Medicine and Health Sciences Commons^™

The Importance Of Family Presence At The Bedside Of Critically Ill Patients, Brenda K. Ramsey

MSN Capstone Projects

The purpose of this paper is to discuss the visitor restrictions on patients and their families during the COVID-19 pandemic. At the beginning of the pandemic, visitation was highly restricted with only telecommunication as a means of “visiting” with your loved one who were hospitalized, especially in the ICU settings. During my research of keeper studies for my capstone project, the articles discussed different forms of communication. The articles discussed interventions such as electronic (e-visits) for physician offices and diaries kept in the ICU for communication between family and staff. Some discussed the effects of visitor restrictions and how it …

Opioid Use Disorder (Oud) And Neonatal Abstinence Syndrome (Nas) Education In An Undergraduate Nursing Program, Tara Flood, Dnp, Rn, Cbc

College of Nursing Posters

Background

In 2018 the American Academy of Nursing urged all nursing schools to adopt curriculum to address the opioid epidemic, although few programs have begun this work.

Minimal background training in nursing school is focused on caring for patients with Opiate use disorder ( OUD) and Neonatal Abstinence Syndrome (NAS) leaving nurses to develop the necessary skills for optimal patient engagement to be formulated in practice. An undergraduate nursing program in an urban setting developed OUD and NAS education into their curriculum.

Undergraduate nursing students are increasingly encountering patients with opioid use disorder in the clinical setting. Previous research indicates …

Addressing Inpatient Substance Use Stigma And Bias: An Examination To Support Training For Healthcare Professionals, Tara Flood, Dnp, Rn, Cbc

College of Nursing Posters

Background

The current opioid crisis is a significant public health issue in the United States, especially amongst women of reproductive age. In the last two decades, the rate of opioid use disorder (OUD) in pregnant women has quadrupled. Women with substance use disorders (SUD) experience more sociodemographic and health disadvantages, pre-existing health conditions, and co-morbid psychiatric diagnoses than their counterparts without SUDs. They are also more likely to experience emergency department visits and hospitalizations during the antenatal period and less likely to utilize prenatal healthcare services.

Acute Inpatient Stabilization Study Primary Stakeholders Evaluation, Tara Flood, Dnp, Rn, Cbc

College of Nursing Posters

Background

The current opioid crisis is a significant public health issue in the United States, especially amongst women of reproductive age. In the last two decades, the rate of opioid use disorder (OUD) in pregnant women has quadrupled. Women with substance use disorders (SUD) experience more sociodemographic and health disadvantages, pre-existing health conditions, and co-morbid psychiatric diagnoses than their counterparts without SUDs. They are also more likely to experience emergency department visits and hospitalizations during the antenatal period and less likely to utilize prenatal healthcare services.

Immunological Monitoring In Hepatitis C Virus Controlled Human Infection Model, Naglaa H Shoukry, Andrea L Cox, Christopher M Walker

Faculty, Staff and Student Publications

Controlled human infection model trials for hepatitis C virus represent an important opportunity to identify correlates of protective immunity against a well-characterized inoculum of hepatitis C virus and how such responses are modified by vaccination. In this article, we discuss the approach to immunological monitoring during such trials, including a set of recommendations for optimal sampling schedule and preferred immunological assays to examine the different arms of the immune response. We recommend that this approach be adapted to different trial designs. Finally, we discuss how these studies can provide surrogate predictors of the success of candidate vaccines.

Evolution Of Immune And Stromal Cell States And Ecotypes During Gastric Adenocarcinoma Progression, Ruiping Wang, Shumei Song, Jiangjiang Qin, Katsuhiro Yoshimura, Fuduan Peng, Yanshuo Chu, Yuan Li, Yibo Fan, Jiankang Jin, Minghao Dang, Enyu Dai, Guangsheng Pei, Guangchun Han, Dapeng Hao, Yating Li, Deyali Chatterjee, Kazuto Harada, Melissa Pool Pizzi, Ailing W Scott, Ghia Tatlonghari, Xinmiao Yan, Zhiyuan Xu, Can Hu, Shaowei Mo, Namita Shanbhag, Yang Lu, Matheus Sewastjanow-Silva, Ahmed Adel Fouad Abdelhakeem, Guang Peng, Samir M Hanash, George A Calin, Cassian Yee, Pawel Mazur, Autumn N Marsden, Andrew Futreal, Zhenning Wang, Xiangdong Cheng, Jaffer A Ajani, Linghua Wang

Faculty, Staff and Student Publications

Understanding tumor microenvironment (TME) reprogramming in gastric adenocarcinoma (GAC) progression may uncover novel therapeutic targets. Here, we performed single-cell profiling of precancerous lesions, localized and metastatic GACs, identifying alterations in TME cell states and compositions as GAC progresses. Abundant IgA+ plasma cells exist in the premalignant microenvironment, whereas immunosuppressive myeloid and stromal subsets dominate late-stage GACs. We identified six TME ecotypes (EC1–6). EC1 is exclusive to blood, while EC4, EC5, and EC2 are highly enriched in uninvolved tissues, premalignant lesions, and metastases, respectively. EC3 and EC6, two distinct ecotypes in primary GACs, associate with histopathological and genomic characteristics, and prognosis. …

