Digital Commons Network^™

The Effect Of Part-Time Vs Full-Time Integrated Clinical Education On Student Physical Therapists’ Self-Efficacy And Clinical Reasoning, William J. Buchala

Student Dissertations

Integrated clinical education (ICE) varies across Doctor of Physical Therapy (DPT) programs, particularly in the use of part-time and full-time clinical experiences. Limited research has examined relationships between ICE structure, self-efficacy, and clinical reasoning. The purpose of this quantitative ex post facto study was to examine relationships between part-time and full-time ICE models and self-efficacy and self-assessed clinical reasoning in DPT students. Survey responses were collected from DPT students who had participated in ICE experiences. Self-efficacy was measured using the Physical Therapist Self-Efficacy Scale, and self-assessed clinical reasoning was measured using the Self-Assessment of Clinical Reflection and Reasoning Scale. Independent-samples …

Examination Of Maternal Mortality, Mental Health Conditions, And Co-Occurring Factors, Laura Eileen Skaarer

Walden Dissertations and Doctoral Studies

Maternal mortality (MM) continues to be a public health concern in the state of Arizona. There is little to no research investigating the relationship between MM and mental health conditions co-occurring with contributing factors among women who have died in Arizona while pregnant or within 1 year of the end of a pregnancy. The purposes of this quantitative study, guided by the three delays model (3DM), were to examine (a) MM and mental health conditions as the primary underlying cause of death; (b) MM and mental health conditions surrounding death; and (c) significant contributing factors (i.e., discrimination, knowledge, lack of …

Feasibility Of Therapeutic Drumming Intervention For Autistic Youth: An Exploratory Study, Zahava L. Friedman, Dina Prisco, Jorge Ochoa, Talia Nuesi, Carmen Guarino, Patricia Higgins, Danielle Centi

The Open Journal of Occupational Therapy

Background: There is a need to identify a wider variety of neurodiversity-affirming interventions within the scope of occupational therapy. Therapeutic drumming, percussive music-making as a therapeutic intervention, holds potential for occupational therapy practice, though few studies have explored its efficacy with this population. The purpose of this study was to explore the design and effectiveness of therapeutic drumming for autistic youth from perspectives of drumming facilitators to identify relevant outcome variables and usefulness in the study and practice of therapeutic drumming.

Methodology: This exploratory feasibility study recruited twelve facilitators and 10 autistic youth. An occupational therapy graduate student …

The Content Validity Of The Functional Cognition Index In Instrumental Activities Of Daily Living (Fci-Iadl) As A Screening Tool For Mild Cognitive Impairment (Mci) In Older Adults In Singapore, Namrata P. Sadarangani, Phyllis Simon

The Open Journal of Occupational Therapy

Background: Mild Cognitive Impairment (MCI) is a syndrome that is considered a transition phase between healthy cognitive aging and dementia. The person may have subjective memory complaints, substantiated by family or caregiver and/or impaired executive function, that lead to difficulties performing complex Instrumental Activities of Daily Living (IADLs). Our objective was to develop a tool to assess functional cognition in IADLs as a screen for MCI in older adults.

Method: A Qualtrics survey questionnaire was rated by 15 content experts on the relevance of the 22 test item questions to the cognitive domains being measured using a 4-point …

Self-Reported Confidence Of Dpt Students In Assessing And Treating Different Body Regions Within Musculoskeletal Physical Therapy Practice, Scott W. Lowe, Jennifer Wiley

The Journal of Integrated Primary Care

Introduction

This study examined Doctorate of Physical Therapy (DPT) students' self-reported confidence in assessing and treating musculoskeletal (MSK) conditions based on body regions. We hypothesized that there would be identifiable differences in self-perceived confidence across the different body regions. Most literature assessing DPT students' readiness for clinical practice has come from the perspective of educators and clinicians, whereas student perspectives have not been reported.

