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Article ; Online: Answering List-Type Questions in Health Domain with Pretrained Large Language Model: A Case for COVID-19 Symptoms.

Jiang, Keyuan / Mujtaba, Mohammed M / Bernard, Gordon R

Studies in health technology and informatics

2024 Volume 310, Page(s) 629–633

Abstract: List-type questions, which can have a varying number of answers, are more common in the health domain where people seek for health-related information from a passage or passages. An example of this type of question answering task is to find COVID-19 ... ...

Abstract	List-type questions, which can have a varying number of answers, are more common in the health domain where people seek for health-related information from a passage or passages. An example of this type of question answering task is to find COVID-19 symptoms from a Twitter post. However, due to the lack of annotated instances for supervised learning, automatic identification of COVID-19 symptoms from Twitter posts is challenging. We investigated detection of symptom mentions in Twitter posts using GPT-3, a pre-trained large language model, along with few-shot learning. Our results of 5-shot and 10-shot learning on a corpus of 655 annotated tweets demonstrate that few-shot learning with pre-trained large language model is a promising approach to answering list-type questions with a minimal amount of effort of annotation.
MeSH term(s)	Humans ; COVID-19 ; Language
Language	English
Publishing date	2024-01-25
Publishing country	Netherlands
Document type	Journal Article
ISSN	1879-8365
ISSN (online)	1879-8365
DOI	10.3233/SHTI231041
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Large Language Model as Unsupervised Health Information Retriever.

Jiang, Keyuan / Mujtaba, Mohammed M / Bernard, Gordon R

Studies in health technology and informatics

2023 Volume 302, Page(s) 833–834

Abstract: Retrieving health information is a task of search for health-related information from a variety of sources. Gathering self-reported health information may help enrich the knowledge body of the disease and its symptoms. We investigated retrieving symptom ... ...

Abstract	Retrieving health information is a task of search for health-related information from a variety of sources. Gathering self-reported health information may help enrich the knowledge body of the disease and its symptoms. We investigated retrieving symptom mentions in COVID-19-related Twitter posts with a pretrained large language model (GPT-3) without providing any examples (zero-shot learning). We introduced a new performance measure of total match (TM) to include exact, partial and semantic matches. Our results show that the zero-shot approach is a powerful method without the need to annotate any data, and it can assist in generating instances for few-shot learning which may achieve better performance.
MeSH term(s)	Humans ; COVID-19 ; Social Media ; Language ; Semantics ; Natural Language Processing
Language	English
Publishing date	2023-05-19
Publishing country	Netherlands
Document type	Journal Article
ISSN	1879-8365
ISSN (online)	1879-8365
DOI	10.3233/SHTI230282
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Article ; Online: Extraction of Medication-Effect Relations in Twitter Data with Neural Embedding and Recurrent Neural Network.

Jiang, Keyuan / Zhang, Dingkai / Bernard, Gordon R

Studies in health technology and informatics

2022 Volume 290, Page(s) 767–771

Abstract: Recently, an active area of research in pharmacovigilance is to use social media such as Twitter as an alternative data source to gather patient-generated information pertaining to medication use. Most of thr published work focuses on identifying ... ...

Abstract	Recently, an active area of research in pharmacovigilance is to use social media such as Twitter as an alternative data source to gather patient-generated information pertaining to medication use. Most of thr published work focuses on identifying mentions of adverse effects in social media data but rarely investigating the relationship between a mentioned medication and any mentioned effect expressions. In this study, we treated this relation extraction task as a classification problem, and represented the Twitter text with neural embedding which was fed to a recurrent neural network classifier. The classification performance of our method was investigated in comparison with 4 baseline word embedding methods on a corpus of 9516 annotated tweets.
MeSH term(s)	Drug-Related Side Effects and Adverse Reactions ; Humans ; Information Storage and Retrieval ; Neural Networks, Computer ; Pharmacovigilance ; Social Media
Language	English
Publishing date	2022-06-08
Publishing country	Netherlands
Document type	Journal Article
ISSN	1879-8365
ISSN (online)	1879-8365
DOI	10.3233/SHTI220182
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Article ; Online: Giants in Chest Medicine: Arthur P. Wheeler, MD, FCCP.

