fraction , and Doppler mitral inflow parameters\", \"time of the early mitral filling wave\", \"diastolic and systolic left ventricular function\", \"diastolic and systolic function\"], \"Participant\": [\"66\", \"chronic heart failure\"]}"
}
] |
science.qasa_abstractive_qa
|
science.qasa_abstractive_qa.920
|
[
{
"role": "user",
"content": "You will be shown an excerpt from a computer science scientific research paper, followed by a question about the paper. Please answer the question. Do not include any text in your response other than the answer.\n\nContext: The two most commonly used attention functions are additive attention [2], and dot-product (multiplicative) attention. Dot-product attention is identical to our algorithm, except for the scaling factor. Additive attention computes the compatibility function using a feed-forward network with a single hidden layer. While the two are similar in theoretical complexity, dot-product attention is much faster and more space-efficient in practice, since it can be implemented using highly optimized matrix multiplication code.\n\nQuestion: What is space meant in \"space-efficient in practice\" ?Does it mean space of search for solutions? or space in memory?"
},
{
"role": "assistant",
"content": "Dot product attention is much faster and more space-efficient than the additive attention. Here the space efficient is referring to the less memory space."
}
] |
science.bc7_litcovid_topic_classification
|
science.bc7_litcovid_topic_classification.1689
|
[
{
"role": "user",
"content": "You are presented with a paragraph from a COVID-19 literature. Classify the topics of this piece of text by choosing from the following categories:\n\n- Epidemic Forecasting: The content relates to predictions about the spread of COVID-19.\n- Treatment: The paragraph discusses therapeutic methods or medication for COVID-19.\n- Prevention: The content covers measures to prevent the spread of COVID-19.\n- Mechanism: The paragraph explains the biological mechanisms of the virus.\n- Case Report: The content is a report of a COVID-19 case.\n- Transmission: The paragraph discusses how COVID-19 is transmitted.\n- Diagnosis: The content is about diagnosing COVID-19 in individuals.\n\nYour classification should be provided as an element within a JSON array. The array should be formatted with topics enclosed in double quotes and separated by commas, following the JSON format, for example: [\"Topic1\", \"Topic2\", ...]. Include all applicable topics within the array. Your output should be a valid JSON array, and no additional text should be included in your response.\n\nArticle:\n\nThe novel coronavirus, SARS-CoV-2, has caused a recent pandemic called COVID-19 and a severe health threat around the world. In the current situation, the virus is rapidly spreading worldwide, and the discovery of a vaccine and potential therapeutics are critically essential. The crystal structure for the main protease (M(pro)) of SARS-CoV-2, 3-chymotrypsin-like cysteine protease (3CL(pro)), was recently made available and is considerably similar to the previously reported SARS-CoV. Due to its essentiality in viral replication, it represents a potential drug target. Herein, a computer-aided drug design (CADD) approach was implemented for the initial screening of 13 approved antiviral drugs. Molecular docking of 13 antivirals against the 3-chymotrypsin-like cysteine protease (3CL(pro)) enzyme was accomplished, and indinavir was described as a lead drug with a docking score of -8.824 and a XP Gscore of -9.466 kcal/mol. Indinavir possesses an important pharmacophore, hydroxyethylamine (HEA), and thus, a new library of HEA compounds (>2500) was subjected to virtual screening that led to 25 hits with a docking score more than indinavir. Exclusively, compound 16 with a docking score of -8.955 adhered to drug-like parameters, and the structure-activity relationship (SAR) analysis was demonstrated to highlight the importance of chemical scaffolds therein. Molecular dynamics (MD) simulation analysis performed at 100 ns supported the stability of 16 within the binding pocket. Largely, our results supported that this novel compound 16 binds with domains I and II, and the domain II-III linker of the 3CL(pro) protein, suggesting its suitability as a strong candidate for therapeutic discovery against COVID-19."
},
{
"role": "assistant",
"content": "[\"Treatment\", \"Mechanism\"]"
}
] |
science.bioasq_factoid_qa
|
science.bioasq_factoid_qa.728
|
[
{
"role": "user",
"content": "You will be shown biomedical passages and your task is to the answer the provided question. Provide a concise and accurate response and do not include any additional text in the response other than the answer.\n\nQuestion: Gallbladder carriage is a well recognised means of spread of which bacteria?\n\nContext: Carriage prevalence of Salmonella enterica serotype Typhi in gallbladders of adult autopsy cases from Mozambique.\nCONCLUSIONS: We report a high prevalence of S. Typhi in gallbladders among adult autopsy cases from Mozambique.\nSalmonella Extracellular Matrix Components Influence Biofilm Formation and Gallbladder Colonization.\nSalmonella enterica serovar Typhi, the causative agent of typhoid fever in humans, forms biofilms encapsulated by an extracellular matrix (ECM). Biofilms facilitate colonization and persistent infection in gallbladders of humans and mouse models of chronic carriage.\nIn vitro modeling of gallbladder-associated Salmonella spp. colonization.\nThe host-pathogen interactions occurring in the gallbladder during Salmonella Typhi colonization contribute to typhoid fever pathogenesis during the acute and chronic stages of disease. The gallbladder is the primary reservoir during chronic typhoid carriage.\nSalmonella chronic carriage: epidemiology, diagnosis, and gallbladder persistence.\nGallbladder carriage has been demonstrated to be mediated by biofilm formation on gallstones and by intracellular persistence in the gallbladder epithelium of mice.\nGallbladder epithelium as a niche for chronic Salmonella carriage.\nThis chronic state is highly associated with the presence of gallstones in the gallbladder of infected carriers upon which Salmonella can form robust biofilms. However, we hypothesize that in addition to gallstones, the gallbladder epithelium aids in the establishment/maintenance of chronic carriage.\nCarriage prevalence of Salmonella enterica serotype Typhi in gallbladders of adult autopsy cases from Mozambique."
},
{
"role": "assistant",
"content": "Salmonella Typhi"
}
] |
science.gnormplus_ner
|
science.gnormplus_ner.354
|
[
{
"role": "user",
"content": "You will be shown an abstract from a biomedical research paper. Given this abstract, your task is to extract all unique entities of the following types: [\"Gene\"].\n\nPlease return the output as a JSON object of the format: {\"Gene\": [\"SSX\", ...]}. The keys should be entity types and values should be lists of extracted entities belonging to the corresponding type. If you cannot find entities belonging to a specific type, the value should be [].\n\nOnly output the JSON object and do not include any additional text.\n\nAbstract:\n\nIdentification of the nuclear localization motif in the ETV6 (TEL) protein. ETV6, or Translocation-Ets-Leukemia (TEL), is an ETS family transcriptional repressor that is essential for establishing hematopoiesis in neonatal bone marrow, and is frequently a target of chromosomal translocations in human cancer. ETV6 is predominantly a nuclear phosphoprotein that represses transcription by binding directly to the promoters of target genes. The nuclear localization mechanism of ETV6, however, is not well understood. In this report, we provide evidence that a nuclear localization signal (NLS) exists in the C-terminal region of ETV6. ETV6 proteins with mutations outside of amino acids 332-452 localize to the nucleus, whereas proteins with mutations within amino acids 332-452 remain in the cytoplasm. Furthermore, when a fragment of ETV6 comprised of amino acids 332-452 was fused to cytoplasmic beta-galactosidase protein, the fusion protein was able to enter the nucleus. These results strongly indicate that residues 332-452 mediate nuclear localization of ETV6."
},
{
"role": "assistant",
"content": "{\"Gene\": [\"ETS family transcriptional repressor\", \"beta-galactosidase\", \"ETV6\", \"Translocation-Ets-Leukemia\", \"TEL\"]}"
}
] |
science.chemprot_ner
|
science.chemprot_ner.923
|
[
{
"role": "user",
"content": "You will be shown an abstract from a biomedical research paper. Given this abstract, your task is to extract all unique entities of the following types: [\"Protein\", \"Chemical\"].\n\nPlease return the output as a JSON object of the format: {\"Chemical\" : [\"Dexamethasone\", ...], \"Protein\" : [\"BRCA-1\", ...]}. The keys should be entity types and values should be lists of extracted entities belonging to the corresponding type. If you cannot find entities belonging to a specific type, the value should be [].\n\nOnly output the JSON object and do not include any additional text.\n\nAbstract:\n\nStudies of the biogenic amine transporters. 13. Identification of \"agonist\" and \"antagonist\" allosteric modulators of amphetamine-induced dopamine release.\nRecent studies identified novel allosteric modulators of the dopamine (DA) transporter (DAT). N-(Diphenylmethyl)-2-phenyl-4-quinazolinamine (SoRI-9804), N-(2,2-diphenylethyl)-2-phenyl-4-quinazolinamine (SoRI-20040), and N-(3,3-diphenylpropyl)-2-phenyl-4-quinazolinamine (SoRI-20041) partially inhibited [(125)I]3beta-(4'-iodophenyl)tropan-2beta-carboxylic acid methyl ester (RTI-55) binding, slowed the dissociation rate of [(125)I]RTI-55 from the DAT, and partially inhibited [(3)H]dopamine uptake. In the present study, we report that SoRI-9804 and SoRI-20040, at doses that do not alter release, partially inhibited d-amphetamine-induced DAT-mediated release of [(3)H]1-methyl-4-phenylpyridinium (MPP(+))or[(3)H]dopamine from striatal synaptosomes (\"DAT-mediated DA release\") in a dose-dependent manner. SoRI-20041, which does not alter DAT-mediated DA release measured with [(3)H]DA, reversed the effect of SoRI-20040. SoRI-20040 and SoRI-9804 also partially inhibited DAT-mediated DA release induced by DA or (+/-)-3,4-methylenedioxyamphetamine, demonstrating that the observed partial inhibition is not specific for a particular DAT substrate. SoRI-9804 and SoRI-20040 did not attenuate D-amphetamine-induced release of [(3)H]5-hydroxytryptamine from serotonergic, or [(3)H]MPP(+) from noradrenergic, nerve terminals. Kinetic experiments demonstrated that SoRI-9804, in contrast to cocaine, slowed D-amphetamine-induced release of [(3)H]MPP(+) from dopaminergic nerve terminals without altering the apparent rate constants. The two major findings of this study are 1) the identification of both \"agonist\" (SoRI-9804 and SoRI-20040) and \"antagonist\" (SoRI-20041) allosteric modulators of D-amphetamine-induced DAT-mediated DA release and 2) [(3)H]DA uptake and d-amphetamine-induced DAT-mediated efflux can be separately modulated. Such agents may have therapeutic potential for the treatment of stimulant addiction, Parkinson's disease, and other psychiatric disorders."
},
{
"role": "assistant",
"content": "{\"Chemical\": [\"MPP(+)\", \"amphetamine\", \"D-amphetamine\", \"DA\", \"dopamine\", \"SoRI-20041\", \"(+/-)-3,4-methylenedioxyamphetamine\", \"SoRI-9804\", \"[(3)H]MPP(+)\", \"N-(2,2-diphenylethyl)-2-phenyl-4-quinazolinamine\", \"[(3)H]DA\", \"SoRI-20040\", \"[(3)H]1-methyl-4-phenylpyridinium\", \"cocaine\", \"[(125)I]3beta-(4\\u0027-iodophenyl)tropan-2beta-carboxylic acid methyl ester\", \"N-(3,3-diphenylpropyl)-2-phenyl-4-quinazolinamine\", \"N-(Diphenylmethyl)-2-phenyl-4-quinazolinamine\", \"RTI-55\", \"[(125)I]RTI-55\", \"d-amphetamine\", \"[(3)H]dopamine\", \"[(3)H]5-hydroxytryptamine\"], \"Protein\": [\"DAT\", \"biogenic amine transporters\", \"dopamine (DA) transporter\"]}"
}
] |
science.cdr_ner
|
science.cdr_ner.451
|
[
{
"role": "user",
"content": "You will be shown an abstract from a biomedical research paper. Given this abstract, your task is to extract all unique entities of the following types: [\"Disease\", \"Chemical\"].\n\nPlease return the output as a JSON object of the format: {\"Chemical\" : [\"Naloxone\", ...], \"Disease\" : [\"Hypotensive\", ...]}. The keys should be entity types and values should be lists of extracted entities belonging to the corresponding type. If you cannot find entities belonging to a specific type, the value should be [].\n\nOnly output the JSON object and do not include any additional text.\n\nAbstract:\n\nEffects of aminophylline on the threshold for initiating ventricular fibrillation during respiratory failure. Cardiac arrhythmias have frequently been reported in association with respiratory failure. The possible additive role of pharmacologic agents in precipitating cardiac disturbances in patients with respiratory failure has only recently been emphasized. The effects of aminophylline on the ventricular fibrillation threshold during normal acid-base conditions and during respiratory failure were studied in anesthetized open chest dogs. The ventricular fibrillation threshold was measured by passing a gated train of 12 constant current pulses through the ventricular myocardium during the vulnerable period of the cardiac cycle. During the infusion of aminophylline, the ventricular fibrillation threshold was reduced by 30 to 40 percent of the control when pH and partial pressures of oxygen (PO2) and carbon dioxide (CO2) were kept within normal limits. When respiratory failure was produced by hypoventilation (pH 7.05 to 7.25; PC02 70 to 100 mm Hg: P02 20 to 40 mm Hg), infusion of aminophylline resulted in an even greater decrease in ventricular fibrillation threshold to 60 percent of the control level. These experiments suggest that although many factors may contribute to the increased incidence of ventricular arrhythmias in respiratory failure, pharmacologic agents, particularly aminophylline, may play a significant role."
},
{
"role": "assistant",
"content": "{\"Chemical\": [\"aminophylline\", \"CO2\", \"PO2\", \"oxygen\", \"carbon dioxide\"], \"Disease\": [\"cardiac disturbances\", \"hypoventilation\", \"Cardiac arrhythmias\", \"ventricular fibrillation\", \"ventricular arrhythmias\", \"respiratory failure\"]}"
}
] |
science.genia_ner
|
science.genia_ner.342
|
[
{
"role": "user",
"content": "You will be shown an abstract from a biomedical research paper. Given this abstract, your task is to extract all unique entities of the following types: [\"RNA\", \"CellLine\", \"Protein\", \"DNA\", \"CellType\"].\n\nPlease return the output as a JSON object of the format: {\"DNA\" : [\"TAL1\", ...], \"RNA\": [\"mRNAs\", ...], \"CellLine\": [\"T cells\", ...], \"CellType\": [\"monocytes\", ...], \"Protein\": [\"IL-2\", ...]}. The keys should be entity types and values should be lists of extracted entities belonging to the corresponding type. If you cannot find entities belonging to a specific type, the value should be [].\n\nOnly output the JSON object and do not include any additional text.\n\nAbstract:\n\nSusceptibility to natural killer cells and down regulation of MHC class I expression in adenovirus 12 transformed cells are regulated by different E1A domains. All human adenoviruses transform rodent cells in vitro, but only cells transformed by serotypes belonging to subgroups A (Ad12) and B (Ad3) are tumorigenic for immunocompetent animals. In these cells, the expression of MHC-class I antigens is repressed and might allow them to escape from recognition by cytotoxic T lymphocytes (CTL) and to develop in tumor. Furthermore, these cell lines appear resistant to lysis by natural killer (NK) cells. To determine the E1A domain (s) responsible for these properties several cell lines were created by transforming baby rat kidney (BRK) cells with a set of plasmids expressing different Ad2 / Ad12 hybrid E1A gene products. The MHC class 1 gene expression was inhibited in cells expressing the Ad12 13S mRNA product and in cells transformed with Ad2 / Ad12 hybrid E1A gene product harboring the C-terminal part of the conserved region (CR) 3 of Ad12. Susceptibility of these transformed cell lines to NK cells was determined by cytolytic assays. The results obtained suggest that two Ad12 E1A domains are required to induce resistance of the cell lines to NK cells."
},
{
"role": "assistant",
"content": "{\"CellLine\": [\"cell lines\", \"adenovirus 12 transformed cells\", \"baby rat kidney (BRK) cells\"], \"CellType\": [\"cytotoxic T lymphocytes\", \"natural killer (NK) cells\", \"natural killer cells\", \"CTL\", \"rodent cells\", \"NK cells\"], \"DNA\": [\"Ad12 E1A domains\", \"plasmids\", \"conserved region (CR) 3\", \"E1A domain\", \"MHC class 1 gene\", \"E1A domains\"], \"Protein\": [\"Ad2 / Ad12 hybrid E1A gene product\", \"Ad2 / Ad12 hybrid E1A gene products\", \"C - terminal part\", \"MHC - class I antigens\", \"MHC\", \"Ad12 13S mRNA product\"], \"RNA\": [\"Ad12 13S mRNA\"]}"
}
] |
science.healthver_entailment
|
science.healthver_entailment.4628
|
[
{
"role": "user",
"content": "You will be shown a claim about public health, and the abstract of a biomedical research paper. Each sentence from the abstract will be on a separate line. Your task is to return a JSON object with two fields:\n\n- \"verdict\": The fact-checking verdict. If the information in the abstract supports the claim, write \"SUPPORT\". If the abstract contradicts the claim, write \"CONTRADICT\". If the abstract does not provide enough information to arrive at a verdict, write \"NEI\" (for \"not enough information\").\n- \"evidence\": An array of sentences providing evidence for the verdict. Please copy all relevant sentences verbatim from the abstract. If the verdict was \"NEI\", then return an empty array.\n\nFor instance, if the model were given the claim \"wearing masks can prevent the spread of COVID\", the output might be\n{\n \"verdict\": \"SUPPORT\",\n \"evidence\": [\"Our findings indicate that mass mask-wearing reduces the transmission rate for COVID-19.\"]\n}\n\nClaim: ngiotensin-converting enzyme inhibitors (ACEi) and angiotensin II receptor blockers (ARB), which are commonly used in patients with hypertension or diabetes and may raise tissue ACE2 levels, could increase the risk of severe COVID-19 infection.\n\nAbstract:\nThe effects of angiotensin-converting enzyme inhibitors (ACEIs) and angiotensin receptor blockers (ARBs) on the risk of COVID-19 infection and disease progression are yet to be investigated.\nThe relationship between ACEI/ARB use and COVID-19 infection was systematically reviewed.\nTo identify relevant studies that met predetermined inclusion criteria, unrestricted searches of the PubMed, Embase, and Cochrane Library databases were conducted.\nThe search strategy included clinical date published until May 9, 2020.\nTwelve articles involving more than 19,000 COVID-19 cases were included.\nTo estimate overall risk, random-effects models were adopted.\nOur results showed that ACEI/ARB exposure was not associated with a higher risk of COVID-19 infection (OR = 0.99; 95 % CI, 0-1.04; P = 0.672).\nAmong those with COVID-19 infection, ACEI/ARB exposure was also not associated with a higher risk of having severe infection (OR = 0.98; 95 % CI, 0.87-1.09; P = 0.69) or mortality (OR = 0.73, 95 %CI, 0.5-1.07; P = 0.111).\nHowever, ACEI/ARB exposure was associated with a lower risk of mortality compared to those on non-ACEI/ARB antihypertensive drugs (OR = 0.48, 95 % CI, 0.29-0.81; P = 0.006).\nIn conclusion, current evidence did not confirm the concern that ACEI/ARB exposure is harmful in patientswith COVID-19 infection.\nThis study supports the current guidelines that discourage discontinuation of ACEIs or ARBs in COVID-19 patients and the setting of the COVID-19 pandemic."