Methods:

The study is a descriptive, observational online survey.  Participants were final-year DPT students in the United States. Participants rated their comfort level in assessing and treating patients with MSK complaints, both in general and specifically …

Small Cell Lung Cancer In A Never-Smoking Patient: A Case Highlighting Diagnostic And Screening Gaps In Primary Care, Edward Hamilton, Alexandra She, Francis Jenney

The Journal of Integrated Primary Care

Small cell lung cancer (SCLC) is best known in relation to tobacco exposure and tends to be seen in advanced disease. Contemporary guidelines in lung cancer screening demonstrate a strong emphasis on smoking exposure, which may serve as a barrier to recognition in never-smokers who lack conventional risk factors. As a result, SCLC in never-smokers remains an important but underrecognized consideration in general and primary care settings. The current case involves a 65-year-old African American man who has never been a smoker but who presented with progressive thoracic pain, shortness of breath, and unintended weight loss, leading to the discovery …

Grated Green Apple And Its Therapeutic Role In Gastrointestinal Disorders: An Analytical Study Of The Effect Of Pectin In Alleviating Diarrhea, Hamza A Saadallah, Mohammed. Ahb. Al-Krdoshi, Noor M Sultan, Farah Y Gaddawi, Marwa R. S Al Shaaban, Abd Al-Bar Al-Farha, Safa M Salim

BioMed Visions Journal

Gastrointestinal disorders, including diarrhea, represent a significant global health burden, necessitating the exploration of effective and accessible therapeutic strategies. Dietary interventions, particularly those containing soluble fibers such as pectin, have emerged as promising solutions due to their profound impact on gut health and its microbiota. This meta-analysis systematically reviews the current scientific understanding of the multifaceted role of pectin in alleviating diarrhea, with a particular focus on the unique contribution of grated green apple. The analysis delves into pectin's physicochemical properties and mechanisms of action—including water binding, modulation of the gut microbiota, production of short-chain fatty acids, and support of …

Pharmacy Students' Perceptions And Attitudes Toward Online Learning: Insights From A Cross-Sectional Study In Iraq, Heba M. Attash, Luma M. Al-Obaidy, Harith Kh. Al-Qazaz, Fahad Saleem

BioMed Visions Journal

Background: The rapid shift to online learning during the pandemic has reshaped pharmacy education in Iraq, yet student perceptions remain underexplored. This study examines how pharmacy students view online and hybrid models, with attention to gender, location, and access to technology. Method: A cross-sectional online survey was conducted between October 2024 and January 2025 with 386 fourth- and fifth-year pharmacy students from differrent universities across Iraq. Data were collected using a structured questionnaire adapted from validated tools, assessing demographics, learning preferences, and attitudes toward digital education. Descriptive and inferential statistics were analyzed using SPSS version 25. Results: Most participants were …

A Systematic Literature Review Of Cvid Reveals Pervasive Detrimental Noninfectious Manifestations, Robert B Lindell, Samir U Sayed, Jose S Campos Duran, Sydney A Sheetz, Apoorva Babu, Montana S Knight, Andrea A Mauracher, Ceire A Hay, Peyton E Conrey, Julie C Fitzgerald, Nadir Yehya, Stephen T Famularo, Teresa Arroyo, Richard Tustin, Hossein Fazelinia, Edward M Behrens, David T Teachey, Lisa R Forbes Satter, Alexandra F Freeman, Jenna Re Bergerson, Steven M Holland, Jennifer W Leiding, Scott L Weiss, Mark W Hall, Deanne M Taylor, Rui Feng, E John Wherry, Nuala J Meyer, Sarah E Henrickson

Faculty, Staff and Students Publications

BACKGROUND

Sepsis is a leading cause of morbidity and mortality in critically ill children, yet heterogeneous immune responses complicate the development of targeted therapies and the host immune factors driving sepsis pathobiology remain unclear.

METHODS

We integrated deep immune phenotyping, plasma proteomics, single-cell transcriptomics, and phosphoflow cytometry in a prospective cohort of 88 critically ill children to elucidate the mechanisms underlying immune heterogeneity.

RESULTS

Unsupervised clustering of plasma cytokines identified 3 immunologic subgroups, including a high-severity group (“Group C”) characterized by hypercytokinemia driven by IL-6 and IFN-γ. Group C exhibited distinct alterations in immune cell frequency and activation, with a …

Perception Of Substance Addiction Among Medical Students Of Al-Zahraa College Of Medicine In Basrah, 2023, Jhood Abdul Samad Molan, Ziyad Tariq Maki, Anfal Mohammed, Fatima Hani Jaber, Noor Alhuda Abdul Wahab, Noor Alhuda Hameed, Noor Riyadh

Iraqi National Journal of Medicine

Background: Substance abuse is a persistent global problem. It can have multiple effects on behavioral and cognitive functions and may lead to psychological symptoms. This global epidemic not only harms individual health but also adversely affects the psychological and moral well-being of society. The prevalence of substance abuse is increasing worldwide, with a more rapid rise in developing countries. Youth constitutes the primary population at risk for substance abuse in each country. Aim: The study aimed to assess substance use-related literacy among the second and fifth-year students of Al-Zahraa College of Medicine in Basrah. Methods: This study included 158 second- …