Bernard, Gordon R

Chest

2016 Volume 149, Issue 5, Page(s) 1126–1127

MeSH term(s)	Critical Care/history ; Education, Medical/history ; History, 20th Century ; History, 21st Century ; Humans ; Teaching/history
Language	English
Publishing date	2016
Publishing country	United States
Document type	Biography ; Editorial ; Historical Article ; Portraits ; Video-Audio Media
ZDB-ID	1032552-9
ISSN	1931-3543 ; 0012-3692
ISSN (online)	1931-3543
ISSN	0012-3692
DOI	10.1016/j.chest.2016.02.645
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Article ; Online: Quantitative assessment of the impact of standard agreement templates on multisite clinical trial start up time.

Lawrence, Colleen E / Bruce, Virginia Nickie M / Salberg, Libby D / Edwards, Terri / Morales, Casi / Palm, Marisha / Bernard, Gordon R

Journal of clinical and translational science

2023 Volume 7, Issue 1, Page(s) e204

Abstract: Contracting delays remain a challenge to the successful initiation of multisite clinical research in the US. The Clinical and Translational Science Awards (CTSA) Contracts Processing Study showed average contract negotiation duration of > 100 days for ... ...

Abstract	Contracting delays remain a challenge to the successful initiation of multisite clinical research in the US. The Clinical and Translational Science Awards (CTSA) Contracts Processing Study showed average contract negotiation duration of > 100 days for industry-sponsored or investigator-initiated contracts. Such delays create enormous costs to sponsors and to patients waiting to use new evidence-based treatments. With support from the National Institutes of Health's National Center for Advancing Translational Sciences, the Accelerated Clinical Trial Agreement (ACTA) was developed by 25 major academic institutions and medical centers engaged in clinical research in collaboration with the University-Industry Demonstration Partnership and with input from pharmaceutical companies. The ACTA also informed the development of subsequent agreements, including the Federal Demonstration Partnership Clinical Trial Subaward Agreement (FDP-CTSA); both ACTA and the FDP-CTSA are largely non-negotiable agreements that represent pre-negotiated compromises in contract terms agreed upon by industry and/or medical center stakeholders. When the involved parties agree to use the CTSA-developed and supported standard agreement templates as a starting point for negotiations, there can be significant time savings for trials. Use of the ACTA resulted in an average savings of 48 days and use of the FDP-CTSA saved an average of 57 days of negotiation duration.
Language	English
Publishing date	2023-09-06
Publishing country	England
Document type	Journal Article
ISSN	2059-8661
ISSN (online)	2059-8661
DOI	10.1017/cts.2023.622
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Article: Taking AIM at serious illness: implementing an access to investigational medicines expanded access program.

Joly, Meghan Morrison / Edwards, Terri L / Jerome, Rebecca N / Mainor, Alex / Bernard, Gordon R / Pulley, Jill M

Frontiers in medicine

2023 Volume 10, Page(s) 1287449

Abstract: When seriously ill patients have exhausted all treatment options available as part of usual care, the use of investigational agents may be warranted. Food and Drug Administration's (FDA) Expanded Access (EA) pathway provides a mechanism for these patient' ...