},
{
"role": "assistant",
"content": "{\"verdict\": \"CONTRADICT\", \"evidence\": [\"In conclusion, current evidence did not confirm the concern that ACEI/ARB exposure is harmful in patientswith COVID-19 infection.\", \"This study supports the current guidelines that discourage discontinuation of ACEIs or ARBs in COVID-19 patients and the setting of the COVID-19 pandemic.\"]}"
}
] |
science.scientific_papers_summarization_single_doc_pubmed
|
science.scientific_papers_summarization_single_doc_pubmed.26574
|
[
{
"role": "user",
"content": "You will be presented with the full text of a biomedical research paper. Please write an abstract for this paper. Your response should include the abstract and no additional text.\n\nPaper text:\nlike most orthopaedic surgical procedures , successful hip arthroscopy is significantly influenced by two factors : the patient selection process for the procedure , and the post - operative rehabilitation .\nobjectively patient selection includes evidence of pathology or clinical circumstances potentially amenable to arthroscopic intervention .\nsubjectively , this also includes an assessment of the patient s expectations of the procedure .\nample evidence supports that the nature of supervised physical therapy following surgery can positively influence the results [ 4 , 5 ] .\nit is generally believed that a reasonably performed surgical procedure can result in a successful outcome when guided by a properly structured post - operative rehabilitation programme .\nconversely , the best operation may fail in the presence of poorly structured post - operative rehabilitation .\northopaedic surgeons represent the cohort most knowledgeable regarding musculoskeletal disorders and treatment ; and thus most qualified for developing properly founded expectations of these procedures , and are most understanding of the post - operative rehabilitation .\nthe purpose of this report is to share observations and outcomes among a cohort of orthopaedic surgeons .\nsince 1993 , all patients undergoing hip arthroscopy are prospectively assessed utilizing a modified harris hip score ( mhhs ) pre- and then post - operatively at 3 , 12 , 24 , 60 and 120 months . from this prospectively gathered database , 24 orthopaedic surgeons ( including one bilateral case ) were identified who had undergone arthroscopic surgery and had achieved minimum 1-year follow - up .\nthe data obtained and presented in this article have been granted exemption status by the institutional review board .\nthe indication for arthroscopy was clinical findings of joint pathology amenable to arthroscopic intervention that had failed conservative treatment , which variously included activity modifications , rehabilitation , oral anti - inflammatory medications , and judicious use of intra - articular injections .\nall procedures were performed using a standard supine method that has been previously reported [ 7 , 8 ] .\npost - operative rehabilitation , begun on the day following surgery , was dictated by the pathology encountered and the procedure performed .\nfemoroplasties were allowed to weight bear as tolerated with crutches for 4 weeks in order to regain protective muscle tone and strength .\nlabral repairs and refixations were maintained with 50% weight bearing for 4 weeks , limiting external rotation and maximal flexion ; while microfractures were kept on a strict protected weight bearing status for 8 weeks .\nstructured rehabilitation , focusing on recover from surgery , was typically maintained for 12 weeks , followed by a functional progression to vigorous activities as dictated by the patient s goals . in general , for orthopaedic surgeons , they were advised to return to a limited clinic schedule at 1 month , and a limited surgical schedule at 2 months .\nstatistical analysis comparing the pre and post - operative scores was performed using a paired samples t - test .\nthe average improvement was 18 points ( preoperative 75 ; post - operative 93 ) which was statistically significant ( p < 0.001 ) ; all improved with excellent or good results .\n1.average mhhs scores over time j.w.t.b \n average mhhs scores over time j.w.t.b there were numerous diagnoses ( table 1 ) and various procedures performed ( table 2 ) . \n\ntable i.diagnosesacetabular chondral lesions24labral tears23fai11 cam ; 6 combined ; 1 pincerloose bodies7femoral chondral lesions6ruptured ligamentum teres3 \n table ii.procedures performedlabral debridement20chondroplasty14femoroplasty11microfracture11acetabuloplasty7 ( 3 with labral refixation)debridement ligamentum teres3 one patient declined and was eventually converted to total hip arthroplasty at 54 months .\none patient sustained a re - injury and underwent repeat arthroscopy at 11 months , again having a successful outcome ( preoperative 85 ; post - operative 96 at 1 year ) .\nthere was one complication : an acute myocardial infarction occurred in the recovery room necessitating coronary artery bypass surgery 4 days later .\n, they resumed patients at an average of 1.6 weeks ( range 2 days4 weeks ) ; and resumed operating at an average of 3.1 weeks ( range 6 days8 weeks ) .\nthe observations shared here span three decades during which the understanding of hip disorders and technological advances in treatment have evolved substantially , thus representing a very heterogeneous study population in terms of diagnoses and procedures performed .\nnonetheless , generally successful results have been recorded in terms of outcome measures and return to vocational activities .\na 4% complication rate may be acceptable , but an acute myocardial infarction reflects that unanticipated , potentially catastrophic problems can occur and thus a responsible approach in the decision on performing any surgical procedure is always paramount .\nfirst , if understanding of the procedure is important to a successful outcome , then this is consistent with the data presented here as all surgeons were uniformly improved , even though one required repeat arthroscopy , one was converted to a total hip arthroplasty and one experienced a significant complication with a myocardial infarction .\nsecond regards compliance with the post - operative rehabilitation process . although the limitations outlined were not strict and were more recommendations to avoid setbacks and flare - ups , this group uniformly exceeded the general guidelines ; returning to patient care and surgery in 40% or less of the recommended time frame .\nthe only one who complied with the recommendations was a resident ; the rest were practicing orthopaedic surgeons .\nit is inherently evident that orthopaedic surgeons should be potentially the most knowledgeable regarding surgical procedures that are recommended to them .\nthis is the only way to avoid falling into the trap of making alterations in what is deemed to be the optimal standard of care .\nshortcuts , and or exceptions in standards of treatment can be fraught with numerous problems and ultimately expose the surgeon being treated to suboptimal care .\nin anterior cruciate ligament reconstructive surgery , we learned that functional progression could exceed the time limits that would be predicted based on biological healing .\nunderstanding the limits and efficacy of these progressive rehabilitation strategies was largely gained through observations of patients who did not exhibit compliance with more cautious rehabilitation strategies . perhaps the same can be learned among hip arthroscopy patients .\nfor example , rehabilitation following labral repair or refixation mostly revolves around protecting the repair site .\nhowever , the labrum has proven to be a hardy structure , as the indications for revision arthroscopy usually include adhesions and incomplete correction of femoroacetabular impingement ( fai ) and , less frequently , failure of a labral repair site [ 12 , 13 ] .\nthus , our rehabilitation strategies can probably be more progressive . however , as we strive to be more progressive , we simply do not want to find the point at which the failure rate starts to rise\n. we do not want to relearn the lessons of the shoulder where lack of post - operative precautions was implicated in failure rates of arthroscopic stabilization .\nsuccessful hip arthroscopy necessitates that patient expectations match the realities of what can be accomplished with the procedure . as a cohort ,\northopaedic surgeons possess the greatest insight into hip arthroscopy , but , as patients , often they must modulate their expectations to match their understanding of the realities of the procedure .\nmarginal compliance with the post - operative rehabilitation did not seem to compromise good results , although this population may be best prepared to understand their individual limits .\nlast , these experiences span three decades during which the understanding of hip disorders and technological advances in treatment have evolved substantially , thus representing a very heterogeneous study population in terms of diagnoses and treatment performed .\nnonetheless , generally successful results have been recorded in terms of outcome measures and return to vocational activities .\nj.w.t.b . is a consultant for and receives research support from smith and nephew endoscopy ; he is a non - paid consultant and has stock in a3 surgical ."
},
{
"role": "assistant",
"content": "successful hip arthroscopy depends on proper patient selection and reasonable patient expectations . \n the purpose of this study is to report the results of hip arthroscopy in orthopaedic surgeons who represent the most informed cohort . \n this report is based on a retrospective review of prospectively collected data among 24 orthopaedic surgeons ( 1 bilateral ) . \n follow - up averaged 48 months ( range 12120 months ) . \n they were all males with an average age of 45 years ( range 3064 years ) . \n all improved with an average of 18 points ( preoperative 75 ; post - operative 93 ) ; although one underwent repeat arthroscopy and one was converted to total hip arthroplasty at 54 months . \n there were numerous diagnoses and procedures performed and one complication ( acute coronary artery occlusion ) . \n they resumed seeing patients at an average of 1.6 weeks ( range 2 days4 weeks ) and operating at an average of 3.1 weeks ( range 6 days8 weeks ) . \n this report spans three decades , thus representing a heterogeneous population in terms of diagnoses and treatment . nonetheless , successful results are noted . as a cohort , \n orthopaedic surgeons possess the greatest insight into hip arthroscopy , but as patients , often they must modulate their expectations in order to match the understanding of the realities of the procedure ."
}
] |
science.bioasq_yesno_qa
|
science.bioasq_yesno_qa.238
|
[
{
"role": "user",
"content": "You have to answer a biomedical question in binary format, i.e. only yes and no are the only acceptable answer formats. A list of paragraphs is provided as context to help you answer the question.\n\nQuestion: Is there a pharmacogenetic test for trastuzumab?\n\nContext: The clinical need for novel approaches to improve drug therapy derives from the high rate of adverse reactions to drugs and their lack of efficacy in many individuals that may be predicted by pharmacogenetic testing.\nthe assessment of the human epidermal growth factor receptor (HER-2) expression for trastuzumab therapy of breast cancer\nHER2 positive breast cancer and the use of the drug Herceptin\nThe dependence on gene copy number or expression levels of HER2 and epidermal growth factor receptor (EGFR) for therapeutic efficacy of trastuzumab and cetuximab (Erbitux), respectively, supports the importance of selecting suitable patient populations based on their pharmacogenetic profile.\nto explore informed consent issues surrounding the use of the drug Herceptin, widely cited as an example of a novel approach to drug development called pharmacogenetics. Drawing on qualitative semi-structured interviews with 25 UK-based breast cancer specialists, this paper explores Herceptin's disputed epistemological status, as an example of pharmacogenetics or as something out of the ordinary in terms of clinical practice.\nThere have been several success stories in the field of pharmacogenetics in recent years, including the analysis of HER2 amplification for trastuzumab selection in breast cancer\nTrastuzumab is standard of care in the treatment of human epidermal growth factor receptor (HER)-2⁺ early and advanced breast cancer.\nHER-2 overexpression as a predictor of response to trastuzumab\nPharmacogenomic analysis aspires to identify individuals with specific genetic characteristics in order to predict a positive response or reduce a negative response to a therapeutic modality.\nAssays are available to detect the HER2 protein receptor or copies of the HER2 gene sequence to determine eligibility for Herceptin treatment or adriamycin treatment in node positive patients, respectively.\nDetermining the HER2 status of breast carcinomas is a prerequisite for the use of the monoclonal antibody trastuzumab (Herceptin), which has recently been licensed for the treatment of metastatic disease.\nLaboratory testing of HER2/neu in breast carcinoma has become vital to patient care following the approval of trastuzumab as the first therapy to target the HER2/neu oncoprotein.\nImmunohistochemical (IHC) analysis was performed with use of a diagnostic test for the assessment of HER2 overexpression, the HercepTest.\nTo test for HER-2/neu overexpression in patients with non-Hodgkin's lymphoma and the possible role of the recombinant monoclonal anti-HER-2/neu antibody trastuzumab (Herceptin) in the treatment of non-Hodgkin's lymphoma.\nTo evaluate concordance between local and central laboratory HER2 testing results in patients from the North Central Cancer Treatment Group (NCCTG) N9831 adjuvant trial of trastuzumab.\nThese findings support the importance of using high-volume, experienced laboratories for HER2 testing to improve the process of selecting patients likely to benefit from trastuzumab therapy.\nwe measured trastuzumab levels in the serum and in cerebrospinal fluid of metastatic breast cancer patients with brain metastases receiving trastuzumab for HER2-overexpressing metastatic breast cancer. In a pilot study, metastatic breast cancer patients with brain metastases and HER2-overexpressing tumors (HercepTest; Dako, Copenhagen, Denmark) were included.\nMonitoring of trastuzumab levels in the serum and cerebrospinal fluid may enable individualized therapy strategies in metastatic breast cancer patients with brain metastases, and lead to a better understanding of trastuzumab pharmacokinetics in the cerebrospinal fluid and serum.\nBiotin-labeled trastuzumab (BiotHER) can be used to test for HER2 by immunohistochemistry.\nThe results support a role for BiotHER testing in better tailoring trastuzumab-based treatments in patients with advanced HER2-amplified breast cancers.\nresponse to anti-human epidermal growth factor receptor 2 (HER2) therapy trastuzumab."
},
{
"role": "assistant",
"content": "yes"
}
] |
science.scientific_lay_summarisation_elife_single_doc_summ
|
science.scientific_lay_summarisation_elife_single_doc_summ.2536
|
[
{
"role": "user",
"content": "You will be presented with the abstract, introduction, and discussion section from a biomedical research article. Your task is to create a summary that a layperson can understand, capturing the essence of the research article. Keep essential scientific terms, but ensure that the language remains clear and the concepts are explained in an uncomplicated manner.\n\nTitle: Microbiota functional activity biosensors for characterizing nutrient metabolism in vivo}\nArticle:\nAbstract:\nMethods for measuring gut microbiota biochemical activities in vivo are needed to characterize its functional states in health and disease. To illustrate one approach, an arabinan-containing polysaccharide was isolated from pea fiber, its structure defined, and forward genetic and proteomic analyses used to compare its effects, versus unfractionated pea fiber and sugar beet arabinan, on a human gut bacterial strain consortium in gnotobiotic mice. We produced ‘Microbiota Functional Activity Biosensors’( MFABs) consisting of glycans covalently linked to the surface of fluorescent paramagnetic microscopic glass beads. Three MFABs, each containing a unique glycan/fluorophore combination, were simultaneously orally gavaged into gnotobiotic mice, recovered from their intestines, and analyzed to directly quantify bacterial metabolism of structurally distinct arabinans in different human diet contexts. Colocalizing pea-fiber arabinan and another polysaccharide( glucomannan) on the bead surface enhanced in vivo degradation of glucomannan. MFABs represent a potentially versatile platform for developing new prebiotics and more nutritious foods.\nIntroduction:\nIncreasing effort is being directed to determining how components of diets consumed by various human populations impact the composition and expressed functional features of their gut microbial communities( e. g., Johnson et al., 2019; Ghosh et al., 2020). A hoped-for benefit is to gain new insights about how food ingredients and their biotransformation by the microbiota are linked to various aspects of human physiology, and new ways to both define and improve nutritional status. However, there are many formidable challenges. The gut microbiota is complex and dynamic and exhibits considerable intra- and interpersonal variation in its configurations( Lloyd-Price et al., 2017). The chemical compositions of food staples are being cataloged at ever-deepening levels of detail using higher throughput analytical methods, such as mass spectrometry. Even as this knowledge is being acquired, how food components are recognized by members of the microbiota, and the pathways through which these chemical entities are metabolized by community members to influence their functions and those of the host remain challenging to define. Furthermore, much needs to be learned about the effects of current methods of food processing on the representation of bioactive food components( Carmody et al., 2015; Wolf et al., 2019), and about the mechanisms that determine whether and how microbes compete and/or cooperate for them. Plant fibers epitomize these challenges. Plant fibers are complex mixtures of biomolecules whose composition varies depending upon their source, method of initial recovery, and the food processing techniques used to incorporate them into food products that have satisfactory organoleptic properties( texture, taste, smell)( Shahidi and Ho, 1998; Caffall and Mohnen, 2009). Plant fibers are composed of but not limited to polysaccharides, proteins, fatty acids, polyphenols, and other plant-derived small molecules( Nicholson et al., 2012; Scalbert et al., 2014). Isolating and/or purifying component polysaccharides from crude plant fiber mixtures for studies of the mechanisms by which they influence members of the microbiota can be very challenging; even if separation is achieved, painstaking analysis is required to define their structures( Pettolino et al., 2012). Nonetheless, knowledge of the genetic underpinnings of how various members of the gut microbiota recognize and metabolize glycans has increased substantially in recent years through a combination of in vitro and in vivo approaches( Brown and Koropatkin, 2020; Kaoutari et al., 2013; Ndeh and Gilbert, 2018). Knowing that a given microbiota member has a suitable complement of genes for acquiring and processing a given glycan structure in vitro does not necessarily predict whether that organism will be a consumer in vivo( Flint et al., 2015). For example, an individual’s microbiota may harbor a number of organisms with the capacity to compete or cooperate with one another for utilization of a given type of glycan. Additionally, the physical and chemical structure of a plant fiber( e. g., its size, surface properties, nutrient composition) in a given region of the gut could influence which set of microbes attach to its surface, how its associated microbes prioritize consumption of its component glycans, and how/whether fiber particle-associated microbes can share products of glycan metabolism with one another. The current study illustrates an approach for identifying bioactive molecules from plant fibers and defining how they affect and how they are processed by members of the human gut microbiota. Pea fiber was selected based on results obtained from a screen we conducted of 34 types of food-grade crude plant fibers obtained from various sources, including the byproducts of food manufacturing( Patnode et al., 2019). The screen was performed in gnotobiotic mice colonized with a defined consortium of cultured sequenced human gut bacterial strains, including several saccharolytic Bacteroides species. Mice were fed a low-fiber diet formulated to represent the upper tertile of saturated fat consumption and lower tertile of fruit and vegetable consumption by individuals living in the USA, as reported in the NHANES database( Ridaura et al., 2013). Supplementation of this ‘HiSF-LoFV’ diet with fiber generated from the seed coat of the pea, Pisum sativum, produced a significant increase in the abundance of Bacteroides thetaiotaomicron( Patnode et al., 2019). We have now isolated a bioactive arabinan-enriched fraction from pea fiber, defined its structure, and characterized how a model human gut community, containing human gut Bacteroides established in gnotobiotic mice, responds to the isolated arabinan-enriched fraction versus unfractionated pea fiber. We go on to describe a generalizable method for covalently attaching different glycans to microscopic paramagnetic glass beads with different covalently bound fluorophores, eliminating the proteinaceous component of an approach published by our group that relies on streptavidin-coated beads and bifunctional biotin-conjugated polysaccharides( Patnode et al., 2019). Introduction of these ‘Microbiota Functional Activity Biosensors’( MFABs) into gnotobiotic mice fed the HiSF-LoFV diet with or without glycan supplementation followed by their recovery from the gut allowed us to directly compare the capacity of these glycans to be degraded by this community. Chemically colocalizing pea fiber arabinan with glucomannan, another type of polysaccharide not found in the diet, in a monolayer on an MFAB surface enhanced the efficiency of microbial community degradation of bead-associated glucomannan when animals were given a pea-fiber-supplemented HiSF-LoFV diet. These findings illustrate how knowledge of the bioactive components of fibers, and the capacity to directly measure microbiota function with MFABs, could provide new approaches for designing ‘next-generation’ prebiotics and foods that are more accessible to, and have a greater impact on, the gut microbiota( and by extension, the host).\nDiscussion:\nWe have used gnotobiotic mice colonized with a defined model human gut microbial community containing 58, 537 known or predicted protein-coding genes together with metaproteomic and forward genetic analyses to demonstrate the sensitivity of a microbiota to structural differences in glycans( arabinans) isolated from two distinct plant sources. Robust isolation procedures and analytical characterization are required to isolate grams of polysaccharide and test their biological effects in gnotobiotic mice. The approach we employed allowed us to isolate 50 g of material to ~85% purity with the remaining material comprised of starch and xylan. Starch can be degraded by host enzymes. The xylan present in our PFABN preparation could, in principle, influence the microbiota response. However, there is arabinoxylan already present in the base HiSF-LoFV diet, and we found that expression of known xylan-responsive PULs in B. cellulosilyticus WH2 and B. ovatus ATCC 8483 was not induced by PFABN supplementation( Figure 2—figure supplement 1; Patnode et al., 2019; McNulty et al., 2013; Martens et al., 2011). The specific activity of each isolated arabinan( in this case the increase in absolute abundance of the responsive Bacteroides per unit mass of diet ingredient consumed per day) was superior to unfractionated pea fiber( Figure 2C), emphasizing, as others have, the importance of characterizing the effects of plant fibers on both the microbiota and host in order to inform future studies at the intersection of food science, nutrition, and human microbial ecology research( Gidley and Yakubov, 2019). Although each of the isolated arabinans had distinct effects on gene expression and organismal fitness, our development of orally administered recoverable and chemically modifiable probes to quantitate community metabolic function revealed their equivalent degradation in specified diet contexts. These findings illustrate how in vivo functional assays can complement and expand current approaches for characterizing microbiomes. The bead-based MFABs described in this report represent a technology for measuring biochemical activities expressed by a microbial community of interest in vivo or ex vivo. Future studies where MFABs are used in conjunction with genetic tools that enable rapid deletion of genes or entire multi-kilobase loci could provide new insights about the mechanisms by which community members acquire/degrade nutrients( polysaccharides). We emphasize that in this study, we use MFABs to quantify community degradative activity and not to analyze community consumption of MFAB-bound polysaccharides and its relationship to bacterial growth. Determining the latter is challenging in our animal model; a typical gavage of 107 beads contained 100 µg of bead-immobilized polysaccharide, 1000 times more polysaccharide was consumed daily in the diet by mice in the polysaccharide-supplemented arms of our experiments. Installing specific functional groups on the surfaces of microscopic paramagnetic glass beads using commercially available organosilane reagents allows ‘modular’ incorporation of different biomolecules. This approach represents an alternative to a procedure we described recently, where bifunctional biotinylated ligands are generated prior to immobilization on glass beads coated with streptavidin( Patnode et al., 2019). Each of these approaches has distinct advantages and disadvantages. By immobilizing ligand directly on the bead surface, MFABs possess a greater number of sites for ligand attachment than streptavidin-coated beads and include no protein constituents. Higher ligand density enables higher levels of ligand loading, which reduces the absolute number of beads that need to be administered, recovered, and processed, and increases the dynamic range of a functional activity readout. A unifying question for food science, microbiome science, and nutrition research is how to decipher the effects of a nutrient and the matrix in which it resides within a food on modulation of microbiota functions( Gidley and Yakubov, 2019; Leitch et al., 2007). Crude plant fibers contain various polysaccharides densely intercalated within a cellulose-lignin matrix( Caffall and Mohnen, 2009). We found that the absolute abundances of B. cellulosilyticus WH2 and Ruminococcaceae sp. TSDC 17. 2 increase significantly when animals were consuming the crude pea fiber-supplemented diet, but not during supplementation with either of the isolated arabinans. The chemistry for covalent polysaccharide attachment to MFABs not only allows for dense ligand presentation, but also enables multiple ligands to be simultaneously immobilized to create ‘hybrid’ beads to model the effects of physical colocalization of different fiber components on microbial degradation. In principle, a wide range of different glycan combinations with varying stoichiometries can be explored owing to the fact that different hybrid bead types, each with its own fluorophore, can be created and tested simultaneously in vitro and in vivo to investigate the mechanism, generality, and biological significance of colocalization of glycans on their degradation by gut microbes. The selection of gut bacterial taxa for in vivo tests of fiber effects in gnotobiotic animal models is critical for yielding ecologically and physiologically relevant results. Characterizing defined communities comprised of organisms beyond those represented in the 14-member consortium will undoubtedly be informative. For example, members of Lactobacillus, Bifidobacterium, and Faecalibacterium are more tolerant of acidic conditions after carbohydrate fermentation and can outcompete acid intolerant bacteria such as Bacteroides; their inclusion would likely change the response of community members to the presence of different plant fiber preparations and the dynamics of plant fiber degradation documented by various collections of MFABs. The approach we describe for ligand immobilization does not require the synthesis of bifunctional ligands( or fluorophores); instead, custom functional groups can be incorporated into the probe through modification of the organosilane donor molecule. As such, the MFAB platform provides an opportunity to develop chemistries for nondestructively releasing ligands for analysis( Bielski and Witczak, 2013). For example, characterizing microbial degradation of polysaccharides needs to move beyond relatively ‘simple’ GC–MS measurements of monosaccharides released from the surface of recovered beads to readouts of glycan structures recovered from the bead surface( prior to and after exposure to microbes). This information would provide a more informed view of functional properties( saccharolytic activities) expressed by model communities comprised of cultured sequenced members of a microbiota representing a population of interest, or their intact uncultured microbiota, as well as greater insights about structure/activity relationships of existing or new candidate prebiotic and synbiotic formulations."