Prevalence Of Cerebrovascular Disease In Patients With Coronary Artery Disease After Pharmacological Stress Test, Eman Mahmoud Abdelfattah, Muhammad Salem Muhammad Hagrass, Khalid Ahmed Elkhashab, Sameh Emil, Hassan Mohamed Ebeid, Lamya Salih, Najah Makhbout Al-Amri, Mostafa Sayed, Haytham Soliman Ghareeb

Journal of the Saudi Heart Association

Objectives: Coronary artery disease (CAD) and cerebrovascular disease (CVD) share common atherosclerotic pathways. However, the clinical significance of headache absence during stress testing remains unexplored. We investigated whether the absence of headache during pharmacological stress testing reflects the presence of subtle cerebrovascular atherosclerosis detectable by transcranial Doppler ultrasonography (TCD).

Methods: This cross-sectional study enrolled 225 patients with CAD undergoing pharmacological stress testing with TCD and myocardial perfusion imaging (MPI) at centers in Egypt (Cardiology Department, Fayoum University). Patients were stratified by headache status during stress testing. Multivariate logistic regression and receiver-operating characteristic (ROC) analysis identified independent predictors of abnormal TCD …

Llm-As-A-Judge For Infection Prevention And Control And Antimicrobial Resistance Impact: Comparing Three Main Llms Vs. Human Experts' Assessment, Marcello Di Pumpo, Leonardo Villani, Maria Rosaria Gualano, Danilo Buonsenso, Francesca Raffaelli, Daniele Donà, Patrizia Laurenti, Vittorio Maio, Stefania Boccia, Walter Ricciardi

College of Population Health Faculty Papers

BACKGROUND: Large language models (LLMs) are increasingly used to generate health information, yet their reliability as evaluators remains unclear. This study investigated the feasibility of an LLM-as-a-judge methodology in the context of infection prevention and antimicrobial resistance (AMR), comparing automated ratings with human expert benchmarks.

METHODS: We performed a secondary analysis of an expert-annotated dataset of health messages. Three leading LLMs (ChatGPT, Claude, Gemini) independently evaluated the same messages using an adapted DISCERN tool across five domains: information reliability, quality, AMR impact, persuasiveness, and overall score. We utilized descriptive statistics, intra-rater reliability tests, and mixed-effects ordinal regression to analyze divergence …

Comments Re: Regulation For Federal Financial Assistance, Fred D. Ledley, Edward Zhou, Brian C. Fox

CISI Publication

This comment focuses on the proposed modifications to §200.205 “Federal Agency Merit Review of Proposals” and §200.340 “Termination and suspension” of Title 2 of the Code of Federal Regulations. We argue that the pre-issuance review, discretionary termination provisions, and other constraints of federal research support that would be established under this proposal create impediments to the scientifically-driven process of discovery and innovation that has long provided the foundation for advances in American prosperity, influence, health, and wellbeing. Our comments focus specifically on federal support for biomedical research by the National Institutes of Health (NIH) for the purpose of advancing healthcare …

Nurses’ Knowledge And Practices Regarding Infection Prevention Measures In Cardiac Intensive Care Unit, Marwa G. Abouheiba, Maha Adel Salem, Jean Bertin Mudenge

Nursing

Abstract: Background: Healthcare-associated infections (HAIs) remain a major global patient safety challenge, contributing substantially to morbidity, mortality, prolonged hospitalization, antimicrobial resistance, and increased healthcare costs. Patients admitted to cardiac intensive care units (ICUs) are particularly vulnerable because of their critical illness, frequent exposure to invasive devices, and complex cardiovascular interventions. Nurses play a pivotal role in preventing HAIs through the consistent implementation of evidence-based infection prevention and control (IPC) measures. Therefore, assessing both nurses' knowledge and their observed clinical practices is essential for identifying strengths, potential gaps, and opportunities for quality improvement. Aim: To assess nurses' knowledge and observed practices …

Depression And Anxiety In Pulmonary Hypertension Associated With Congenital Heart Disease: Pathophysiology And Clinical Implications Of The Heart–Brain Axis, Nicodemus N. Triatmojo, Valerinna Y.S. Putri

Journal of the Saudi Heart Association

Pulmonary hypertension associated with congenital heart disease or PH-CHD is an increasingly prevalent disorder in modern cardiology. It is characterized by progressive pulmonary vascular remodeling, chronic right ventricular (RV) pressure overload, and abnormal cardiopulmonary hemodynamic. Due to advances in congenital cardiology and treatments for pulmonary hypertension, survival rates have increased. As a result, the focus has switched to long-term functional status and quality of life. Depression and anxiety are currently recognized as prevalent and clinically significant manifestations in PH-CHD; nonetheless, they remain underdiagnosed and undertreated within cardiovascular care frameworks.