Abstract	When seriously ill patients have exhausted all treatment options available as part of usual care, the use of investigational agents may be warranted. Food and Drug Administration's (FDA) Expanded Access (EA) pathway provides a mechanism for these patient's physicians to pursue use of an investigational agent outside of a clinical trial when trial enrollment is not a feasible option. Though FDA has recently implemented processes to significantly streamline the regulatory portion of the process, the overall pathway has several time-consuming components including communication with the pharmaceutical company and the associated institutional requirements for EA use (contracting, Institutional Review Board [IRB], pharmacy, billing). Here, we present our experience building infrastructure at the Vanderbilt University Medical Center (VUMC) to support physicians and patients in pursuing EA, called the Access to Investigational Medicines (AIM) Platform, aligning the needs and responsibilities of institutional stakeholders and streamlining to ensure efficiency and regulatory compliance. Since its launch, the AIM team has experienced steady growth, supporting 40 EA cases for drugs/biologics, including both single patient cases and intermediate-size EA protocols in the emergent and non-emergent setting. As the EA pathway is a complex process that requires expert facilitation, we propose prioritizing EA support infrastructure at major academic medical centers as an essential regulatory knowledge function.
Language	English
Publishing date	2023-10-09
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2775999-4
ISSN	2296-858X
ISSN	2296-858X
DOI	10.3389/fmed.2023.1287449
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Article ; Online: Repurposing N-acetylcysteine for management of non-acetaminophen induced acute liver failure: an evidence scan from a global health perspective.

Jerome, Rebecca N / Zahn, Laura A / Abner, Jessica J / Joly, Meghan M / Shirey-Rice, Jana K / Wallis, Robert S / Bernard, Gordon R / Pulley, Jill M

Translational gastroenterology and hepatology

2024 Volume 9, Page(s) 2

Abstract: Background: The World Health Organization (WHO)'s Essential Medicines List (EML) plays an important role in advocating for access to key treatments for conditions affecting people in all geographic settings. We applied our established drug repurposing ... ...

Abstract	Background: The World Health Organization (WHO)'s Essential Medicines List (EML) plays an important role in advocating for access to key treatments for conditions affecting people in all geographic settings. We applied our established drug repurposing methods to one EML agent, N-acetylcysteine (NAC), to identify additional uses of relevance to the global health community beyond its existing EML indication (acetaminophen toxicity). Methods: We undertook a phenome-wide association study (PheWAS) of a variant in the glutathione synthetase ( Results: PheWAS of Conclusions: This body of literature indicates efficacy and safety of NAC in non-acetaminophen induced ALF. Given the presence of NAC on the EML, this medication is likely to be available across a range of resource settings; promulgating its use in this novel subset of ALF can provide healthcare professionals and patients with a valuable and safe complement to supportive care for this disease.
Language	English
Publishing date	2024-01-18
Publishing country	China
Document type	Journal Article
ISSN	2415-1289
ISSN (online)	2415-1289
DOI	10.21037/tgh-23-40
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Article ; Online: Systemic inflammation and delirium during critical illness.

Brummel, Nathan E / Hughes, Christopher G / McNeil, J Brennan / Pandharipande, Pratik P / Thompson, Jennifer L / Orun, Onur M / Raman, Rameela / Ware, Lorraine B / Bernard, Gordon R / Harrison, Fiona E / Ely, E Wesley / Girard, Timothy D

Intensive care medicine

2024

Abstract: Purpose: The purpose of this study was to determine associations between markers of inflammation and endogenous anticoagulant activity with delirium and coma during critical illness.: Methods: In this prospective cohort study, we enrolled adults with ...