},
{
"role": "assistant",
"content": "Tens of trillions of microbes living in the gut help humans and other animals digest their food . In the process , the microbes provide necessary nutrients for themselves and the animal . Learning more about the interaction of food components and gut bacteria could help scientists to better understand how different diets affect human health . Currently , studying these complex interactions is challenging , but new technologies that measure microbial nutrient processing in the gut could help . Now , Wesener et al . show that swallowable microscopic biosensors can measure how gut bacteria break down nutrients from food . To make the biosensors , Wesener et al . attached complex carbohydrates extracted from peas and fluorescent tags to microscopic beads . In the experiments , mice colonized with human gut microbes were fed the beads along with a traditional low fiber , Western diet . Some of the animals also received fiber supplements . The microscopic beads were then recovered from the intestines after digestion and the remaining carbohydrates on the beads were measured . The genetic makeup of the gut microbiome and the expression of microbial genes was also examined . The experiments revealed which pea carbohydrates the gut microbes consumed and showed that pairing certain carbohydrates together on the microbead surface increased their digestion in mice that received fiber supplements . If future studies prove that the microbead biosensors created by Wesener et al . are safe for humans to ingest , they could be used to help diagnose how well a person’s gut microbiota can process different foods . Studies using the microbead sensors may also help scientists develop more nutritious foods or supplements that promote the growth of microbes important for health ."
}
] |
science.scicite_classification
|
science.scicite_classification.2984
|
[
{
"role": "user",
"content": "You will be presented with a citation segment from the section of a research paper. Classify the intent behind this citation by choosing from one of the following categories:\n\n- Method: Cites the paper for its methodology or procedure.\n- Background: Cites the paper to provide background information.\n- Result: Cites the paper for its findings or results.\n\nYour answer should be a single word from the following list of options: [\"Method\", \"Background\", \"Result\"]. Do not include any other text in your response.\n\nCitation sentence:\n\nWard, Wender, and Reimherr (1993) developed a psychiatric instrument, the Wender Utah Rating Scale (WURS), specifically designed retrospectively to assess ADHD symptoms in adult subjects."
},
{
"role": "assistant",
"content": "Background"
}
] |
science.multixscience_multidoc_summarization
|
science.multixscience_multidoc_summarization.30298
|
[
{
"role": "user",
"content": "You are provided with the abstract of a scientific paper and the abstracts of the papers it references. Your task is to write a Related Work section for the main paper. This section should concisely summarize and integrate the key points from the cited abstracts, reflecting how they relate to the main paper's contributions and context. In your summary, use numerical citation markers like [1], [2], etc., to refer to the corresponding papers.\n\nMain Abstract:\nIn predicate abstraction, exact image computation is problematic, requiring in the worst case an exponential number of calls to a decision procedure. For this reason, software model checkers typically use a weak approximation of the image. This can result in a failure to prove a property, even given an adequate set of predicates. We present an interpolant-based method for strengthening the abstract transition relation in case of such failures. This approach guarantees convergence given an adequate set of predicates, without requiring an exact image computation. We show empirically that the method converges more rapidly than an earlier method based on counterexample analysis.\n\nCited Abstract(s):\n[1]: The success of model checking for large programs depends crucially on the ability to efficiently construct parsimonious abstractions. A predicate abstraction is parsimonious if at each control location, it specifies only relationships between current values of variables, and only those which are required for proving correctness. Previous methods for automatically refining predicate abstractions until sufficient precision is obtained do not systematically construct parsimonious abstractions: predicates usually contain symbolic variables, and are added heuristically and often uniformly to many or all control locations at once. We use Craig interpolation to efficiently construct, from a given abstract error trace which cannot be concretized, a parsominous abstraction that removes the trace. At each location of the trace, we infer the relevant predicates as an interpolant between the two formulas that define the past and the future segment of the trace. Each interpolant is a relationship between current values of program variables, and is relevant only at that particular program location. It can be found by a linear scan of the proof of infeasibility of the trace.We develop our method for programs with arithmetic and pointer expressions, and call-by-value function calls. For function calls, Craig interpolation offers a systematic way of generating relevant predicates that contain only the local variables of the function and the values of the formal parameters when the function was called. We have extended our model checker Blast with predicate discovery by Craig interpolation, and applied it successfully to C programs with more than 130,000 lines of code, which was not possible with approaches that build less parsimonious abstractions."
},
{
"role": "assistant",
"content": "[1] , interpolants are used to choose new predicates to refine a predicate abstraction. Here, we use interpolants to refine an approximation of the abstract transition relation for a given set of predicates."
}
] |
science.bioasq_factoid_qa
|
science.bioasq_factoid_qa.1009
|
[
{
"role": "user",
"content": "You will be shown biomedical passages and your task is to the answer the provided question. Provide a concise and accurate response and do not include any additional text in the response other than the answer.\n\nQuestion: Which molecule is targeted by Asciminib?\n\nContext: Asciminib, an allosteric ABL1 inhibitor, could demonstrate a higher capacity in overcoming common TKIs resistant mutations, including T315I, but clinical findings are needed.\nMoreover, allosteric targeting has been identified to consequentially inhibit Bcr-Abl activity, which led to the recent development of ABL-001 (asciminib) that selectively binds the myristoyl pocket.\nAsciminib (previously ABL001), which binds the myristate-binding pocket of the Bcr-Abl kinase domain, is in phase I clinical trials as monotherapy and in combination with imatinib, nilotinib and dasatinib for the treatment of patients with refractory CML or Ph+ ALL.\nAsciminib (ABL001) is an orally administered allosteric inhibitor of the BCR-ABL tyrosine kinase.\nDiscovery of Asciminib (ABL001), an Allosteric Inhibitor of the Tyrosine Kinase Activity of BCR-ABL1.\nWe describe the discovery of asciminib (ABL001), the first allosteric BCR-ABL1 inhibitor to reach the clinic. Asciminib binds to the myristate pocket of BCR-ABL1 and maintains activity against TKI-resistant ATP-site mutations.\nHere we characterize ABL001 (asciminib), a potent and selective allosteric ABL1 inhibitor that is undergoing clinical development testing in patients with CML and Philadelphia chromosome-positive (Ph+) acute lymphoblastic leukaemia.\nWe describe the discovery of asciminib (ABL001), the first allosteric BCR-ABL1 inhibitor to reach the clinic.\nAsciminib binds to the myristate pocket of BCR-ABL1 and maintains activity against TKI-resistant ATP-site mutations.\nDisposition of asciminib, a potent BCR-ABL1 tyrosine kinase inhibitor, in healthy male subjects.\nAsciminib ( previously ABL001) , which binds the myristate-binding pocket of the Bcr-Abl kinase domain , is in phase I clinical trials as monotherapy and in combination with imatinib , nilotinib and dasatinib for the treatment of patients with refractory CML or Ph+ ALL .\nAsciminib is an allosteric inhibitor that binds a myristoyl site of the BCR-ABL1 protein , locking BCR-ABL1 into an inactive conformation through a mechanism distinct from those for all other ABL kinase inhibitors .\nDiscovery of Asciminib ( ABL001) , an Allosteric Inhibitor of the Tyrosine Kinase Activity of BCR-ABL1 .\nAsciminib binds to the myristate pocket of BCR-ABL1 and maintains activity against TKI-resistant ATP-site mutations.\nWe describe the discovery of asciminib (ABL001), the first allosteric BCR-ABL1 inhibitor to reach the clinic.\nAsciminib (previously ABL001), which binds the myristate-binding pocket of the Bcr-Abl kinase domain, is in phase I clinical trials as monotherapy and in combination with imatinib, nilotinib and dasatinib for the treatment of patients with refractory CML or Ph+ ALL.\nAsciminib, a highly selective non-ATP competitive inhibitor of BCR-ABL, has demonstrated to be a promising drug for patients with chronic myeloid leukemia.\nThe obtained results indicate that the mutations have adversely influence on the binding of Asciminib to BCR-ABL, as the nonpolar contributions decline in the two mutants.\nAsciminib is a potent, specific BCR-ABL1 inhibitor being developed for the treatment of patients with chronic myelogenous leukemia (CML) and Philadelphia chromosome positive acute lymphoblastic leukemia (Ph + ALL).\nAsciminib, an allosteric inhibitor targeting the myristoyl-binding pocket of BCR-ABL1, is active against most single mutants but ineffective against all tested compound mutants.\nHere we characterize ABL001 (asciminib), a potent and selective allosteric ABL1 inhibitor that is undergoing clinical development testing in patients with CML and Philadelphia chromosome-positive (Ph\nAsciminib, an allosteric ABL1 inhibitor, could demonstrate a higher capacity in overcoming common TKIs resistant mutations, including T315I, but clinical findings are needed.\nAsciminib, an allosteric inhibitor targeting the myristoyl-binding pocket of BCR-ABL1, is active against most single mutants but ineffective against all tested compound mutants."
},
{
"role": "assistant",
"content": "BCR-ABL tyrosine kinase"
}
] |
science.bioasq_general_qa
|
science.bioasq_general_qa.934
|
[
{
"role": "user",
"content": "You will be shown a question, followed by excerpts from biomedical research papers. Please answer the question based on the provided context. Do not include any text in your response other than the answer.\n\nQuestion: What was fingolimod synthesized from?\n\nContext: Pioneering in this field was the synthesis of FTY720 (fingolimod, Gilenya®) from myriocin, one of the metabolites of the fungus Isaria sinclairii known from traditional Chinese medicine for its antibacterial and energy boosting effect."
},
{
"role": "assistant",
"content": "FTY720 (fingolimod, Gilenya®) was synthesized from myriocin, one of the metabolites of the fungus Isaria sinclairii known from traditional Chinese medicine for its antibacterial and energy boosting effect."
}
] |
science.data_reco_mcq_mc
|
science.data_reco_mcq_mc.1246
|
[
{
"role": "user",
"content": "You are provided with a research question, keyphrases about the question, a description of candidate datasets and dataset options. Read the description of popular datasets provided below and select the ones that can be used to validate the following research question. Use your knowledge of machine learning datasets to make the best judgement.\nYour response should be formatted as a `json` array. For instance, for the query \"Semi supervised image classification\", a sample response might be: [\"CIFAR-10\", \"CIFAR-100\"]. Do not include any extra text in the response other than the answer array.\n\nQuery: I want to train a deep neural network for image classification.\n\nKeyphrases: image classification images\n\nDataset description:\nGoPro: The GoPro dataset for deblurring consists of 3,214 blurred images with the size of 1,280×720 that are divided into 2,103 training images and 1,111 test images. The dataset consists of pairs of a realistic blurry image and the corresponding ground truth shapr image that are obtained by a high-speed camera.\nCOWC: The Cars Overhead With Context (COWC) data set is a large set of annotated cars from overhead. It is useful for training a device such as a deep neural network to learn to detect and/or count cars.\nCIFAR-10: The CIFAR-10 dataset (Canadian Institute for Advanced Research, 10 classes) is a subset of the Tiny Images dataset and consists of 60000 32x32 color images. The images are labelled with one of 10 mutually exclusive classes: airplane, automobile (but not truck or pickup truck), bird, cat, deer, dog, frog, horse, ship, and truck (but not pickup truck).\nImageNet: The ImageNet dataset contains 14,197,122 annotated images according to the WordNet hierarchy. Since 2010 the dataset is used in the ImageNet Large Scale Visual Recognition Challenge (ILSVRC), a benchmark in image classification and object detection.\nUNSW-NB15: UNSW-NB15 is a network intrusion dataset. It contains nine different attacks, includes DoS, worms, Backdoors, and Fuzzers.\n\nOptions:- A: GoPro B: COWC C: CIFAR-10 D: ImageNet E: UNSW-NB15"
},
{
"role": "assistant",
"content": "[\"CIFAR-10\", \"ImageNet\"]"
}
] |
science.genia_ner
|
science.genia_ner.803
|
[
{
"role": "user",
"content": "You will be shown an abstract from a biomedical research paper. Given this abstract, your task is to extract all unique entities of the following types: [\"RNA\", \"CellLine\", \"Protein\", \"DNA\", \"CellType\"].\n\nPlease return the output as a JSON object of the format: {\"DNA\" : [\"TAL1\", ...], \"RNA\": [\"mRNAs\", ...], \"CellLine\": [\"T cells\", ...], \"CellType\": [\"monocytes\", ...], \"Protein\": [\"IL-2\", ...]}. The keys should be entity types and values should be lists of extracted entities belonging to the corresponding type. If you cannot find entities belonging to a specific type, the value should be [].\n\nOnly output the JSON object and do not include any additional text.\n\nAbstract:\n\nInhibition of IL-4-inducible gene expression in human monocytes by type I and type II interferons. The Th2-type cytokines, interleukin-4 (IL-4) and interleukin-13 (IL-13), induce expression of a distinct subset of genes in human monocytes, including FcepsilonRIIb (CD23), 15-lipoxygenase, IL-1 receptor antagonist (IL-1ra), and type I and type II IL-1 receptors (IL-1R). Type I interferons (IFN-alpha and IFN-beta) and type II interferon (IFN-gamma) inhibit induction of these genes by IL-4 and IL-13. However, the mechanism by which IFNs mediate this inhibition has not been defined. In this overview, we discuss the role of the transcription factor, STAT6 (signal transducer and activator of transcription-6) in mediating IL-4-and IL-13-induced gene expression in monocytes. We also discuss our recent findings that type I and type II IFNs suppress IL-4 / IL-13-inducible gene expression by inhibiting tyrosine phosphorylation and nuclear translocation of STAT6. The ability of type I and type II IFNs to inhibit IL-4 / IL-13-induced STAT6 activity is dose-and time-dependent, and is not unique to monocytes because IFNs induce the same effects in fibroblasts. Inhibition of STAT6 activity is not evident unless cells are preincubated with IFN for at least 1 h before IL-4 stimulation. Furthermore, inhibition can be blocked by actinomycin D, indicating a requirement for de novo transcription. We propose a model in which stimulation of monocytes by IFN activates de novo synthesis of an inhibitory factor, possibly one or more members of the SOCS / SSI / CIS gene family, capable of suppressing activation of STAT6 by IL-4 and IL-13. Because STAT6 activation plays an essential role in IL-4 / IL-13-induced gene expression, the ability of IFN-beta and IFN-gamma to inhibit STAT6 activity provides an explanation for how IFNs can suppress IL-4 / IL-13-inducible gene expression."