More study shows the disease's severity or symptom count cannot explain …

A Phase Ii Trial Of Defactinib Combined With Avutometinib In Patients With Metastatic Uveal Melanoma, Rino S. Seedor, Mizue Terai, Sergei A. Koshkin, Andrew E. Aplin, Marlana Orloff, Erin Sharpe-Mills, Madeleine Naccarato, Aurora Mills, Alfredo A. Molinolo, J. Silvio Gutkind, Takami Sato

Kimmel Cancer Center Faculty Papers

Background: Treatment options are limited, and outcomes remain poor for patients with metastatic uveal melanoma (MUM). We conducted an investigator-initiated, prospective, single-arm, single-institution, phase II study evaluating the combination of an FAK inhibitor (defactinib) with a RAF/MEK inhibitor (avutometinib) for the treatment of MUM. Methods: From February 2021 through January 2023, 12 patients with MUM were treated with the combination of defactinib and avutometinib. Defactinib was given 200 mg twice daily, and avutometinib was given 3.2 mg twice a week. Both drugs were given for 3 weeks on and 1 week off (28-day cycle). Disease control rate was the primary …

Signal And Substance: Why Methodological Sophistication Fails To Guarantee Inference, Aamir Rashid, Rizwana Rasheed

Publications and Research

Despite increasing analytical sophistication, empirical research in organization studies continues to suffer from fragile inference, uneven theoretical accumulation, and contested credibility. This paper seeks to explain why these problems persist by shifting attention from authors’ methodological choices to the evaluative dynamics of peer review. Adopting a conceptual and theory-analytic approach, the paper theorizes peer review as an inferential gatekeeping system. Drawing on research design, theory evaluation, and philosophy-of-science literatures, this study develops an analytical framework to examine how evaluative routines shape what constitutes empirical rigor during the review process. The analysis identifies five recurring reviewer blind spots: inferential scope inflation, …

Fall Prevention Education Among Older Adults At Townson Assisted Living Facility (Talf), Yolana Farrell-Williams

Walden Dissertations and Doctoral Studies

Falls in the elderly are a significant cause of injury, disability, and preventable medical expenditure; thus, fall prevention is an issue to assisted living homes like Townson Assisted Living Facility (TALF). The internal incident reports showed that persistent fall incidents were associated with inconsistent knowledge among the staff and unequal observed compliance with fall-prevention guidelines, indicating a practice gap in the systematized education of nurses. Educational interventions are effective in achieving high-quality staff, adherence to protocols, and outcomes concerning falls. Consequently, the current project was conducted to determine whether a specialized falls-prevention education program would enhance the knowledge and competency …

The Association Between Food Insecurity, Housing Insecurity, Self-Care Practice And Depression Among Black Immigrants In The United States, Beatrice Ngozi Mbaocha

Walden Dissertations and Doctoral Studies

The prevalence and poor prognosis of depressive symptoms remain significant among adult Black immigrants in the United States. This study examined the complex interplay between food insecurity, housing insecurity, self-care practices, and depression among adult Black immigrants in the United States. Grounded in the socioecological model, this quantitative cross-sectional study analyzed data from N = 469 noninstitutionalized Black immigrant adults (54.2% female, 45.8% male) using the 2023 National Health Interview Survey. Binary logistic regression was employed to assess the probability of depressive symptoms as a function of food insecurity, housing insecurity, and self-care practices, controlling for age, gender, and employment …

Evaluation Of Diclazuril And Amprolium Against Eimeria Spp. In Vietnamese Broilers: Implications For Intestinal Integrity And Claudin Gene Expression, Nguyen Thi Hoa, Pham Hoang Son Hung, Le Dinh Phung, Le Duc Thao, Nguyen Van Chao, Tran Thi Na, Tran Cao My Linh, Ho Thi Dung