Abstract	Purpose: The purpose of this study was to determine associations between markers of inflammation and endogenous anticoagulant activity with delirium and coma during critical illness. Methods: In this prospective cohort study, we enrolled adults with respiratory failure and/or shock treated in medical or surgical intensive care units (ICUs) at 5 centers. Twice per day in the ICU, and daily thereafter, we assessed mental status using the Richmond Agitation Sedation Scale (RASS) and the Confusion Assessment Method-Intensive Care Unit (CAM-ICU). We collected blood samples on study days 1, 3, and 5, measuring levels of C-reactive protein (CRP), interferon gamma (IFN-γ), interleukin (IL)-1 beta (IL-1β), IL-6, IL-8, IL-10, IL-12, matrix metalloproteinase-9 (MMP-9), tumor necrosis factor-alpha (TNF-α), tumor necrosis factor receptor 1 (TNFR1), and protein C using validated protocols. We used multinomial logistic regression to analyze associations between biomarkers and the odds of delirium or coma versus normal mental status the following day, adjusting for age, sepsis, Sequential Organ Failure Assessment (SOFA), study day, corticosteroids, and sedatives. Results: Among 991 participants with a median age (interquartile range, IQR) of 62 [53-72] years and enrollment SOFA of 9 [7-11], higher concentrations of IL-6 (odds ratio [OR] [95% CI]: 1.8 [1.4-2.3]), IL-8 (1.3 [1.1-1.5]), IL-10 (1.5 [1.2-1.8]), TNF-α (1.2 [1.0-1.4]), and TNFR1 (1.3 [1.1-1.6]) and lower concentrations of protein C (0.7 [0.6-0.8])) were associated with delirium the following day. Higher concentrations of CRP (1.4 [1.1-1.7]), IFN-γ (1.3 [1.1-1.5]), IL-6 (2.3 [1.8-3.0]), IL-8 (1.8 [1.4-2.3]), and IL-10 (1.5 [1.2-2.0]) and lower concentrations of protein C (0.6 [0.5-0.8]) were associated with coma the following day. IL-1β, IL-12, and MMP-9 were not associated with mental status. Conclusion: Markers of inflammation and possibly endogenous anticoagulant activity are associated with delirium and coma during critical illness.
Language	English
Publishing date	2024-04-22
Publishing country	United States
Document type	Journal Article
ZDB-ID	80387-x
ISSN	1432-1238 ; 0340-0964 ; 0342-4642 ; 0935-1701
ISSN (online)	1432-1238
ISSN	0340-0964 ; 0342-4642 ; 0935-1701
DOI	10.1007/s00134-024-07388-6
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Article ; Online: Therapeutic Targets in Sepsis: Past, Present, and Future.

Seeley, Eric J / Bernard, Gordon R

Clinics in chest medicine

2016 Volume 37, Issue 2, Page(s) 181–189

Abstract: Antibiotics and fluids have been standard treatment for sepsis since World War II. Many molecular mediators of septic shock have since been identified. In models of sepsis, blocking these mediators improved organ injury and decreased mortality. Clinical ... ...

Abstract	Antibiotics and fluids have been standard treatment for sepsis since World War II. Many molecular mediators of septic shock have since been identified. In models of sepsis, blocking these mediators improved organ injury and decreased mortality. Clinical trials, however, have failed. The absence of new therapies has been vexing to clinicians, clinical researchers, basic scientists, and the pharmaceutical industry. This article examines the evolution of sepsis therapy and theorizes about why so many well-reasoned therapies have not worked in human trials. We review new molecular targets for sepsis and examine trial designs that might lead to successful treatments for sepsis.
MeSH term(s)	Anti-Bacterial Agents/therapeutic use ; Humans ; Sepsis/drug therapy ; Shock, Septic/drug therapy
Chemical Substances	Anti-Bacterial Agents
Language	English
Publishing date	2016
Publishing country	United States
Document type	Journal Article ; Review ; Comment
ZDB-ID	447455-7
ISSN	1557-8216 ; 0272-5231
ISSN (online)	1557-8216
ISSN	0272-5231
DOI	10.1016/j.ccm.2016.01.015
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Article ; Online: The definition of ARDS revisited: 20 years later.

Bernard, Gordon R / Artigas, Antonio

Intensive care medicine

2016 Volume 42, Issue 5, Page(s) 640–642

MeSH term(s)	Biomarkers ; Consensus Development Conferences as Topic ; Humans ; Positive-Pressure Respiration ; Respiratory Distress Syndrome, Adult/classification ; Respiratory Distress Syndrome, Adult/diagnostic imaging ; Respiratory Distress Syndrome, Adult/physiopathology ; Respiratory Distress Syndrome, Adult/therapy ; Societies, Medical
Chemical Substances	Biomarkers
Language	English
Publishing date	2016-05
Publishing country	United States
Document type	Editorial
ZDB-ID	80387-x
ISSN	1432-1238 ; 0340-0964 ; 0342-4642 ; 0935-1701
ISSN (online)	1432-1238
ISSN	0340-0964 ; 0342-4642 ; 0935-1701
DOI	10.1007/s00134-016-4281-z
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