},
{
"role": "assistant",
"content": "{\"CellLine\": [], \"CellType\": [\"fibroblasts\", \"monocytes\", \"human monocytes\"], \"DNA\": [], \"Protein\": [\"inhibitory factor\", \"IFN\", \"IFN - gamma\", \"type I and type II IL - 1 receptors\", \"STAT6\", \"interleukin - 4\", \"IFNs\", \"IFN - beta\", \"CD23\", \"IFN - alpha\", \"15 - lipoxygenase\", \"type I and type II IFNs\", \"type II interferon\", \"SOCS / SSI / CIS gene family\", \"IL - 13\", \"IL - 1ra\", \"interleukin - 13\", \"FcepsilonRIIb\", \"IL - 1R\", \"Th2 - type cytokines\", \"Type I interferons (IFN - alpha and IFN - beta) and type II interferon (IFN - gamma)\", \"Type I interferons\", \"IL - 4\", \"type I and type II interferons\", \"IL - 1 receptor antagonist\", \"transcription factor\", \"signal transducer and activator of transcription - 6\"], \"RNA\": []}"
}
] |
science.scientific_lay_summarisation_plos_single_doc_summ
|
science.scientific_lay_summarisation_plos_single_doc_summ.7432
|
[
{
"role": "user",
"content": "You will be presented with the abstract, introduction, and discussion section from a biomedical research article. Your task is to create a summary that a layperson can understand, capturing the essence of the research article. Keep essential scientific terms, but ensure that the language remains clear and the concepts are explained in an uncomplicated manner.\n\nTitle: Structure and Evolution of Streptomyces Interaction Networks in Soil and In Silico}\nArticle:\nAbstract:\nSoil grains harbor an astonishing diversity of Streptomyces strains producing diverse secondary metabolites. However, it is not understood how this genotypic and chemical diversity is ecologically maintained. While secondary metabolites are known to mediate signaling and warfare among strains, no systematic measurement of the resulting interaction networks has been available. We developed a high-throughput platform to measure all pairwise interactions among 64 Streptomyces strains isolated from several individual grains of soil. We acquired more than 10, 000 time-lapse movies of colony development of each isolate on media containing compounds produced by each of the other isolates. We observed a rich set of such sender-receiver interactions, including inhibition and promotion of growth and aerial mycelium formation. The probability that two random isolates interact is balanced; it is neither close to zero nor one. The interactions are not random: the distribution of the number of interactions per sender is bimodal and there is enrichment for reciprocity—if strain A inhibits or promotes B, it is likely that B also inhibits or promotes A. Such reciprocity is further enriched in strains derived from the same soil grain, suggesting that it may be a property of coexisting communities. Interactions appear to evolve rapidly: isolates with identical 16S rRNA sequences can have very different interaction patterns. A simple eco-evolutionary model of bacteria interacting through antibiotic production shows how fast evolution of production and resistance can lead to the observed statistical properties of the network. In the model, communities are evolutionarily unstable—they are constantly being invaded by strains with new sets of interactions. This combination of experimental and theoretical observations suggests that diverse Streptomyces communities do not represent a stable ecological state but an intrinsically dynamic eco-evolutionary phenomenon.\nIntroduction:\nSampling DNA from diverse ecosystems has revealed a breathtaking diversity of microbial life[1],[2], especially in soil[3]–[5]. But we have barely begun to explore, both experimentally and theoretically, how these complex communities coexist and function. We know that microbes can interact via secretion of a wide array of small molecules, most notably antibiotic compounds. But how prevalent, diverse, and specific are such interactions? How is the incredible diversity of microbes and their natural products maintained and promoted by complex and spatially structured networks of interactions? To tackle these questions, we isolated bacterial strains from individual grains of soil and systematically measured all pair-wise interactions among them. We measured compound-mediated interactions, where a “sender” strain affects a “receiver” strain by secreting metabolites, antibiotics, or other compounds( Figure 1AB). We focused on bacteria from the genus Streptomyces, which are the most prolific producers of small molecules, are abundant in soil[6], and exhibit diverse production and resistance capabilities[6]–[8] that are modular and prone to Horizontal Gene Transfer( HGT)[9]. Sixty-four Streptomyces from four individual grains of soil were isolated( Figure 1C), phenotyped for all possible pair-wise interactions, and genotyped for 16S rRNA. We explored the statistical properties of the resulting network and juxtaposed them with those emerging from a simple ecological model of bacteria evolving production of and resistance to antibiotics[10],[11]. We developed a high-throughput platform for measuring directional pairwise interactions by observing how the products of one bacterial strain affect the colony growth of another. A fine-pored filter is placed on a nutrient agar surface, a lawn of the sender strain is grown on top, and the filter is removed—leaving behind sterile agar that has been altered or conditioned by the sender strain. The conditioned agar is then resupplied with concentrated liquid nutrients to compensate for the nutrients consumed by the donor. A receiver strain is point-inoculated onto the sterile conditioned agar and time-lapse movie of the growing colony is taken. A high-throughput implementation of this assay allowed us to acquire 11, 500 movies along 15 d at 4 h time resolution, covering all pairwise interactions within our collection of 64 strains in duplicate( Figure 1D, Materials and Methods). By comparing colony growth of the receiver strains on conditioned and non-conditioned agar, we identify interactions between strains. We quantified the first time point in which each colony becomes visible on the images( appearance time) to identify growth inhibitory and growth promotion interactions. In addition, we visually scored instances of inhibition of aerial mycelium formation( and subsequent sporulation).\nDiscussion:\nWe find that Streptomyces isolates from soil grains exhibit diverse and rich interaction patterns. The interaction matrix they form has a balanced frequency of interactions—the probability that two random strains interact is neither close to zero nor to one. The sender-degree distribution is broad and bimodal—isolates tend to inhibit almost everyone or almost no one, which makes the interactions statistically controlled more by the properties of the sender than the receiver. This sender-receiver asymmetry, while pronounced, is not extreme, indicating the importance of resistance to compounds produced by others. These properties make this network very different from other ecological networks, which have monotonic degree distributions, and typically exhibit much lower interaction frequency. Finally, the community is enriched in reciprocal interactions—interaction pairs are enriched in mutual inhibitory interactions and mutual growth promotions, while it is rare to find cases in which one strain promotes a second, but this second strain inhibits the first. This reciprocity is further enriched among strains derived from the same grain of soil, thus revealing spatial structuring of interactions. These properties of the interaction network have emerged from a long evolutionary process, which we probed by juxtaposing interactions and phylogeny. We found that the interactions of an isolate can change dramatically even over short evolutionary time( indicated by very close 16S sequences), with evolution changing the production profiles more than the resistance profiles. Incorporating such fast evolution in a dynamic ecological model of antibiotic interactions, we find that most of the observed properties of the network are reproduced under a broad range of parameters. The community compositions are not static—increase in production of an antibiotic promotes resistance, which promotes sensitivity, and invites production again. As the community undergoes cycles with respect to different antibiotics, different combinations of production and resistance become favorable, which makes it evolutionary unstable. In our model both ecological interactions and continuous turnover of interaction phenotypes are required to maintain functional diversity. Our work has several important limitations. Perhaps the main one is that interactions are measured in the lab and actual interactions in the soil may be more complex or different. We were also limited to studying only the interactions among Streptomyces strains; interactions between Streptomyces and other microbes could be of major importance. Higher order interactions, such as synergy or antagonism between natural products, or induction of small molecule production by other small molecules, are not captured by the pairwise measurements. Many of these shortcomings are inherent to most current studies of microbial species interactions. However, the systematic and high-throughput nature of the current study allows us to ask questions at the statistical level, and might therefore be less prone to some of these difficulties. Furthermore, the high-throughput interaction platform developed here and the simulations offer a natural foundation for many subsequent studies of microbial communities, which will address some of the above concerns, potentially yielding important biological insights. For example, it is now possible to probe how the statistical properties of networks, such as the relative significance of positive and negative interactions, are affected by media composition and the presence of other small molecules. This enables investigations of the regulatory roles of and epistatic effects between small molecules. It would also be interesting to see whether the effects of a sender on a receiver will be modified if the sender is co-incubated with the receiver. Finally, the interaction platform can be used to follow the evolutionary and ecological dynamics of synthetic laboratory communities of interacting microbial strains. The observed network properties do not seem to correspond to an ecologically stable state maintained by antibiotic interactions alone. Instead, the model and observations suggest that they are supported by a constant evolutionary change. The distribution of production and resistance in the community is poised so that simple changes in production capabilities of a strain can alter its interactions with many other strains potentially to a great ecological advantage. This evolutionarily unstable ecological state seems complemented by the modular nature of the secondary metabolite gene clusters, which enable such changes and, thus, lead to turnover of interaction phenotypes of different strains and species. This continuous turnover might in turn be important for the emergence and maintenance of the modularity and clustering of small molecule production and resistance genes and their recruitment to mobile genetic elements[21]. This reasoning suggests a unified view of network structure, network evolution, and modularity of secondary metabolism to be further explored."
},
{
"role": "assistant",
"content": "Soil harbors a diverse spectrum of bacteria that secrete small molecules such as antibiotics . Streptomyces bacteria , considered the most prolific producers , have been mined for decades for novel products with therapeutic applications , yet little is known about the properties of the interaction networks these compounds mediate . These networks can hold clues about how the diversity of small molecules and of Streptomyces strains with different production and resistance capabilities is maintained and promoted . To explore the network properties , we developed a high-throughput platform for measuring pairwise phenotypic interactions mediated by secreted metabolites , and used it to measure the interaction network among 64 random Streptomyces isolates from several grains of soil . We found many strong but specific interactions that are on average determined more by metabolite production than by metabolite sensitivity . We found reciprocity between strains , whereby if one strain inhibits or promotes the growth of a second strain , it's likely that the second strain affects the first strain in a similar manner . These interactions are not correlated with phylogeny , as very closely related strains exhibit different interaction patterns . We could explain these findings with a mathematical model requiring interplay between ecological dynamics and evolution of antibiotic production and resistance , suggesting that the bacterial and small molecule diversity of these communities is maintained by constant evolutionary turnover of interaction phenotypes ."
}
] |
science.scitldr_aic
|
science.scitldr_aic.1232
|
[
{
"role": "user",
"content": "Below are the abstract, introduction, and conclusion of a computer science research paper. Please summarize the main contribution of the work in a single sentence. Your response should include the summary and no additional text.\n\nPaper text:\n\nWe study the problem of learning similarity functions over very large corpora using neural network embedding models.\nThese models are typically trained using SGD with random sampling of unobserved pairs, with a sample size that grows quadratically with the corpus size, making it expensive to scale.\n\nWe propose new efficient methods to train these models without having to sample unobserved pairs.\nInspired by matrix factorization, our approach relies on adding a global quadratic penalty and expressing this term as the inner-product of two generalized Gramians.\nWe show that the gradient of this term can be efficiently computed by maintaining estimates of the Gramians, and develop variance reduction schemes to improve the quality of the estimates.\nWe conduct large-scale experiments that show a significant improvement both in training time and generalization performance compared to sampling methods.\nWe consider the problem of learning a similarity function h : X × Y → R, that maps each pair of items, represented by their feature vectors (x, y) ∈ X × Y, to a real number h(x, y), representing their similarity.\nWe will refer to x and y as the left and right feature vectors, respectively.\nMany problems can be cast in this form: In natural language processing, x represents a context (e.g. a bag of words), y represents a candidate word, and the target similarity measures the likelihood to observe y in context x BID14 BID16 BID13 .\nIn recommender systems, x represents a user query, y represents a candidate item, and the target similarity is a measure of relevance of item y to query x, e.g. a movie rating BID0 , or the likelihood to watch a given movie BID12 Rendle, 2010) .\nOther applications include image similarity, where x and y are pixel-representations of images BID5 BID6 Schroff et al., 2015) , and network embedding models BID10 Qiu et al., 2018) , where x and y are nodes in a graph and the similarity is whether an edge connects them.A popular approach to learning similarity functions is to train an embedding representation of each item, such that items with high similarity are mapped to vectors that are close in the embedding space.\nA common property of such problems is that only a small subset of all possible pairs X × Y is present in the training set, and those examples typically have high similarity.\nTraining exclusively on observed examples has been demonstrated to yield poor generalization performance.\nIntuitively, when trained only on observed pairs, the model places the embedding of a given item close to similar items, but does not learn to place it far from dissimilar ones (Shazeer et al., 2016; Xin et al., 2017) .\nTaking into account unobserved pairs is known to improve the embedding quality in many applications, including recommendation BID12 BID1 and word analogy tasks (Shazeer et al., 2016) .\nThis is often achieved by adding a low-similarity prior on all pairs, which acts as a repulsive force between all embeddings.\nBut because it involves a number of terms quadratic in the corpus size, this term is computationally intractable (except in the linear case), and it is typically optimized using sampling: for each observed pair in the training set, a set of random unobserved pairs is sampled and used to compute an estimate of the repulsive term.\nBut as the corpus size increases, the quality of the estimates deteriorates unless the sample size is increased, which limits scalability.In this paper, we address this issue by developing new methods to efficiently estimate the repulsive term, without sampling unobserved pairs.\nOur approach is inspired by matrix factorization models, which correspond to the special case of linear embedding functions.\nThey are typically trained using alternating least squares BID12 , or coordinate descent methods BID2 , which circumvent the computational burden of the repulsive term by writing it as a matrix-inner-product of two Gramians, and computing the left Gramian before optimizing over the right embeddings, and viceversa.\nUnfortunately, in non-linear embedding models, each update of the model parameters induces a simulateneous change in all embeddings, making it impractical to recompute the Gramians at each iteration.\nAs a result, the Gramian formulation has been largely ignored in the non-linear setting, where models are instead trained using stochastic gradient methods with sampling of unobserved pairs, see BID7 .\nVincent et al. (2015) were, to our knowledge, the first to attempt leveraging the Gramian formulation in the non-linear case.\nThey consider a model where only one of the embedding functions is non-linear, and show that the gradient can be computed efficiently in that case.\nTheir result is remarkable in that it allows exact gradient computation, but this unfortunately does not generalize to the case where both embedding functions are non-linear.Contributions We propose new methods that leverage the Gramian formulation in the non-linear case, and that, unlike previous approaches, are efficient even when both left and right embeddings are non-linear.\nOur methods operate by maintaining stochastic estimates of the Gram matrices, and using different variance reduction schemes to improve the quality of the estimates.\nWe perform several experiments that show these methods scale far better than traditional sampling approaches on very large corpora.We start by reviewing preliminaries in Section 2, then derive the Gramian-based methods and analyze them in Section 3.\nWe conduct large-scale experiments on the Wikipedia dataset in Section 4, and provide additional experiments in the appendix.\nAll the proofs are deferred to Appendix A.\nWe showed that the Gramian formulation commonly used in low-rank matrix factorization can be leveraged for training non-linear embedding models, by maintaining estimates of the Gram matrices and using them to estimate the gradient.\nBy applying variance reduction techniques to the Gramians, one can improve the quality of the gradient estimates, without relying on large sample size as is done in traditional sampling methods.\nThis leads to a significant impact on training time and generalization quality, as indicated by our experiments.\nWhile we focused on problems with very large vocabulary size, where traditional approaches are inefficient, it will be interesting to evaluate our methods on other applications such as word-analogy tasks BID14 Schnabel et al. (2015) .\nAnother direction of future work is to extend this formulation to a larger family of penalty functions, such as the spherical loss family studied in (Vincent et al., 2015; BID8"
},
{
"role": "assistant",
"content": "We develop efficient methods to train neural embedding models with a dot-product structure, by reformulating the objective function in terms of generalized Gram matrices, and maintaining estimates of those matrices."
}
] |
science.chemdner_ner
|
science.chemdner_ner.1579
|
[
{
"role": "user",
"content": "You will be shown an abstract from a biomedical research paper. Given this abstract, your task is to extract all unique entities of the following types: [\"Chemical\"].\n\nPlease return the output as a JSON object of the format: {\"Chemical\": [\"Arsenic\", ...]}. The keys should be entity types and values should be lists of extracted entities belonging to the corresponding type. If you cannot find entities belonging to a specific type, the value should be [].\n\nOnly output the JSON object and do not include any additional text.\n\nAbstract:\n\nPhenolic glycosides from Curculigo orchioides Gaertn. Five new chlorophenolic glucosides, curculigine E (1), curculigine F (2), curculigine G (3), curculigine H (5), curculigine I (6) and one new phenolic glycoside, orcinoside H (4), together with eight known phenolic glycosides (7-14) were isolated from the Curculigo orchioides Gaertn. Their structures were established by spectroscopic techniques (IR, UV, MS, 1D and 2D NMR). The isolated phenolic glycosides were evaluated for antiosteoporotic activity against MC3T3-E1 cell line using MTT assays. Compounds 1, 2, 3, and 5 showed moderate antiosteoporotic activity with the proliferation rate of 10.1-14.1%."