The Thai Journal of Veterinary Medicine

This study aimed to assess the resistance status of Eimeria spp. in Vietnam to diclazuril and amprolium and to evaluate their effects on intestinal recovery following infection. One hundred 12-day-old chicks were randomly allotted to four groups: a non-infected negative control (NC), an infected untreated as positive control (PC), an infected group treated with diclazuril (DI), and an infected group treated with amprolium (AM). At day 14, chicks from all groups except NC were orally challenged with 2 × 10⁴ sporulated Eimeria oocysts (E. tenella, E. maxima, E. acervulina, and E. mitis). On day 7 …

Phenomenological Analysis Of Trust In Science For The Design Of Ai-Based Health And Social Policies, Kochav Koren

All Duquesne Faculty Scholarship

The promises of artificial intelligence (AI) as a solution to challenges facing health systems increasingly link technological innovation with improvements in efficiency and access. However, the legitimacy of AI-supported health policies depends not only on scientific competence but also on public trust in scientific institutions. Using data from the international Trust in Science Project (71,922 respondents across 68 countries), this study analyses multidimensional trust and communication ecologies to reconstruct relational configurations of trust, termed ‘Figures of Relevance’. Findings reveal that whilst scientific competence is widely recognised, perceptions of institutional openness vary markedly, shaping heterogeneity in trust. The study identifies four …

Multiple Event Segmentation Mechanisms In The Human Brain, Tan T Nguyen, Joset A Etzel, Matthew A Bezdek, Jeffrey M Zacks

2020-Current year OA Pubs

The human brain segments continuous experience into discrete events, with theoretical accounts proposing two distinct mechanisms: creating boundaries at points of high

Association Between Trainee Involvement During Pediatric And Congenital Cardiac Catheterization And Procedural Outcomes., Natalie Jayaram, John A. Spertus, Kevin F. Kennedy, Andrew C. Glatz

Manuscripts, Articles, Book Chapters and Other Papers

BACKGROUND: Participation in the cardiac catheterization laboratory is a requirement of cardiology fellowship training. We sought to determine whether trainee presence is associated with outcomes during pediatric and congenital cardiac catheterization.

METHODS: We identified catheterizations between January 2011 and September 2020 within the IMPACT (Improving Pediatric and Adult Congenital Treatment) Registry. Multivariable multilevel regression was used to determine the association between trainee presence and procedural outcomes.

RESULTS: Of 122 760 catheterizations at 107 academic hospitals, a trainee was present in 71 651 (58.4%) cases. Rates of major adverse events were similar between trainee and nontrainee cases (9.0% versus 8.0%). Contrast …

Urinary Incontinence's Prevalence, Risk Factors, And Quality Of Life Impact On Working Women In Saudi Arabia, Ahmed Mansor, Hatim Tagalsir Osman Ali, Maha Ali, Arwa Abd Al Salam Ashry, Ghala Abdullah Alharbi, Khalid Albasheer, Omer Munder, Isam Mohamed Babbiker Ahmed

Saudi Medical Journal

Background: This study aimed to investigate the prevalence and severity of Urinary incontinence (UI) among working women in Saudi Arabia (SA), identify the associated demographic, lifestyle, medical, and obstetric risk factors, and assess its effect on quality of life and work productivity. The UI is a common underreported condition that affects women's daily functioning and life quality, particularly in the workplace. Methods: During 2025, 390 working women in SA who were at least 18 years old and from various work sectors participated in a descriptive cross-sectional survey. Data were gathered using a validated, structured questionnaire; statistical analysis was carried out …

Artificial Intelligence In Pharmaceutical Care: Transforming Drug Discovery, Development, And Patient-Care Delivery, Abdulrahman G. Alharbi, Abdulrahman A. Aljabri

Saudi Medical Journal

The integration of artificial intelligence (AI) into pharmaceutical care represents a paradigm shift in healthcare delivery, offering unprecedented opportunities to revolutionize medication management, accelerate drug development, and enhance patient outcomes. This comprehensive review synthesized evidence from global literature (2021–2025) examining AI applications across drug discovery and development, clinical trials optimization, medication therapy management, and pharmacy operations. The AI demonstrated prediction accuracies of 86–98% in drug discovery, 80% improvement in clinical trial recruitment efficiency, and 32.7% increase in medication adherence over standard care. The global AI drug discovery market, valued at \$1.5 billion (2023), is projected to reach \$11.8 billion by …