},
{
"role": "assistant",
"content": "{\"Chemical\": [\"chlorophenolic glucosides\", \"curculigine G\", \"curculigine H\", \"curculigine I\", \"phenolic glycosides\", \"Phenolic glycosides\", \"orcinoside H\", \"curculigine F\", \"phenolic glycoside\", \"MTT\", \"curculigine E\"]}"
}
] |
science.covid_deepset_qa
|
science.covid_deepset_qa.1561
|
[
{
"role": "user",
"content": "You will be shown a paragraph from a biomedical research paper, followed by a question about the paper. Please extract text from the paragraph to answer the question. Do not include any text in your repsonse other than the answer.\n\nParagraph: The disease can manifest in both the upper airway (such as chronic rhinosinusitis, CRS) and lower airway (such as asthma and chronic obstructive pulmonary disease, COPD) which greatly affect the patients' quality of life (Calus et al., 2012; Bao et al., 2015) . Treatment and management vary greatly in efficacy due to the complexity and heterogeneity of the disease. This is further complicated by the effect of episodic exacerbations of the disease, defined as worsening of disease symptoms including wheeze, cough, breathlessness and chest tightness (Xepapadaki and Papadopoulos, 2010) . Such exacerbations are due to the effect of enhanced acute airway inflammation impacting upon and worsening the symptoms of the existing disease (Hashimoto et al., 2008; Viniol and Vogelmeier, 2018) . These acute exacerbations are the main cause of morbidity and sometimes mortality in patients, as well as resulting in major economic burdens worldwide. However, due to the complex interactions between the host and the exacerbation agents, the mechanisms of exacerbation may vary considerably in different individuals under various triggers. Acute exacerbations are usually due to the presence of environmental factors such as allergens, pollutants, smoke, cold or dry air and pathogenic microbes in the airway (Gautier and Charpin, 2017; Viniol and Vogelmeier, 2018) . These agents elicit an immune response leading to infiltration of activated immune cells that further release inflammatory mediators that cause acute symptoms such as increased mucus production, cough, wheeze and shortness of breath. Among these agents, viral infection is one of the major drivers of asthma exacerbations accounting for up to 80-90% and 45-80% of exacerbations in children and adults respectively (Grissell et al., 2005; Xepapadaki and Papadopoulos, 2010; Jartti and Gern, 2017; Adeli et al., 2019) . Viral involvement in COPD exacerbation is also equally high, having been detected in 30-80% of acute COPD exacerbations (Kherad et al., 2010; Jafarinejad et al., 2017; Stolz et al., 2019) . Whilst the prevalence of viral exacerbations in CRS is still unclear, its prevalence is likely to be high due to the similar inflammatory nature of these diseases (Rowan et al., 2015; Tan et al., 2017) . One of the reasons for the involvement of respiratory viruses' in exacerbations is their ease of transmission and infection (Kutter et al., 2018) . In addition, the high diversity of the respiratory viruses may also contribute to exacerbations of different nature and severity (Busse et al., 2010; Costa et al., 2014; Jartti and Gern, 2017) . Hence, it is important to identify the exact mechanisms underpinning viral exacerbations in susceptible subjects in order to properly manage exacerbations via supplementary treatments that may alleviate the exacerbation symptoms or prevent severe exacerbations. While the lower airway is the site of dysregulated inflammation in most chronic airway inflammatory diseases, the upper airway remains the first point of contact with sources of exacerbation. Therefore, their interaction with the exacerbation agents may directly contribute to the subsequent responses in the lower airway, in line with the \"United Airway\" hypothesis. To elucidate the host airway interaction with viruses leading to exacerbations, we thus focus our review on recent findings of viral interaction with the upper airway. We compiled how viral induced changes to the upper airway may contribute to chronic airway inflammatory disease exacerbations, to provide a unified elucidation of the potential exacerbation mechanisms initiated from predominantly upper airway infections. Despite being a major cause of exacerbation, reports linking respiratory viruses to acute exacerbations only start to emerge in the late 1950s (Pattemore et al., 1992) ; with bacterial infections previously considered as the likely culprit for acute exacerbation (Stevens, 1953; Message and Johnston, 2002) . However, with the advent of PCR technology, more viruses were recovered during acute exacerbations events and reports implicating their role emerged in the late 1980s (Message and Johnston, 2002) . Rhinovirus (RV) and respiratory syncytial virus (RSV) are the predominant viruses linked to the development and exacerbation of chronic airway inflammatory diseases (Jartti and Gern, 2017) . Other viruses such as parainfluenza virus (PIV), influenza virus (IFV) and adenovirus (AdV) have also been implicated in acute exacerbations but to a much lesser extent (Johnston et al., 2005; Oliver et al., 2014; Ko et al., 2019) . More recently, other viruses including bocavirus (BoV), human metapneumovirus (HMPV), certain coronavirus (CoV) strains, a specific enterovirus (EV) strain EV-D68, human cytomegalovirus (hCMV) and herpes simplex virus (HSV) have been reported as contributing to acute exacerbations . The common feature these viruses share is that they can infect both the upper and/or lower airway, further increasing the inflammatory conditions in the diseased airway (Mallia and Johnston, 2006; Britto et al., 2017) . Respiratory viruses primarily infect and replicate within airway epithelial cells . During the replication process, the cells release antiviral factors and cytokines that alter local airway inflammation and airway niche (Busse et al., 2010) . In a healthy airway, the inflammation normally leads to type 1 inflammatory responses consisting of activation of an antiviral state and infiltration of antiviral effector cells. This eventually results in the resolution of the inflammatory response and clearance of the viral infection (Vareille et al., 2011; Braciale et al., 2012) . However, in a chronically inflamed airway, the responses against the virus may be impaired or aberrant, causing sustained inflammation and erroneous infiltration, resulting in the exacerbation of their symptoms (Mallia and Johnston, 2006; Dougherty and Fahy, 2009; Busse et al., 2010; Britto et al., 2017; Linden et al., 2019) . This is usually further compounded by the increased susceptibility of chronic airway inflammatory disease patients toward viral respiratory infections, thereby increasing the frequency of exacerbation as a whole (Dougherty and Fahy, 2009; Busse et al., 2010; Linden et al., 2019) . Furthermore, due to the different replication cycles and response against the myriad of respiratory viruses, each respiratory virus may also contribute to exacerbations via different mechanisms that may alter their severity. Hence, this review will focus on compiling and collating the current known mechanisms of viral-induced exacerbation of chronic airway inflammatory diseases; as well as linking the different viral infection pathogenesis to elucidate other potential ways the infection can exacerbate the disease. The review will serve to provide further understanding of viral induced exacerbation to identify potential pathways and pathogenesis mechanisms that may be targeted as supplementary care for management and prevention of exacerbation. Such an approach may be clinically significant due to the current scarcity of antiviral drugs for the management of viral-induced exacerbations. This will improve the quality of life of patients with chronic airway inflammatory diseases. Once the link between viral infection and acute exacerbations of chronic airway inflammatory disease was established, there have been many reports on the mechanisms underlying the exacerbation induced by respiratory viral infection. Upon infecting the host, viruses evoke an inflammatory response as a means of counteracting the infection. Generally, infected airway epithelial cells release type I (IFNα/β) and type III (IFNλ) interferons, cytokines and chemokines such as IL-6, IL-8, IL-12, RANTES, macrophage inflammatory protein 1α (MIP-1α) and monocyte chemotactic protein 1 (MCP-1) (Wark and Gibson, 2006; Matsukura et al., 2013) . These, in turn, enable infiltration of innate immune cells and of professional antigen presenting cells (APCs) that will then in turn release specific mediators to facilitate viral targeting and clearance, including type II interferon (IFNγ), IL-2, IL-4, IL-5, IL-9, and IL-12 (Wark and Gibson, 2006; Singh et al., 2010; Braciale et al., 2012) . These factors heighten local inflammation and the infiltration of granulocytes, T-cells and B-cells (Wark and Gibson, 2006; Braciale et al., 2012) . The increased inflammation, in turn, worsens the symptoms of airway diseases. Additionally, in patients with asthma and patients with CRS with nasal polyp (CRSwNP), viral infections such as RV and RSV promote a Type 2-biased immune response (Becker, 2006; Jackson et al., 2014; Jurak et al., 2018) . This amplifies the basal type 2 inflammation resulting in a greater release of IL-4, IL-5, IL-13, RANTES and eotaxin and a further increase in eosinophilia, a key pathological driver of asthma and CRSwNP (Wark and Gibson, 2006; Singh et al., 2010; Chung et al., 2015; Dunican and Fahy, 2015) . Increased eosinophilia, in turn, worsens the classical symptoms of disease and may further lead to life-threatening conditions due to breathing difficulties. On the other hand, patients with COPD and patients with CRS without nasal polyp (CRSsNP) are more neutrophilic in nature due to the expression of neutrophil chemoattractants such as CXCL9, CXCL10, and CXCL11 (Cukic et al., 2012; Brightling and Greening, 2019) . The pathology of these airway diseases is characterized by airway remodeling due to the presence of remodeling factors such as matrix metalloproteinases (MMPs) released from infiltrating neutrophils (Linden et al., 2019) . Viral infections in such conditions will then cause increase neutrophilic activation; worsening the symptoms and airway remodeling in the airway thereby exacerbating COPD, CRSsNP and even CRSwNP in certain cases (Wang et al., 2009; Tacon et al., 2010; Linden et al., 2019) . An epithelial-centric alarmin pathway around IL-25, IL-33 and thymic stromal lymphopoietin (TSLP), and their interaction with group 2 innate lymphoid cells (ILC2) has also recently been identified (Nagarkar et al., 2012; Hong et al., 2018; Allinne et al., 2019) . IL-25, IL-33 and TSLP are type 2 inflammatory cytokines expressed by the epithelial cells upon injury to the epithelial barrier (Gabryelska et al., 2019; Roan et al., 2019) . ILC2s are a group of lymphoid cells lacking both B and T cell receptors but play a crucial role in secreting type 2 cytokines to perpetuate type 2 inflammation when activated (Scanlon and McKenzie, 2012; Li and Hendriks, 2013) . In the event of viral infection, cell death and injury to the epithelial barrier will also induce the expression of IL-25, IL-33 and TSLP, with heighten expression in an inflamed airway (Allakhverdi et al., 2007; Goldsmith et al., 2012; Byers et al., 2013; Shaw et al., 2013; Beale et al., 2014; Jackson et al., 2014; Uller and Persson, 2018; Ravanetti et al., 2019) . These 3 cytokines then work in concert to activate ILC2s to further secrete type 2 cytokines IL-4, IL-5, and IL-13 which further aggravate the type 2 inflammation in the airway causing acute exacerbation (Camelo et al., 2017) . In the case of COPD, increased ILC2 activation, which retain the capability of differentiating to ILC1, may also further augment the neutrophilic response and further aggravate the exacerbation (Silver et al., 2016) . Interestingly, these factors are not released to any great extent and do not activate an ILC2 response during viral infection in healthy individuals (Yan et al., 2016; Tan et al., 2018a) ; despite augmenting a type 2 exacerbation in chronically inflamed airways (Jurak et al., 2018) . These classical mechanisms of viral induced acute exacerbations are summarized in Figure 1 . As integration of the virology, microbiology and immunology of viral infection becomes more interlinked, additional factors and FIGURE 1 | Current understanding of viral induced exacerbation of chronic airway inflammatory diseases. Upon virus infection in the airway, antiviral state will be activated to clear the invading pathogen from the airway. Immune response and injury factors released from the infected epithelium normally would induce a rapid type 1 immunity that facilitates viral clearance. However, in the inflamed airway, the cytokines and chemokines released instead augmented the inflammation present in the chronically inflamed airway, strengthening the neutrophilic infiltration in COPD airway, and eosinophilic infiltration in the asthmatic airway. The effect is also further compounded by the participation of Th1 and ILC1 cells in the COPD airway; and Th2 and ILC2 cells in the asthmatic airway. Frontiers in Cell and Developmental Biology | www.frontiersin.org mechanisms have been implicated in acute exacerbations during and after viral infection (Murray et al., 2006) . Murray et al.\n\nQuestion: Where can this disease manifest?"
},
{
"role": "assistant",
"content": "in both the upper airway (such as chronic rhinosinusitis, CRS) and lower airway (such as asthma and chronic obstructive pulmonary disease, COPD)"
}
] |
science.data_reco_mcq_sc
|
science.data_reco_mcq_sc.10171
|
[
{
"role": "user",
"content": "Given a short query with keyphrases about a research idea in 2018 in the domain of artificial intelligence, recommend the relevant datasets to validate the research idea from options provided. A short description of the datasets is also provided to help you.\n\nQuery: This paper presents a detailed analysis of existing end-to-end neural models on the Stanford Question\n\nKeyphrases: machine reading comprehension text\n\nDataset description:\nARCD: Composed of 1,395 questions posed by crowdworkers on Wikipedia articles, and a machine translation of the Stanford Question Answering Dataset (Arabic-SQuAD).\nJamendo Lyrics: Dataset for lyrics alignment and transcription evaluation. It contains 20 music pieces under CC license from the Jamendo website along with their lyrics, with: Manual annotations indicating the start time of each word in the audio file Predictions of start and end times for each word from both of the models presented in the paper\nE2E: End-to-End NLG Challenge (E2E) aims to assess whether recent end-to-end NLG systems can generate more complex output by learning from datasets containing higher lexical richness, syntactic complexity and diverse discourse phenomena.\nSQuAD: The Stanford Question Answering Dataset (SQuAD) is a collection of question-answer pairs derived from Wikipedia articles. In SQuAD, the correct answers of questions can be any sequence of tokens in the given text.\n\nOptions:- A: ARCD B: Jamendo Lyrics C: E2E D: SQuAD"
},
{
"role": "assistant",
"content": "SQuAD"
}
] |
science.craftchem_ner
|
science.craftchem_ner.9963
|
[
{
"role": "user",
"content": "You will be presented a sentence from biomedical research text. Extract all terms that correspond to chemical entities of biological interest (ChEBI).\nReturn your identified terms in a JSON array, formatted like this: [\"Entity1\", \"Entity2\", ...].\nIf no such entities are detected, respond by providing an empty JSON array [].\n\nBiomedical context:\nRawsignalintensitiesofeachprobewereobtainedfromdataanalysissoftware(Beadstudio;Illumina)andimportedintoGeneSpringGX7.3(AgilentTechnologies,PaloAlto,CA,USA)."
},
{
"role": "assistant",
"content": "[]"
}
] |
science.qasper_extractive_qa
|
science.qasper_extractive_qa.467.0
|
[
{
"role": "user",
"content": "You will be shown sections from a scientific research paper, together with a question about the paper. Your task is to answer the question based on the contents of the paper. Your response should be a `json` object with two fields:\n\n\"answer\": An array of strings extracted directly from the paper which, collectively, answer the question.\n\"evidence\": An array of strings. Each should be an excerpt from the paper, in which one or more of the extracted answers can be found.\n\nFor instance, for the question \"What baselines did the authors compare against?\", a sample response might be:\n\n{\n \"answer\": [\"BERT\", \"RoBERTa\"],\n \"evidence\": [\"In our experiments, we compare the performance of our model against BERT and RoBERTa.\"]\n}\n\nDo not include any text in your response other than the json.\n\nIf the question is unanswerable given the provided excerpts, respond with the single word \"null\".\n\nPaper: Large Arabic Twitter Dataset on COVID-19\n\nThe 2019 coronavirus disease (COVID-19), emerged late December 2019 in China, is now rapidly spreading across the globe. At the time of writing this paper, the number of global confirmed cases has passed one million and half with over 75,000 fatalities. Many countries have enforced strict social distancing policies to contain the spread of the virus. This has changed the daily life of tens of millions of people, and urged people to turn their discussions online, e.g., via online social media sites like Twitter. In this work, we describe the first Arabic tweets dataset on COVID-19 that we have been collecting since March 1st, 2020. The dataset would help researchers and policy makers in studying different societal issues related to the pandemic. Many other tasks related to behavioral change, information sharing, misinformation and rumors spreading can also be analyzed.\n\nIntroduction\nOn December 31, 2019, Chinese public health authorities reported several cases of a respiratory syndrome caused by an unknown disease, which subsequently became known as COVID-19 in the city of Wuhan, China. This highly contagious disease continued to spread worldwide, leading the World Health Organization (WHO) to declare a global health emergency on January 30, 2020. On March 11, 2020 the disease has been identified as pandemic by WHO, and many countries around the world including Saudi Arabia, United States, United Kingdom, Italy, Canada, and Germany have continued reporting more cases of the disease BIBREF0. As the time of writing this paper, this pandemic is affecting more than 208 countries around the globe with more than one million and half confirmed cases BIBREF1.\nSince the outbreak of COVID-19, many governments around the world enforced different measures to contain the spread of the virus. The measures include travel restrictions, curfews, ban of mass gatherings, social distancing, and probably cities lock-down. This has impacted the routine of people around the globe, and many of them have turned to social media platforms for both news and communication. Since the emergence of COVID-19, Twitter platform plays a significant role in crisis communications where millions of tweets related to the virus are posted daily. Arabic is the official language of more than 22 countries with nearly 300 million native speakers worldwide. Furthermore, there is a large daily Arabic content in Twitter as millions of Arabic users use the social media network to communicate. For instance, Saudi Arabia alone has nearly 15 million Twitter users as of January, 2020 BIBREF2. Hence, it is important to analyze the Arabic users' behavior and sentiment during this pandemic. Other Twitter COVID-19 datasets have been recently proposed BIBREF3, BIBREF4 but with no significant content for the Arabic language.\nIn this work, we provide the first dataset dedicated to Arabic tweets related to COVID-19. The dataset is available at https://github.com/SarahAlqurashi/COVID-19-Arabic-Tweets-Dataset. We have been collecting data in real-time from Twitter API since January 1, 2020, by tracking COVID-19 related keywords which resulted in more than 3,934,610 Arabic tweets so far. The presented dataset is believed to be helpful for both researchers and policy makers in studying the pandemic from social perspective, as well as analyzing the human behaviour and information spreading during pandemics.\nIn what follows, we describe the dataset and the collection methods, present the initial data statistics, and provide information about how to use the dataset.\n\nDataset Description\nWe collected COVID-19 related Arabic tweets from January 1, 2020 until April 15, 2020, using Twitter streaming API and the Tweepy Python library. We have collected more than 3,934,610 million tweets so far. In our dataset, we store the full tweet object including the id of the tweet, username, hashtags, and geolocation of the tweet. We created a list of the most common Arabic keywords associated with COVID-19. Using Twitter’s streaming API, we searched for any tweet containing the keyword(s) in the text of the tweet. Table TABREF1 shows the list of keywords used along with the starting date of tracking each keyword. Furthermore, Table TABREF2 shows the list of hashtags we have been tracking along with the number of tweets collected from each hashtag. Indeed, some tweets were irrelevant, and we kept only those that were relevant to the pandemic.\nA summary over the dataset is given in Table TABREF3. While collecting data, we have observed that the number of retweets increased significantly in late March. This is likely due to the exponential increase in confirmed COVID-19 cases worldwide, including the Arabic speaking countries. A relatively small percentage of tweets were geotagged. Figure FIGREF6 presents the location of tweets observed as of 14 April 2020.\n\nDataset Access\nThe dataset is accessible on GitHub at this address: https://github.com/SarahAlqurashi/COVID-19-Arabic-Tweets-Dataset\nHowever, to comply with Twitter’s content redistribution policy, we are distributing only the IDs of the collected tweets. There are several tools (such as Hydrator) that can be used to retrieve the full tweet object. We also plan to provide more details on the pre-processing phase in the GitHub page.\n\nFuture Work\nWe are continuously updating the dataset to maintain more aspects of COVID-19 Arabic conversations and discussions happening on Twitter. We also plan to study how different groups respond to the pandemic and analyze information sharing behavior among the users.\n\nAcknowledgements\nThe authors wish to express their thanks to Batool Mohammed Hmawi for her help in data collection.\n\nTable 2: Hashtags used in collecting this dataset.\n\nTable 1: The list of keywords that we used to collect the tweets.\n\nTable 3: Summary statistics for the collected tweets\n\nFigure 1: The location of geotagged tweets\n\nQuestion: What additional information is found in the dataset?"
},
{
"role": "assistant",
"content": "{\"answer\": [\"the full tweet object including the id of the tweet, username, hashtags, and geolocation of the tweet\"], \"evidence\": [\"We collected COVID-19 related Arabic tweets from January 1, 2020 until April 15, 2020, using Twitter streaming API and the Tweepy Python library. We have collected more than 3,934,610 million tweets so far. In our dataset, we store the full tweet object including the id of the tweet, username, hashtags, and geolocation of the tweet. We created a list of the most common Arabic keywords associated with COVID-19. Using Twitter\\u2019s streaming API, we searched for any tweet containing the keyword(s) in the text of the tweet. Table TABREF1 shows the list of keywords used along with the starting date of tracking each keyword. Furthermore, Table TABREF2 shows the list of hashtags we have been tracking along with the number of tweets collected from each hashtag. Indeed, some tweets were irrelevant, and we kept only those that were relevant to the pandemic.\"]}"
}
] |
science.scicite_classification
|
science.scicite_classification.4044
|
[
{
"role": "user",
"content": "You will be presented with a citation segment from the section of a research paper. Classify the intent behind this citation by choosing from one of the following categories:\n\n- Method: Cites the paper for its methodology or procedure.\n- Background: Cites the paper to provide background information.\n- Result: Cites the paper for its findings or results.\n\nYour answer should be a single word from the following list of options: [\"Method\", \"Background\", \"Result\"]. Do not include any other text in your response.\n\nCitation sentence:\n\nIn our previous study of slow regular saccades, we demonstrated the invariance of saccadic latencies with target angular displacement (Darrien et al., 2001) but had diYculty in reconciling the results with those of previous studies which showed an increase in latency (Fuller, 1996; Kalesnykas &…"
},
{
"role": "assistant",
"content": "Result"
}
] |
science.scicite_classification
|
science.scicite_classification.3511
|
[
{
"role": "user",
"content": "You will be presented with a citation segment from the section of a research paper. Classify the intent behind this citation by choosing from one of the following categories:\n\n- Method: Cites the paper for its methodology or procedure.\n- Background: Cites the paper to provide background information.\n- Result: Cites the paper for its findings or results.\n\nYour answer should be a single word from the following list of options: [\"Method\", \"Background\", \"Result\"]. Do not include any other text in your response.\n\nCitation sentence:\n\nCell viability results showing that lung cancer cells exhibit resistance to the cytotoxicity of high concentration of ATP in comparison to normal cells are consistent with published data that showed low (nearly undetectable) expression levels of P2X7R in lung cancer cells (20, 21, 39)."
},
{
"role": "assistant",
"content": "Result"
}
] |
science.chemdner_ner
|
science.chemdner_ner.3499
|
[
{
"role": "user",
"content": "You will be shown an abstract from a biomedical research paper. Given this abstract, your task is to extract all unique entities of the following types: [\"Chemical\"].\n\nPlease return the output as a JSON object of the format: {\"Chemical\": [\"Arsenic\", ...]}. The keys should be entity types and values should be lists of extracted entities belonging to the corresponding type. If you cannot find entities belonging to a specific type, the value should be [].\n\nOnly output the JSON object and do not include any additional text.\n\nAbstract:\n\nRepression of mammary adipogenesis by genistein limits mammosphere formationof human MCF-7 cells. Mammary adipose tissue may contribute to breast cancer development and progression by altering neighboring epithelial cell behavior and phenotype through paracrine signaling. Dietary exposure to soy foods is associated with lower mammary tumor risk and reduced body weight and adiposity in humans and in rodent breast cancer models. Despite the suggested linkage between obesity and breast cancer, the local influence of bioactive dietary components on mammary adiposity for anti-tumor effects remains unknown. Herein, we report that post-weaning dietary exposure to soy protein isolate and its bioactive isoflavone genistein lowered mammary adiposity and increased mammary tumor suppressor PTEN and E-cadherin expression in female mice, relative to control casein diet. To ascertain genistein's role in mammary adipose deposition that may affect underlying epithelial cell phenotype, we evaluated genistein's effects on SV40-immortalized mouse mammary stromal fibroblast-like (MSF) cells during differentiation to adipocytes. MSF cultured in differentiation medium with 40 nM genistein showed reductions in mature adipocyte numbers, triglyceride accumulation, and PPARγ and fatty acid synthase transcript levels. Genistein inhibition of adipose differentiation was accompanied by increased estrogen receptor (ER)-β gene expression and was modestly recapitulated by ERβ selective agonist 2,3-bis (4-hydroxyphenyl)-propionitrile (DPN). Reduction of ERβ expression by siRNA targeting increased PPARγ transcript levels and stromal fibroblast differentiation into mature adipocytes; the latter was reversed by genistein but not DPN. Conditioned medium from genistein-treated adipocytes diminished anchorage-independent mammosphere formation of human MCF-7 breast cancer cells. Our results suggest a mechanistic pathway to support direct regulation by genistein of mammary adiposity for breast cancer prevention."
},
{
"role": "assistant",
"content": "{\"Chemical\": []}"
}
] |
science.chia_ner
|
science.chia_ner.303
|
[
{
"role": "user",
"content": "You will be shown inclusion or exclusion criteria for a clinical trial. Given these criteria, your task is to extract all unique entities of the following types: [\"Observation\", \"Condition\", \"Procedure\", \"Drug\", \"Temporal\", \"Multiplier\", \"Qualifier\", \"Negation\", \"ReferencePoint\", \"Scope\", \"Value\", \"Mood\", \"Device\", \"Visit\", \"Measurement\", \"Person\"].\n\nPlease return the output as a JSON object of the format: {\"Condition\" : [\"breast cancer\", ...], \"Device\" : [\"ports\", ...], \"Drug\" : [\"Atenolol\", ...], \"Measurement\" : [\"blood pressure\", ...], \"Mood\" : [\"suspected\", ...], \"Multiplier\" : [\"more than two\", ...], \"Negation\" : [\"no\", ...], \"Observation\" : [\"history\", ...], \"Person\" : [\"male\", ...], \"Procedure\" : [\"surgery\", ...], \"Qualifier\" : [\"severe\", ...], \"ReferencePoint\" : [\"enrollment\", ...], \"Scope\" : [\"infection\", ...], \"Temporal\" : [\"one day\", ...], \"Value\" : [\"50%\", ...], \"Visit\" : [\"ICU\", ...]}. The keys should be entity types and values should be lists of extracted entities belonging to the corresponding type. If you cannot find entities belonging to a specific type, the value should be [].\n\nOnly output the JSON object and do not include any additional text.\n\nAbstract:\n\nPatients must have histologic proof of a malignancy suitable for radiation therapy. \nPatients must have received prior external beam radiation therapy to the region proposed for HDR brachytherapy treatment; evaluation of doses previously delivered to spinal cord/cauda equine, pelvis, and other critical structures (bowel, kidneys, rectum) will be taken into consideration. \nIf repeat irradiation would exceed any normal tissue constraint set by MSKCC Radiation Oncology Department dose constraint criteria, the patient will potentially be eligible. \nIf the total prior radiation dose to the cord or pelvis exceeds 100 Gy BED equivalent, the patient will be potentially eligible, where a total of 100 BED Gy equivalent is determined by the biological equivalent dose (BED) calculation; BED = nd(1 + d/α/β), where n = number of fractions and d = dose per fraction; α/β is the constant for spinal cord late effect and equals 2. [Rades 2005, Nieder 2005, Sahgal 2012] \nKPS ≥ 60 \nAge ≥ 18 years old"
},
{
"role": "assistant",
"content": "{\"Condition\": [\"malignancy\"], \"Device\": [], \"Drug\": [], \"Measurement\": [\"KPS\", \"MSKCC Radiation Oncology Department dose constraint criteria\"], \"Mood\": [], \"Multiplier\": [], \"Negation\": [], \"Observation\": [], \"Person\": [\"Age\"], \"Procedure\": [\"histologic\", \"HDR brachytherapy\", \"external beam radiation therapy\", \"repeat irradiation\", \"radiation therapy\"], \"Qualifier\": [\"to the region proposed for HDR brachytherapy treatment\", \"suitable for radiation therapy\"], \"ReferencePoint\": [], \"Scope\": [], \"Temporal\": [\"prior\"], \"Value\": [\"\\u2265 60\", \"\\u2265 18 years old\", \"exceed any normal tissue constraint\", \"proof\"], \"Visit\": []}"
}
] |
science.qasa_abstractive_qa
|
science.qasa_abstractive_qa.1279
|
[
{
"role": "user",
"content": "You will be shown an excerpt from a computer science scientific research paper, followed by a question about the paper. Please answer the question. Do not include any text in your response other than the answer.\n\nContext: In order to make a model invariant to input permutation, three strategies exist: 1) sort input into a canonical order; 2) treat the input as a sequence to train an RNN, but augment the training data by all kinds of permutations; 3) use a simple symmetric function to aggregate the information from each point. Here, a symmetric function takes n vectors as input and outputs a new vector that is invariant to the input order. For example, + and * operators are symmetric binary functions. Key to our approach is the use of a single symmetric function, max pooling. Effectively the network learns a set of optimization functions/criteria that select interesting or informative points of the point cloud and encode the reason for their selection. The final fully connected layers of the network aggregate these learnt optimal values into the global descriptor for the entire shape as mentioned above (shape classification) or are used to predict per point labels (shape segmentation).\n\nQuestion: Is the reason for using max pooling for permutation invariant in the paper above?"
},
{
"role": "assistant",
"content": "[Note:The question is not phrased correctly. In order to make a model invariant to input permutation, one of the strategies is to use a simple symmetric function to aggregate the information from each point. In the paper, a symmetric function takes n vectors as input and outputs a new vector that is invariant to the input order. For example, + and * operators are symmetric binary functions. The key to the paper's approach is the use of a single symmetric function, max pooling.]"
}
] |
science.multixscience_multidoc_summarization
|
science.multixscience_multidoc_summarization.18535
|
[
{
"role": "user",
"content": "You are provided with the abstract of a scientific paper and the abstracts of the papers it references. Your task is to write a Related Work section for the main paper. This section should concisely summarize and integrate the key points from the cited abstracts, reflecting how they relate to the main paper's contributions and context. In your summary, use numerical citation markers like [1], [2], etc., to refer to the corresponding papers.\n\nMain Abstract:\nDeep learning has improved state-of-the-art results in many important fields, and has been the subject of much research in recent years, leading to the development of several systems for facilitating deep learning. Current systems, however, mainly focus on model building and training phases, while the issues of data management, model sharing, and lifecycle management are largely ignored. Deep learning modeling lifecycle generates a rich set of data artifacts, such as learned parameters and training logs, and comprises of several frequently conducted tasks, e.g., to understand the model behaviors and to try out new models. Dealing with such artifacts and tasks is cumbersome and largely left to the users. This paper describes our vision and implementation of a data and lifecycle management system for deep learning. First, we generalize model exploration and model enumeration queries from commonly conducted tasks by deep learning modelers, and propose a high-level domain specific language (DSL), inspired by SQL, to raise the abstraction level and accelerate the modeling process. To manage the data artifacts, especially the large amount of checkpointed float parameters, we design a novel model versioning system (dlv), and a read-optimized parameter archival storage system (PAS) that minimizes storage footprint and accelerates query workloads without losing accuracy. PAS archives versioned models using deltas in a multi-resolution fashion by separately storing the less significant bits, and features a novel progressive query (inference) evaluation algorithm. Third, we show that archiving versioned models using deltas poses a new dataset versioning problem and we develop efficient algorithms for solving it. We conduct extensive experiments over several real datasets from computer vision domain to show the efficiency of the proposed techniques.\n\nCited Abstract(s):\n[1]: An important issue in the design and implementation of a neural network is the sensitivity of its output to input and weight perturbations. In this paper, we discuss the sensitivity of the most popular and general feedforward neural networks-multilayer perceptron (MLP). The sensitivity is defined as the mathematical expectation of the output errors of the MLP due to input and weight perturbations with respect to all input and weight values in a given continuous interval. The sensitivity for a single neuron is discussed first and an analytical expression that is a function of the absolute values of input and weight perturbations is approximately derived. Then an algorithm is given to compute the sensitivity for the entire MLP. As intuitively expected, the sensitivity increases with input and weight perturbations, but the increase has an upper bound that is determined by the structural configuration of the MLP, namely the number of neurons per layer and the number of layers. There exists an optimal value for the number of neurons in a layer, which yields the highest sensitivity value. The effect caused by the number of layers is quite unexpected. The sensitivity of a neural network may decrease at first and then almost keeps constant while the number increases.\n\n[2]: An analysis is made of the sensitivity of feedforward layered networks of Adaline elements (threshold logic units) to weight errors. An approximation is derived which expresses the probability of error for an output neuron of a large network (a network with many neurons per layer) as a function of the percentage change in the weights. As would be expected, the probability of error increases with the number of layers in the network and with the percentage change in the weights. The probability of error is essentially independent of the number of weights per neuron and of the number of neurons per layer, as long as these numbers are large (on the order of 100 or more). >\n\n[3]: The sensitivity of a neural network's output to its inputs' perturbations is an important measure for evaluating the network's performance. To make the sensitivity be a practical tool for designing and implementing Multilayer Perceptrons (MLPs), this paper proposes a general approach to quantify the sensitivity of MLPs. The sensitivity is defined as the mathematical expectation of absolute output deviations due to input perturbations with respect to all possible inputs, and computed following a bottom-up way, in which the sensitivity of a neuron is first considered and then is that of the entire network. The main contribution of the approach is that it requests a weak assumption on the input, that is, input elements need only to be independent of each other without being restricted to have a certain type of distribution and thus is more applicable to real applications. Some experimental results on artificial datasets and real datasets demonstrate the proposed approach is highly accurate."
},
{
"role": "assistant",
"content": "Stability Analysis Results Stability analysis of is studied in the literature [2] [1] [3] , where the problem setting is perturbation analysis regardless specific data, rather focus on statistical measures of stability. uses basic perturbation analysis techniques and focus on novel progressive query answering in a segmented float storage."
}
] |
science.mslr2022_cochrane_multidoc_summarization
|
science.mslr2022_cochrane_multidoc_summarization.1653
|
[
{
"role": "user",
"content": "You will be provided with the titles and abstracts of a collection of medical RCT reports studying a clinical question -- for instance, the efficacy of an intervention on some medical outcome. Please write a few sentences synthesizing the findings of these reports, which could serve as a conclusion section for a systematic review article. Your response should not include any other text. The RCT reports are below.\n\n\n\nTitle 1:\nSteroid versus placebo injection for trigger finger.\nAbstract 1:\nThe ability of a single injection of steroid and lidocaine to bring about cure of primary trigger finger was determined and compared with a control placebo injection of only lidocaine. Twenty-four patients were randomized to the therapeutic or control group and were followed prospectively. One physician administered the injection, another the clinical examination after injection, and a third evaluated the results blindly. Patients were not told to which group they were assigned. Nine of the 14 patients in the steroid group versus two of the ten patients in the placebo group were cured of trigger finger at final follow-up examination. After injection, seven patients had immediate but temporary relief of triggering because of flexor sheath distention. One injection cured 64% [corrected] of patients with primary trigger finger with no side effect and is the recommended nonsurgical treatment.\n\n\nTitle 2:\nControlled study of the use of local steroid injection in the treatment of trigger finger and thumb.\nAbstract 2:\nA controlled double-blind prospective study of injection of methylprednisolone acetate plus local anaesthetic against a control injection of a local anaesthetic in the treatment of trigger finger and thumb has shown a 60% success rate for the steroid injection against 16% for the control group (p less than 0.05). This is the first controlled trial of local steroid therapy in this condition."
},
{
"role": "assistant",
"content": "The effectiveness of local corticosteroid injections was studied in only two small randomized controlled trials of poor methodological quality. Both studies showed better short-term effects of corticosteroid injection combined with lidocaine compared to lidocaine alone on the treatment success outcome. In one study the effects of corticosteroid injections lasted up to four months. No adverse effects were observed. The available evidence for the effectiveness of intra-tendon sheath corticosteroid injection for trigger finger can be graded as a silver level evidence for superiority of corticosteroid injections combined with lidocaine over injections with lidocaine alone."
}
] |
science.scitldr_aic
|
science.scitldr_aic.420
|
[
{
"role": "user",
"content": "Below are the abstract, introduction, and conclusion of a computer science research paper. Please summarize the main contribution of the work in a single sentence. Your response should include the summary and no additional text.\n\nPaper text:\n\nQuantum machine learning methods have the potential to facilitate learning using extremely large datasets.\nWhile the availability of data for training machine learning models is steadily increasing, oftentimes it is much easier to collect feature vectors that to obtain the corresponding labels.\nOne of the approaches for addressing this issue is to use semi-supervised learning, which leverages not only the labeled samples, but also unlabeled feature vectors.\nHere, we present a quantum machine learning algorithm for training Semi-Supervised Kernel Support Vector Machines.\nThe algorithm uses recent advances in quantum sample-based Hamiltonian simulation to extend the existing Quantum LS-SVM algorithm to handle the semi-supervised term in the loss, while maintaining the same quantum speedup as the Quantum LS-SVM.\nData sets used for training machine learning models are becoming increasingly large, leading to continued interest in fast methods for solving large-scale classification problems.\nOne of the approaches being explored is training the predictive model using a quantum algorithm that has access to the training set stored in quantum-accessible memory.\nIn parallel to research on efficient architectures for quantum memory (Blencowe, 2010) , work on quantum machine learning algorithms and on quantum learning theory is under way (see for example Refs.\n(Biamonte et al., 2017; Dunjko & Briegel, 2018; Schuld & Petruccione, 2018) and (Arunachalam & de Wolf, 2017) for review).\nAn early example of this approach is Quantum LS-SVM (Rebentrost et al., 2014a) , which achieves exponential speedup compared to classical LS-SVM algorithm.\nQuantum LS-SVM uses quadratic least-squares loss and squared-L 2 regularizer, and the optimization problem can be solved using the seminal HHL (Harrow et al., 2009 ) algorithm for solving quantum linear systems of equations.\nWhile progress has been made in quantum algorithms for supervised learning, it has been recently advocated that the focus should shift to unsupervised and semi-supervised setting (Perdomo-Ortiz et al., 2018) .\nIn many domains, the most laborious part of assembling a training set is the collection of sample labels.\nThus, in many scenarios, in addition to the labeled training set of size m we have access to many more feature vectors with missing labels.\nOne way of utilizing these additional data points to improve the classification model is through semi-supervised learning.\nIn semi-supervised learning, we are given m observations x 1 , ..., x m drawn from the marginal distribution p(x), where the l (l m) first data points come with labels y 1 , ..., y l drawn from conditional distribution p(y|x).\nSemi-supervised learning algorithms exploit the underlying distribution of the data to improve classification accuracy on unseen samples.\nIn the approach considered here, the training samples are connected by a graph that captures their similarity.\nHere, we introduce a quantum algorithm for semi-supervised training of a kernel support vector machine classification model.\nWe start with the existing Quantum LS-SVM (Rebentrost et al., 2014a) , and use techniques from sample-based Hamiltonian simulation (Kimmel et al., 2017) to add a semisupervised term based on Laplacian SVM (Melacci & Belkin, 2011) .\nAs is standard in quantum machine learning (Li et al., 2019) , the algorithm accesses training points and the adjacency matrix of the graph connecting samples via a quantum oracle.\nWe show that, with respect to the oracle, the proposed algorithm achieves the same quantum speedup as LS-SVM, that is, adding the semisupervised term does not lead to increased computational complexity."
},
{
"role": "assistant",
"content": "We extend quantum SVMs to semi-supervised setting, to deal with the likely problem of many missing class labels in huge datasets."