Healthcare-Associated Infection Causes And Mitigation Strategies: A Systematic Review, Mohammad Irfan, Nahed Alquwez

Saudi Medical Journal

Objective: To describe the landscape of healthcare-associated infections (HAI) and, in particular, to pay attention to the types of infection that are usually seen, the most common infectious agents involved and the effective prevention strategies. Methods: A detailed search was performed using Google and PubMed, and studies that exclusively addressed healthcare associated infections or their mitigation. Studies published since 2000 were included. Data from individual articles were extracted and categorized by study focus, type of infection, causes and contributing factors, and documented mitigation strategies. Editorials, reviews, case studies, meta-analyses, and systematic reviews were excluded. Results: The analysis showed that infections …

The Role Of The Nlrp3 Inflammasome In Preeclampsia And Implantation Failure: A Molecular Review, Ari Budi Suryawinata, Mariel Tania Darmayani, Listyani Suhargo

Chulalongkorn Medical Journal

The NOD-like receptor family pyrin domain containing 3 (NLRP3) inflammasome is a critical multiprotein complex of the innate immune system that functions as a molecular sensor for a wide array of danger signals. While its activation is essential for host defense and tissue homeostasis, its dysregulation is increasingly implicated in the pathophysiology of numerous inflammatory disorders. This review article synthesizes the current molecular understanding of the NLRP3 inflammasome, focusing on its dual role in health and disease. We first provide a concise overview of the canonical two-step mechanism of NLRP3 activation and the intricate molecular checkpoints including genetic factors, post-translational …

Subunit Composition Of The Katp Channels That Modulate Contractility Of Skeletal Muscle During Fatigue, Rosa Scala, Yuezhou Chen, Berk Mizrak, Gretchen A Meyer, Colin G Nichols

2020-Current year OA Pubs

ATP-sensitive potassium (KATP) channels are among the most expressed ion channels in skeletal muscle sarcolemma. While all KATP subunits can be detected in skeletal muscles, transcripts are enriched for KCNJ11 and ABCC9, suggesting that noncanonical Kir6.2/SUR2A assembly may constitute the majority of sarcolemmal KATP channels, but there has been no systematic dissection of KATP makeup in skeletal muscles. Here, we used a unique collection of murine lines selectively lacking specific channel-forming subunits (knockout, KO), and combined a genetic and pharmacological approach to determine which subunits of KATP channels are functionally relevant for skeletal muscle contraction. Under fatiguing conditions, isometric tetanic …

Aberrant Ciliogenesis Induced By Enhanced Bmp Signaling Causes Heterotopic Ossification, Hiroyuki Yamaguchi, Jianbo Wang, Fangfang Yan, Jiarui Bi, Radbod Darabi, William R. Lagor, Zhongming Zhao, Aris N. Economides, Yuji Mishina, Yoshihiro Komatsu

Faculty, Staff and Student Publications

Bone morphogenetic protein (BMP) signaling is a principal driver of heterotopic ossification (HO), yet how aberrant BMP activity structurally reprograms cellular signaling machinery to develop HO remains unclear. Here, we identify BMP signaling as a direct upstream regulator of ciliogenesis that coordinates a multi-stage, pro-osteochondrogenic signaling relay during HO. Using a conditional gain-of-function BMP mouse model (Acvr1Q207D/+), we demonstrate that enhanced BMP signaling promotes primary cilium biogenesis and axonemal elongation through canonical Smad1/5/9-dependent transcriptional activation of intraflagellar transport (IFT) Ift20, a core component of the IFT machinery. Rather than operating via a singular downstream cascade, these elongated …

Advancing Bioinformatics With Language Models: Components, Applications, And Perspectives, Jiajia Liu, Mengyuan Yang, Yankai Yu, Haixia Xu, Tiangang Wang, Kang Li, Xiaobo Zhou

Faculty, Staff and Student Publications

Large language models (LLMs) are deep learning-based artificial intelligence models that have achieved remarkable success in natural language processing. Typically composed of neural networks with billions of parameters, they are trained on massive unlabeled datasets using self-supervised or semi-supervised learning. Beyond language, LLMs hold immense potential for addressing complex bioinformatics challenges. This review provides a comprehensive overview of transformer-based model applications in genomics, transcriptomics, proteomics, drug discovery, and single-cell analysis. We discuss critical components, including tokenization strategies for diverse biological data, transformer architectures, attention mechanisms, and pretraining approaches. We also survey currently available foundation models and their downstream applications across …