}
] |
science.anat_em_ner
|
science.anat_em_ner.81
|
[
{
"role": "user",
"content": "You will be shown an abstract from a biomedical research paper. Given this abstract, your task is to extract all unique entities of the following types: [\"AnatomicalEntity\"].\n\nPlease return the output as a JSON object of the format: {\"AnatomicalEntity\": [\"tumor cells\", ...]}. The keys should be entity types and values should be lists of extracted entities belonging to the corresponding type. If you cannot find entities belonging to a specific type, the value should be [].\n\nOnly output the JSON object and do not include any additional text.\n\nAbstract:\n\nWater emerging from the yoke adapter of the nitrous oxide hose"
},
{
"role": "assistant",
"content": "{\"AnatomicalEntity\": []}"
}
] |
science.chemprot_re
|
science.chemprot_re.907
|
[
{
"role": "user",
"content": "Given an abstract from a research paper, your task is to identify and label relationships between chemical compounds and genes mentioned in the abstract.\n\nThe relationship type must be one of ['DOWNREGULATOR', 'SUBSTRATE', 'INDIRECT-REGULATOR', 'PART-OF', 'MODULATOR-ACTIVATOR', 'REGULATOR', 'INHIBITOR', 'COFACTOR', 'UPREGULATOR', 'ACTIVATOR', 'ANTAGONIST', 'NOT', 'INDIRECT-DOWNREGULATOR', 'SUBSTRATE_PRODUCT-OF', 'INDIRECT-UPREGULATOR', 'AGONIST', 'PRODUCT-OF', 'MODULATOR', 'DIRECT-REGULATOR', 'UNDEFINED', 'AGONIST-INHIBITOR', 'AGONIST-ACTIVATOR', 'MODULATOR-INHIBITOR'].\n\nPlease format your output as a JSON array. Each entry in the array should express a single relation, formatted as [\"<Entity_A>\", \"<RELATION_A_B>\", \"<Entity_B>\"]. If no relations can be found, please output an empty JSON array [].\n\nAbstract:\n\nGliotransmission and brain glucose sensing: critical role of endozepines. Hypothalamic glucose sensing is involved in the control of feeding behavior and peripheral glucose homeostasis, and glial cells are suggested to play an important role in this process. Diazepam-binding inhibitor (DBI) and its processing product the octadecaneuropeptide (ODN), collectively named endozepines, are secreted by astroglia, and ODN is a potent anorexigenic factor. Therefore, we investigated the involvement of endozepines in brain glucose sensing. First, we showed that intracerebroventricular administration of glucose in rats increases DBI expression in hypothalamic glial-like tanycytes. We then demonstrated that glucose stimulates endozepine secretion from hypothalamic explants. Feeding experiments indicate that the anorexigenic effect of central administration of glucose was blunted by coinjection of an ODN antagonist. Conversely, the hyperphagic response elicited by central glucoprivation was suppressed by an ODN agonist. The anorexigenic effects of centrally injected glucose or ODN agonist were suppressed by blockade of the melanocortin-3/4 receptors, suggesting that glucose sensing involves endozepinergic control of the melanocortin pathway. Finally, we found that brain endozepines modulate blood glucose levels, suggesting their involvement in a feedback loop controlling whole-body glucose homeostasis. Collectively, these data indicate that endozepines are a critical relay in brain glucose sensing and potentially new targets in treatment of metabolic disorders."
},
{
"role": "assistant",
"content": "[[\"glucose\", \"INDIRECT-UPREGULATOR\", \"DBI\"]]"
}
] |
science.scitldr_aic
|
science.scitldr_aic.1240
|
[
{
"role": "user",
"content": "Below are the abstract, introduction, and conclusion of a computer science research paper. Please summarize the main contribution of the work in a single sentence. Your response should include the summary and no additional text.\n\nPaper text:\n\nAn unintended consequence of feature sharing is the model fitting to correlated tasks within the dataset, termed negative transfer. \nIn this paper, we revisit the problem of negative transfer in multitask setting and find that its corrosive effects are applicable to a wide range of linear and non-linear models, including neural networks.\nWe first study the effects of negative transfer in a principled way and show that previously proposed counter-measures are insufficient, particularly for trainable features.\nWe propose an adversarial training approach to mitigate the effects of negative transfer by viewing the problem in a domain adaptation setting.\nFinally, empirical results on attribute prediction multi-task on AWA and CUB datasets further validate the need for correcting negative sharing in an end-to-end manner.\nAdvances in machine learning have led to proficient supervised learning models with powerful representations in various prediction tasks.\nWe now expect an ideal classification model to restrict itself to a pertinent set of evidences available to it from the input for prediction.\nFurther, we expect the model to disregard any unrelated evidences in the data to enable better generalization.\nFigure 1: A supervised classifier 'cheetah vs. snow-leopard' that uses unrelated evidence (of habitat) over relevant evidence (of fur patterns).\nAs shown by the pixel importance maps, the model suffers from the negative transfer prevalent in a typical animal image dataset skewed towards the animal's typical habitat and fails to generalize to rare samples.Let us consider the task of training an animal classifier \"cheetah vs. snow-leopards\" from a dataset of images of these animals, such as those illustrated in Figure 1 -a task which ideally should focus on the animal's appearance features.\nHowever, a large portion of these images also contain various cues of the typical habitat of the animals in the background, i.e., tall grass and snow (see Figures 1\n(a) and\n(b)) which are, in principle, unrelated to the animal's appearance.\nAn archetypal model is deceived by the co-occurrence of such unrelated, yet easily detectable cues of habitat over the animal's appearance features such as complex fur patterns.\nHowever, a proficient supervised learning model must identify relevant evidences for the label of interest and at the same time discard various unrelated evidences such as presence of snow, even though it tends to co-occur frequently with snow-leopard.\nConsequently, it would be more likely that such a model would perform better on rare-instances (such as those in Figures 1\n(c) and\n(d)) and generalize better to unseen instances.This phenomenon of co-occurring but unrelated evidences being present in training data and thereby having a debilitating effect on model performance has been described in literature BID8 ; BID16 ; BID9 ; BID13 ; BID15 ).\nThese techniques utilize the easy availability of labels for unrelated evidences (e.g. background habitat labels above), called negative labels which constitutes an auxiliary task, and seek to mitigate its debilitating performance on the primary task (e.g. animal classification above) with techniques referred to as negative-sharing or negative-transfer.While all of these techniques have tackled this problem utilizing various forms of regularization, we describe several shortcomings of this class of approaches, most notable of which is their inapplicability to the popular paradigm of trainable features obtained via neural representation learning.\nMotivated by these limitations, in this paper we depart from the direction of regularization-based approaches and examine methods inspired from a domain-adaptation viewpoint to propose an adversarial training-based formulation.\nWe uniquely view such a scenario as an instance of adversarial multi-task learning, where the classification tasks are either the primary task of interest (i.e., predicting the presence of fur pattern and color) or the auxiliary negative tasks (i.e., characteristics of habitat) to be avoided.\nSince the 2 tasks are unrelated, any label correlation between primary and auxiliary labels in the training data is only by chance and therefore from a domain-adaptation perspective, we envision a target-domain as possibly having a different correlation between the primary and auxiliary labels.\nThe effects of negative transfer are hence mitigated when the classification task is trained in this domain.We discuss advantages of our proposed formulation, inspired from domain-adaptation, to alleviate the negative transfer over existing techniques, including ready applicability to neural networks in an end-to-end fashion.\nIt must be noted that, while the formulation of the problem is motivated with multi-task learning, negative-transfer is a disposition of any supervised learning task from simple binary classification to recent popular supervised tasks such as image detection, captioning, or visual dialog.\nWe present motivating literature that prelude this work next.\nIn this work, we show that adversarial learning is the natural answer to prevent negative transfer.\nThis leads to potential improvement in any supervised learning of natural data that is seeking generalization.\nWe find that even in relatively straight-forward linear models presented above, co-occurrence of unrelated labels hampers performance and must be explicitly treated.\nWe address the problem of negative transfer in a multi-task scenario, and also show the applicability of our solution in any supervised task.\nSupervised learning practitioners can utilize domain expertise to acquire and leverage additional negative labels for this purpose.\nRecent work in explainability of machine learning models can also be appropriately leveraged to facilitate this task."
},
{
"role": "assistant",
"content": "We look at negative transfer from a domain adaptation point of view to derive an adversarial learning algorithm."
}
] |
science.craftchem_ner
|
science.craftchem_ner.3440
|
[
{
"role": "user",
"content": "You will be presented a sentence from biomedical research text. Extract all terms that correspond to chemical entities of biological interest (ChEBI).\nReturn your identified terms in a JSON array, formatted like this: [\"Entity1\", \"Entity2\", ...].\nIf no such entities are detected, respond by providing an empty JSON array [].\n\nBiomedical context:\nAntibodiesareagainstmarkersofnormalepidermaldifferentiation,andincludeK5(abasallyexpressedkeratin),K1(asuprabasalkeratin,expressedinspinouslayercells),involucrin(Inv;asuprabasallyexpressedcornifiedenvelopeproteinfoundinupperspinousandgranularlayercells),loricrin(Lor;acornifiedenvelopeproteinexpressedinthegranularlayer),andfilaggrin(Fil;aproteinthatbundleskeratinfilamentsinthegranularlayerandstratumcorneum)."
},
{
"role": "assistant",
"content": "[\"protein\", \"protein\", \"protein\"]"
}
] |
science.anat_em_ner
|
science.anat_em_ner.304
|
[
{
"role": "user",
"content": "You will be shown an abstract from a biomedical research paper. Given this abstract, your task is to extract all unique entities of the following types: [\"AnatomicalEntity\"].\n\nPlease return the output as a JSON object of the format: {\"AnatomicalEntity\": [\"tumor cells\", ...]}. The keys should be entity types and values should be lists of extracted entities belonging to the corresponding type. If you cannot find entities belonging to a specific type, the value should be [].\n\nOnly output the JSON object and do not include any additional text.\n\nAbstract:\n\nL-Carnitine ameliorates methotrexate-induced oxidative organ injury and inhibits leukocyte death. \nMethotrexate (MTX), a folic acid antagonist widely used for the treatment of a variety of tumors and inflammatory diseases, affects normal tissues that have a high rate of proliferation, including the hematopoietic cells of the bone marrow and the gastrointestinal mucosal cells. To elucidate the role of free radicals and leukocytes in MTX-induced oxidative organ damage and the putative protective effect of L-carnitine (L-Car), Wistar albino rats were administered a single dose of MTX (20 mg/kg) followed by either saline or L-Car (500 mg/kg) for 5 days. After decapitation of the rats, trunk blood was obtained, and the ileum, liver, and kidney were removed for histological examination and for the measurement of malondialdehyde (MDA) and glutathione (GSH) levels, myeloperoxidase (MPO) activity, and collagen content. Our results showed that MTX administration increased the MDA and MPO activities and collagen content and decreased GSH levels in all tissues, while these alterations were reversed in L-Car-treated group. The elevated serum TNF-alpha level observed following MTX treatment was depressed with L-Car. The oxidative burst of neutrophils stimulated by Annexin V was reduced in the saline-treated MTX group, while L-Car abolished this inhibition. Similarly, flow cytometric measurements revealed that leukocyte apoptosis was increased in MTX-treated animals, while L-Car reversed these effects. Severe degeneration of the intestinal mucosa, liver parenchyma, and glomerular and tubular epithelium observed in the saline-treated MTX group was improved by L-Car treatment. These results suggest that L-Car, possibly via its free radical scavenging and antioxidant properties, ameliorates MTX-induced oxidative organ injury and inhibits leukocyte apoptosis. Thus, supplementation with L-Carnitine as an adjuvant therapy may be promising in alleviating the systemic side-effects of chemotherapeutics."
},
{
"role": "assistant",
"content": "{\"AnatomicalEntity\": [\"organ\", \"leukocytes\", \"ileum\", \"tumors\", \"bone marrow\", \"tissues\", \"neutrophils\", \"intestinal mucosa\", \"serum\", \"liver parenchyma\", \"gastrointestinal mucosal cells\", \"hematopoietic cells\", \"tubular epithelium\", \"glomerular\", \"trunk blood\", \"leukocyte\", \"kidney\", \"liver\"]}"
}
] |
science.scireviewgen_multidoc_summarization
|
science.scireviewgen_multidoc_summarization.30756
|
[
{
"role": "user",
"content": "You are presented with multiple paper abstracts, alongside the associated literature review and chapter titles. Given the provided information, you are going to do a literature review. Please generate a coherent literature review that synthesizes the content, draws connections between different works, highlights major findings, and identifies any gaps in the existing research.\n\nLiterature Review Title: Self-Driving Cars: A Survey \nChapter Title: B. Motion Planning \n1. Abstract of Cited Paper (BIB001): Self-driving vehicles are a maturing technology with the potential to reshape mobility by enhancing the safety, accessibility, efficiency, and convenience of automotive transportation. Safety-critical tasks that must be executed by a self-driving vehicle include planning of motions through a dynamic environment shared with other vehicles and pedestrians, and their robust executions via feedback control. The objective of this paper is to survey the current state of the art on planning and control algorithms with particular regard to the urban setting. A selection of proposed techniques is reviewed along with a discussion of their effectiveness. The surveyed approaches differ in the vehicle mobility model used, in assumptions on the structure of the environment, and in computational requirements. The side-by-side comparison presented in this survey helps to gain insight into the strengths and limitations of the reviewed approaches and assists with system level design choices.\n\nLiterature Review:"
},
{
"role": "assistant",
"content": "The motion planning subsystem is responsible for computing a path or trajectory from the self-driving car's current state to the next local goal state defined by the behavior selection subsystem. The motion plan executes the local driving behavior, satisfies car's kinematic and dynamic constraints, provides comfort to the passenger, and avoids collisions with static and moving obstacles in the environment. A motion plan can be a path or a trajectory. The path is a sequence of car's states that does not define how car's states evolve over time. This task can be entrusted to other subsystem (e.g., the behavior selection subsystem) or a velocity profile can be defined as a function of curvature and proximity to obstacles. The trajectory is a path that specifies the evolution of car's states through time. Various methods for motion planning have been proposed in the literature. We review those that were designed for onroad motion planning 1 and evaluated experimentally using real-world autonomous vehicles. For more comprehensive reviews on these methods, readers are referred to González et al. BIB001 and Paden et al. BIB002 ."
}
] |
science.scitldr_aic
|
science.scitldr_aic.1124
|
[
{
"role": "user",
"content": "Below are the abstract, introduction, and conclusion of a computer science research paper. Please summarize the main contribution of the work in a single sentence. Your response should include the summary and no additional text.\n\nPaper text:\n\nKnowledge graph embedding research has overlooked the problem of probability calibration.\nWe show popular embedding models are indeed uncalibrated.\nThat means probability estimates associated to predicted triples are unreliable.\nWe present a novel method to calibrate a model when ground truth negatives are not available, which is the usual case in knowledge graphs.\nWe propose to use Platt scaling and isotonic regression alongside our method.\nExperiments on three datasets with ground truth negatives show our contribution leads to well calibrated models when compared to the gold standard of using negatives.\nWe get significantly better results than the uncalibrated models from all calibration methods.\nWe show isotonic regression offers the best the performance overall, not without trade-offs.\nWe also show that calibrated models reach state-of-the-art accuracy without the need to define relation-specific decision thresholds.\nKnowledge graph embedding models are neural architectures that learn vector representations (i.e. embeddings) of nodes and edges of a knowledge graph.\nSuch knowledge graph embeddings have applications in knowledge graph completion, knowledge discovery, entity resolution, and link-based clustering, just to cite a few (Nickel et al., 2016a) .\nDespite burgeoning research, the problem of calibrating such models has been overlooked, and existing knowledge graph embedding models do not offer any guarantee on the probability estimates they assign to predicted facts.\nProbability calibration is important whenever you need the predictions to make probabilistic sense, i.e., if the model predicts a fact is true with 80% confidence, it should to be correct 80% of the times.\nPrior art suggests to use a sigmoid layer to turn logits returned by models into probabilities (Nickel et al., 2016a ) (also called the expit transform), but we show that this provides poor calibration.\nFigure 1 shows reliability diagrams for off-the-shelf TransE and ComplEx.\nThe identity function represents perfect calibration.\nBoth models are miscalibrated: all TransE combinations in Figure 1a under-forecast the probabilities (i.e. probabilities are too small), whereas ComplEx under-forecasts or over-forecasts according to which loss is used (Figure1b).\nCalibration is crucial in high-stakes scenarios such as drug-target discovery from biological networks, where end-users need trustworthy and interpretable decisions.\nMoreover, since probabilities are not calibrated, when classifying triples (i.e. facts) as true or false, users must define relationspecific thresholds, which can be awkward for graphs with a great number of relation types.\nTo the best of our knowledge, this is the first work to focus on calibration for knowledge embeddings.\nOur contribution is two-fold: First, we use Platt Scaling and isotonic regression to calibrate knowledge graph embedding models on datasets that include ground truth negatives.\nOne peculiar feature of knowledge graphs is that they usually rely on the open world assumption (facts not present are not necessarily false, they are simply unknown).\nThis makes calibration troublesome because of the lack of ground truth negatives.\nFor this reason, our second and main contribution is a calibration heuristics that combines Platt-scaling or isotonic regression with synthetically generated negatives.\nExperimental results show that we obtain better-calibrated models and that it is possible to calibrate knowledge graph embedding models even when ground truth negatives are not present.\nWe also experiment with triple classification, and we show that calibrated models reach state-of-the-art accuracy without the need to define relation-specific decision thresholds.\nWe propose a method to calibrate knowledge graph embedding models.\nWe target datasets with and without ground truth negatives.\nWe experiment on triple classification datasets and apply Platt scaling and isotonic regression with and without synthetic negatives controlled by our heuristics.\nAll calibration methods perform significantly better than uncalibrated scores.\nWe show that isotonic regression brings better calibration performance, but it is computationally more expensive.\nAdditional experiments on triple classification shows that calibration allows to use a single decision threshold, reaching state-of-the-art results without the need to learn per-relation thresholds.\nFuture work will evaluate additional calibration algorithms, such as beta calibration (Kull et al., 2017) or Bayesian binning (Naeini et al., 2015) .\nWe will also experiment on ensembling of knowledge graph embedding models, inspired by (Krompaß & Tresp, 2015) .\nThe rationale is that different models operate on different scales, but calibrating brings them all to the same probability scale, so their output can be easily combined."
},
{
"role": "assistant",
"content": "We propose a novel method to calibrate knowledge graph embedding models without the need of negative examples."
}
] |
science.data_reco_mcq_sc
|
science.data_reco_mcq_sc.2660
|
[
{
"role": "user",
"content": "Given a short query with keyphrases about a research idea in 2015 in the domain of artificial intelligence, recommend the relevant datasets to validate the research idea from options provided. A short description of the datasets is also provided to help you.\n\nQuery: We propose a novel algorithm, SNaCK, to learn a low-dimensional embedding of a\n\nKeyphrases: prime number recognition image\n\nDataset description:\nHopkins155: The Hopkins 155 dataset consists of 156 video sequences of two or three motions. Each video sequence motion corresponds to a low-dimensional subspace.\nPA-100K: PA-100K is a recent-proposed large pedestrian attribute dataset, with 100,000 images in total collected from outdoor surveillance cameras. It is split into 80,000 images for the training set, and 10,000 for the validation set and 10,000 for the test set.\nFood-101: The Food-101 dataset consists of 101 food categories with 750 training and 250 test images per category, making a total of 101k images. The labels for the test images have been manually cleaned, while the training set contains some noise.\nRL Unplugged: RL Unplugged is suite of benchmarks for offline reinforcement learning. The RL Unplugged is designed around the following considerations: to facilitate ease of use, the datasets are provided with a unified API which makes it easy for the practitioner to work with all data in the suite once a general pipeline has been established.\n\nOptions:- A: Hopkins155 B: PA-100K C: Food-101 D: RL Unplugged"
},
{
"role": "assistant",
"content": "Food-101"
}
] |
science.covidfact_entailment
|
science.covidfact_entailment.12
|
[
{
"role": "user",
"content": "You will be shown a claim related to the COVID-19 pandemic, and the abstract of a biomedical research paper. Each sentence from the abstract will be on a separate line. Your task is to return a JSON object with two fields:\n\n- \"verdict\": The fact-checking verdict. If the information in the abstract supports the claim, write \"SUPPORT\". If the abstract contradicts the claim, write \"CONTRADICT\".\n- \"evidence\": An array of sentences providing evidence for the verdict. Please copy all relevant sentences verbatim from the abstract.\n\nFor instance, if the model were given the claim \"the COVID vaccine is safe for healthy adults\", the output might be\n{\n \"verdict\": \"SUPPORT\",\n \"evidence\": [\"Our findings indicate that the risks of severe COVID vaccine side effects are low for healthy adults.\"]\n}\n\nClaim: Gns561 exhibits potent in vitro antiviral activity against sars-cov-2 through autophagy inhibition\n\nAbstract:\nSince December 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2/2019-nCoV) has spread quickly worldwide, with more than 29 million cases and 920,000 deaths.\nInterestingly, coronaviruses were found to subvert and hijack the autophagic process to allow their viral replication.\nOne of the spotlights had been focused on the autophagy inhibitors as a target mechanism effective in the inhibition of SARS-CoV-2 infection.\nConsequently, chloroquine (CQ) and hydroxychloroquine (HCQ), a derivative of CQ, was suggested as the first potentially be therapeutic strategies as they are known to be autophagy inhibitors.\nThen, they were used as therapeutics in SARS-CoV-2 infection along with remdesivir, for which the FDA approved emergency use authorization.\nHere, we investigated the antiviral activity and associated mechanism of GNS561, a small basic lipophilic molecule inhibitor of late-stage autophagy, against SARS-CoV-2.\nOur data indicated that GNS561 showed the highest antiviral effect for two SARS-CoV-2 strains compared to CQ and remdesivir.\nFocusing on the autophagy mechanism, we showed that GNS561, located in LAMP2-positive lysosomes, together with SARS-CoV-2, blocked autophagy by increasing the size of LC3-II spots and the accumulation of autophagic vacuoles in the cytoplasm with the presence of multilamellar bodies characteristic of a complexed autophagy.\nFinally, our study revealed that the combination of GNS561 and remdesivir was associated with a strong synergistic antiviral effect against SARS-CoV-2.\nOverall, our study highlights GNS561 as a powerful drug in SARS-CoV-2 infection and supports that the hypothesis that autophagy inhibitors could be an alternative strategy for SARS-CoV-2 infection."
},
{
"role": "assistant",
"content": "{\"verdict\": \"SUPPORT\", \"evidence\": [\"Here, we investigated the antiviral activity and associated mechanism of GNS561, a small basic lipophilic molecule inhibitor of late-stage autophagy, against SARS-CoV-2.\", \"Our data indicated that GNS561 showed the highest antiviral effect for two SARS-CoV-2 strains compared to CQ and remdesivir.\", \"Finally, our study revealed that the combination of GNS561 and remdesivir was associated with a strong synergistic antiviral effect against SARS-CoV-2.\", \"Overall, our study highlights GNS561 as a powerful drug in SARS-CoV-2 infection and supports that the hypothesis that autophagy inhibitors could be an alternative strategy for SARS-CoV-2 infection.\"]}"
}
] |
science.pico_ner
|
science.pico_ner.2568
|
[
{
"role": "user",
"content": "You will be shown an abstract from a biomedical research paper. Given this abstract, your task is to extract all unique entities of the following types: [\"Outcome\", \"Participant\", \"Intervention\"].\n\nPlease return the output as a JSON object of the format: {\"Participant\" : [\"patients with COPD\", ...], \"Intervention\" : [\"Atenolol\", ...], \"Outcome\" : [\"blood pressure\", ...]}. The keys should be entity types and values should be lists of extracted entities belonging to the corresponding type. If you cannot find entities belonging to a specific type, the value should be [].\n\nOnly output the JSON object and do not include any additional text.\n\nAbstract:\n\nInfrared LED irradiation applied during high-intensity treadmill training improves maximal exercise tolerance in postmenopausal women : a 6-month longitudinal study . Reduced aerobic fitness is associated with an increased risk of cardiovascular diseases among the older population . The aim of this study was to investigate the effects of LED irradiation ( 850 nm ) applied during treadmill training on the maximal exercise tolerance in postmenopausal women . At the beginning of the study , 45 postmenopausal women were assigned randomly to three groups , and 30 women completed the entire 6 months of the study . The groups were : ( 1 ) the LED group ( treadmill training associated with phototherapy , n = 10 ) , ( 2 ) the exercise group ( treadmill training , n = 10 ) , and ( 3 ) the sedentary group ( neither physical training nor phototherapy , n = 10 ) . The training was performed for 45 min twice a week for 6 months at intensities between 85 % and 90 % maximal heart rate ( HRmax ) . The irradiation parameters were 39 mW/cm ( 2 ) , 45 min and 108 J/cm ( 2 ) . The cardiovascular parameters were measured at baseline and after 6 months . As expected , no significant differences were found in the sedentary group ( p ≥ 0.05 ) . The maximal time of tolerance ( Tlim ) , metabolic equivalents ( METs ) and Bruce stage reached significantly higher values in the LED group and the exercise group ( p < 0.01 ) . Furthermore , the HR , double product and Borg score at isotime were significantly lower in the LED group and in the exercise group ( p < 0.05 ) . However , the time of recovery showed a significant decrease only in the LED group ( p = 0.003 ) . Moreover , the differences between before and after training ( delta values ) for the Tlim , METs and HR at isotime were greater in the LED group than in the exercise group with a significant intergroup difference ( p < 0.05 ) . Therefore , the infrared LED irradiation during treadmill training can improve maximal performance and post-exercise recovery in postmenopausal women ."
},
{
"role": "assistant",
"content": "{\"Intervention\": [\"LED irradiation\", \"Infrared LED irradiation\"], \"Outcome\": [\"effects\", \"maximal exercise tolerance\"], \"Participant\": []}"
}
] |
science.chemprot_ner
|
science.chemprot_ner.809
|
[
{
"role": "user",
"content": "You will be shown an abstract from a biomedical research paper. Given this abstract, your task is to extract all unique entities of the following types: [\"Protein\", \"Chemical\"].\n\nPlease return the output as a JSON object of the format: {\"Chemical\" : [\"Dexamethasone\", ...], \"Protein\" : [\"BRCA-1\", ...]}. The keys should be entity types and values should be lists of extracted entities belonging to the corresponding type. If you cannot find entities belonging to a specific type, the value should be [].\n\nOnly output the JSON object and do not include any additional text.\n\nAbstract:\n\nResistance to conventional insecticides in Pakistani populations of Musca domestica L. (Diptera: Muscidae): a potential ectoparasite of dairy animals.\nThe house fly, Musca domestica L., is an important hygienic pest of humans and dairy animals with the potential to develop resistance to most chemical classes of insecticides. Six adult house fly strains from dairy farms in Punjab, Pakistan were evaluated for resistance to selected insecticides from organochlorine, organophosphate, carbamate and pyrethroid classes. For a chlorocyclodiene and two organophosphates tested, the resistance ratios (RR) at LC50 were in the range of 5.60-22.02 fold for endosulfan, 7.66-23.24 fold for profenofos and 2.47-7.44 fold for chlorpyrifos. For two pyrethroids and one carbamate, the RR values at LC50 were 30.22-70.02 for cypermethrin, 5.73-18.31 for deltamethrin, and 4.39-15.50 for methomyl. This is the first report of resistance to different classes of insecticides in Pakistani dairy populations of house flies. Regular insecticide resistance monitoring programs on dairy farms are needed to prevent field control failures. Moreover, integrated approaches including the judicious use of insecticides are needed to delay the development of insecticide resistance in house flies."
},
{
"role": "assistant",
"content": "{\"Chemical\": [\"organophosphate\", \"chlorpyrifos\", \"carbamate\", \"organophosphates\", \"endosulfan\", \"pyrethroids\", \"chlorocyclodiene\", \"cypermethrin\", \"methomyl\", \"deltamethrin\", \"pyrethroid\", \"organochlorine\"], \"Protein\": []}"
}
] |
science.chemprot_ner
|
science.chemprot_ner.591
|
[
{
"role": "user",
"content": "You will be shown an abstract from a biomedical research paper. Given this abstract, your task is to extract all unique entities of the following types: [\"Protein\", \"Chemical\"].\n\nPlease return the output as a JSON object of the format: {\"Chemical\" : [\"Dexamethasone\", ...], \"Protein\" : [\"BRCA-1\", ...]}. The keys should be entity types and values should be lists of extracted entities belonging to the corresponding type. If you cannot find entities belonging to a specific type, the value should be [].\n\nOnly output the JSON object and do not include any additional text.\n\nAbstract:\n\nTemporal profile of brain and pituitary GnRHs, GnRH-R and gonadotropin mRNA expression and content during early development in European sea bass (Dicentrarchus labrax L.).\nA likely endocrine control mechanism for sexual differentiation in size-graded populations of European sea bass (Dicentrarchus labrax) is proposed by evaluating the brain expression and pituitary content of two forms of gonadotropin-releasing hormone (GnRH), namely sea bream (sbGnRH) and salmon (sGnRH), the pituitary expression of one subtype of GnRH receptor (dlGnRH-R-2A) and the three gonadotropin (GtH) subunits, namely glycoprotein alpha (GPalpha), follicle-stimulating hormone beta (FSHbeta) and luteinizing hormone beta (LHbeta), as well as the pituitary and plasma LH levels between 50 and 300 days post-hatching (dph). Four gradings were conducted between 2 and 8 months after hatching, resulting in a population of large and small individuals, having 96.5% females (female-dominant population) and 69.2% males (male-dominant population), respectively, after the last grading. The onset of gonadal differentiation was different in the two sexes, and coincided with a peak of expression of sbGnRH or sGnRH. Furthermore, the expression of these GnRHs was correlated with the expression of dlGnRH-R-2A. Sex-related differences in the brain and pituitary content of sbGnRH were also found at the time of sexual differentiation. Moreover, the observed sexual dimorphism at the transcriptional or synthesis level of these GnRH forms suggests that a different neuro-hormonal regulation is operating according to sex. At the onset of sex differentiation, FSHbeta transcriptional activity reached maximal values, which were maintained until the completion of the process. The present study suggests a role for sbGnRH, sGnRH and the dlGnRH-R-2A during gonadal differentiation, possibly through enhancement of FSHbeta gene expression. In males, a different endocrine regulation seems to exist also during spermiogenesis and spermiation, when gene transcription, peptide synthesis and release of LH are of greater importance."
},
{
"role": "assistant",
"content": "{\"Chemical\": [\"GnRHs\", \"gonadotropin-releasing hormone\", \"GnRH\"], \"Protein\": [\"LHbeta\", \"GnRH\", \"follicle-stimulating hormone beta\", \"GnRHs\", \"FSHbeta\", \"gonadotropin-releasing hormone\", \"sbGnRH\", \"dlGnRH-R-2A\", \"GnRH-R\", \"sGnRH\", \"luteinizing hormone beta\", \"GtH\", \"GnRH receptor\", \"gonadotropin\", \"glycoprotein alpha\", \"LH\", \"GPalpha\"]}"
}
] |
science.multixscience_multidoc_summarization
|
science.multixscience_multidoc_summarization.10519
|
[
{
"role": "user",
"content": "You are provided with the abstract of a scientific paper and the abstracts of the papers it references. Your task is to write a Related Work section for the main paper. This section should concisely summarize and integrate the key points from the cited abstracts, reflecting how they relate to the main paper's contributions and context. In your summary, use numerical citation markers like [1], [2], etc., to refer to the corresponding papers.\n\nMain Abstract:\nThis article presents fraudulent activity that are done by the unscrupulous desire of people to make the personal benefits by manipulating the tax in taxing system. Taxpayers manipulate the money paid to the tax authorities through avoidance and evasion activities. In this paper, we deal with a specific technique used by the tax-evaders known as a circular trading. We define an algorithm for detection and analysis of circular trade. To detect these circular trade, we have modeled whole system as a directed graph with actors being vertices and the transactions among them as directed edges. We have proposed an algorithm for detecting these circular trade. The commercial tax dataset is given by Telangana, India. This dataset contains the transaction details of participants involved in a known circular trade.\n\nCited Abstract(s):\n[1]: Market manipulation remains the biggest concern of investors in today's securities market, despite fast and strict responses from regulators and exchanges to market participants that pursue such practices. The existing methods in the industry for detecting fraudulent activities in securities market rely heavily on a set of rules based on expert knowledge. The securities market has deviated from its traditional form due to new technologies and changing investment strategies in the past few years. The current securities market demands scalable machine learning algorithms supporting identification of market manipulation activities. In this paper we use supervised learning algorithms to identify suspicious transactions in relation to market manipulation in stock market. We use a case study of manipulated stocks during 2003. We adopt CART, conditional inference trees, C5.0, Random Forest, Naive Bayes, Neural Networks, SVM and kNN for classification of manipulated samples. Empirical results show that Naive Bayes outperform other learning methods achieving F 2 measure of 53 (sensitivity and specificity are 89 and 83 respectively).\n\n[2]: \n\n[3]: Many mal-practices in stock market trading--e.g., circular trading and price manipulation--use the modus operandi of collusion. Informally, a set of traders is a candidate collusion set when they have \"heavy trading\" among themselves, as compared to their trading with others. We formalize the problem of detection of collusion sets, if any, in the given trading database. We show that naive approaches are inefficient for real-life situations. We adapt and apply two well-known graph clustering algorithms for this problem. We also propose a new graph clustering algorithm, specifically tailored for detecting collusion sets. A novel feature of our approach is the use of Dempster---Schafer theory of evidence to combine the candidate collusion sets detected by individual algorithms. Treating individual experiments as evidence, this approach allows us to quantify the confidence (or belief) in the candidate collusion sets. We present detailed simulation experiments to demonstrate effectiveness of the proposed algorithms.\n\n[4]: In financial markets, abnormal trading behaviors pose a serious challenge to market surveillance and risk management. What is worse, there is an increasing emergence of abnormal trading events that some experienced traders constitute a collusive clique and collaborate to manipulate some instruments, thus mislead other investors by applying similar trading behaviors for maximizing their personal benefits. In this paper, a method is proposed to detect the potential collusive cliques involved in an instrument of future markets by first calculating the correlation coefficient between any two eligible unified aggregated time series of signed order volume, and then combining the connected components from multiple sparsified weighted graphs constructed by using the correlation matrices where each correlation coefficient is over a user-specified threshold. Experiments conducted on real order data from the Shanghai Futures Exchange show that the proposed method can effectively detect suspect collusive cliques, which have been verified by financial experts. A tool based on the proposed method has been deployed in the exchange as a pilot application for futures market surveillance and risk management.\n\n[5]: In this paper, we analyze the trading behavior of users in an experimental stock market with a special emphasis on irregularities within the set of regular trading operations. To this end the market is represented as a graph of traders that are connected by their transactions. Our analysis is executed from two perspectives: On a micro scale view fraudulent transactions between traders are introduced and described in terms of the patterns they typically produce in the market’s graph representation. On a macro scale, we use a spectral clustering method based on the eigensystem of complex Hermitian adjacency matrices to characterize the trading behavior of the traders and thus characterize the market. Thereby, we can show the gap between the formal definition of the market and the actual behavior within the market where deviations from the allowed trading behavior can be made visible. These questions are for instance relevant with respect to the forecast efficiency of experimental stock markets since manipulations tend to decrease the precision of the market’s results. To demonstrate this we show some results of the analysis of a political stock market that was set up for the 2006 state parliament elections in Baden-Wuerttemberg, Germany."
},
{
"role": "assistant",
"content": "Most of the work on @math are concentrated on stock market trading. In [3] , [5] , [2] , [4] and [1] the authors have investigated on @math and other related collusion techniques used in stock market trading. A brief overview on some of these techniques is given below."
}
] |
science.genia_ner
|
science.genia_ner.244
|
[
{
"role": "user",
"content": "You will be shown an abstract from a biomedical research paper. Given this abstract, your task is to extract all unique entities of the following types: [\"RNA\", \"CellLine\", \"Protein\", \"DNA\", \"CellType\"].\n\nPlease return the output as a JSON object of the format: {\"DNA\" : [\"TAL1\", ...], \"RNA\": [\"mRNAs\", ...], \"CellLine\": [\"T cells\", ...], \"CellType\": [\"monocytes\", ...], \"Protein\": [\"IL-2\", ...]}. The keys should be entity types and values should be lists of extracted entities belonging to the corresponding type. If you cannot find entities belonging to a specific type, the value should be [].\n\nOnly output the JSON object and do not include any additional text.\n\nAbstract:\n\nFunctional block for 1 alpha, 25-dihydroxyvitamin D3-mediated gene regulation in human B lymphocytes. Elements necessary for the steroid hormone 1 alpha, 25-dihydroxyvitamin D3 (1 alpha, 25- (OH) 2D3) to induce a biological response include the presence of specific intracellular receptors (vitamin D3 receptors (VDR)) and modulation of gene expression via hormone-activated receptor binding to regulatory regions of target genes. These parameters were examined in normal and Epstein-Barr virus-immortalized human B cells and compared with 1 alpha, 25- (OH) 2D3-responsive cells of the T and monocytic lineages. Although resting tonsillar B cells did not express VDR mRNA, activation of these cells with interleukin-4 induced VDR in the absence of exogenously supplemented 1 alpha, 25- (OH) 2D3. As indicators of hormone-mediated gene regulation we analyzed modulation of CD23, a common B cell / monocyte surface antigen, and 24-hydroxylase. 1 alpha, 25- (OH) 2D3 inhibited CD23 expression in U937 cells, yet failed to modulate CD23 expression in B cells. Furthermore, 1 alpha, 25- (OH) 2D3 induced 24-hydroxylase mRNA expression and metabolic activity in both U937 cells and lectin-activated T cells, yet failed to induce 24-hydroxylase mRNA or its metabolic activity in B cells. These findings suggest that although human B lymphocytes can express VDR mRNA and protein, they exhibit a functional block for vitamin D-dependent gene regulation."
},
{
"role": "assistant",
"content": "{\"CellLine\": [\"U937 cells\", \"Epstein - Barr virus - immortalized human B cells\", \"1 alpha , 25 - (OH) 2D3 - responsive cells\"], \"CellType\": [\"T and monocytic lineages\", \"human B lymphocytes\", \"B cells\", \"lectin - activated T cells\"], \"DNA\": [\"target genes\"], \"Protein\": [\"intracellular receptors\", \"protein\", \"common B cell / monocyte surface antigen\", \"CD23\", \"24 - hydroxylase\", \"interleukin - 4\", \"VDR\", \"vitamin D3 receptors\", \"regulatory regions\"], \"RNA\": [\"24 - hydroxylase mRNA\", \"VDR mRNA\"]}"
}
] |
science.craftchem_ner
|
science.craftchem_ner.9340
|
[
{
"role": "user",
"content": "You will be presented a sentence from biomedical research text. Extract all terms that correspond to chemical entities of biological interest (ChEBI).\nReturn your identified terms in a JSON array, formatted like this: [\"Entity1\", \"Entity2\", ...].\nIf no such entities are detected, respond by providing an empty JSON array [].\n\nBiomedical context:\nRedarrowshowsthebonemarrowcavityin(E)and(I)."
},
{
"role": "assistant",
"content": "[]"
}
] |
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