Loss Of Syncrip Unleashes Apobec-Driven Mutagenesis, Tumor Heterogeneity, And Ar-Targeted Therapy Resistance In Prostate Cancer, Xiaoling Li, Yunguan Wang, Su Deng, Guanghui Zhu, Choushi Wang, Nickolas A Johnson, Zeda Zhang, Carla Rodriguez Tirado, Yaru Xu, Lauren A Metang, Julisa Gonzalez, Atreyi Mukherji, Jianfeng Ye, Yuqiu Yang, Wei Peng, Yitao Tang, Mia Hofstad, Zhiqun Xie, Heewon Yoon, Liping Chen, Xihui Liu, Sujun Chen, Hong Zhu, Douglas Strand, Han Liang, Ganesh Raj, Housheng Hansen He, Joshua T Mendell, Bo Li, Tao Wang, Ping Mu

Faculty, Staff and Student Publications

Tumor mutational burden and heterogeneity has been suggested to fuel resistance to many targeted therapies. The cytosine deaminase APOBEC proteins have been implicated in the mutational signatures of more than 70% of human cancers. However, the mechanism underlying how cancer cells hijack the APOBEC mediated mutagenesis machinery to promote tumor heterogeneity, and thereby foster therapy resistance remains unclear. We identify SYNCRIP as an endogenous molecular brake which suppresses APOBEC-driven mutagenesis in prostate cancer (PCa). Overactivated APOBEC3B, in SYNCRIP-deficient PCa cells, is a key mutator, representing the molecular source of driver mutations in some frequently mutated genes in PCa, including FOXA1, …

Bacteroides Uniformis-Induced Perturbations In Colonic Microbiota And Bile Acid Levels Inhibit Th17 Differentiation And Ameliorate Colitis Developments, Yiting Yan, Yu Lei, Ying Qu, Zhen Fan, Ting Zhang, Yangbin Xu, Qian Du, Daniel Brugger, Yulin Chen, Ke Zhang, Enping Zhang

Faculty, Staff and Student Publications

Inflammatory bowel disease (IBD) is associated with gut dysbiosis and can lead to colitis-associated malignancies. Bacteroides uniformis (Bu) regulates animal intestinal homeostasis; however, the mechanism by which it alleviates colitis in mice remains unknown. We investigated the effects of B. uniformis JCM5828 and its metabolites on female C57BL/6J mice with dextran sulfate sodium salt (DSS) induced colitis. Treatment with Bu considerably alleviated colitis progression and restored the mechanical and immune barrier protein expression. Additionally, Bu increased the abundance of the symbiotic bacteria Bifidobacterium and Lactobacillus vaginalis while decreasing that of pathogenic Escherichia-Shigella, and modulated intestinal bile acid metabolism. Bu largely …

Environmental Toxins And Their Impact On Neurological Health, Maria Allesandra Elsasser

Master's Projects and Capstones

This paper evaluates the impact of environmental toxins on neurological health from a public health perspective. Employing a comprehensive review of literature across various databases, the study sheds light on the mechanisms through which environmental neurotoxicity influences health, highlighting key correlations between toxin exposure and the onset of neurodegenerative disorders. The research identifies significant gaps in current approaches to managing these risks, particularly concerning policy regulations and public awareness. Based on these findings, strategic recommendations are proposed to address and mitigate the identified challenges, with implications emphasizing the broader benefits for public health.

Community Members’ Experiences Training As Medical Journal Reviewers, Jeri Jewett-Tennant, Kurt C. Stange, Ashwini R. Sehgal

Faculty Scholarship

Purpose: Although medical research dissemination is intended to benefit members of society, few members of society actually participate in the process of publishing findings. This study shares findings from community members’ (including patients and the public) experiences being trained as medical journal reviewers. Methods: We analyzed findings from two focus group interviews of community reviewers (N = 29) to identify themes in their experiences with the training program. Results: Community members trained as journal reviewers appreciated learning the context under which manuscript development and review occur from authors and funders, the value of the community member perspectives to science, and …

Impact Of A Double Catastrophe, War And Covid-19, On Health Service Utilization Of A Tertiary Care Hospital In Tigray: An Interrupted Time-Series Study, Hiluf Ebuy Abraha, L Lewis Wall, Et Al.

2020-Current year OA Pubs

BACKGROUND: In developing nations with fragile healthcare systems, the effect of war is likely to be much worse than it would be in more developed countries. The presence of COVID-19 will also likely exacerbate the war's impact. This study set out to determine the effect of armed conflict and the COVID-19 pandemic on health service utilization at Ayder Comprehensive Specialized Hospital, in the Tigray region of Ethiopia.

METHODS: An interrupted time-series study design was used to analyze patient visits over forty-eight consecutive months (from July 2017 to June 2021) at inpatient, outpatient, and emergency departments. Data were analyzed using segmented …

Analysis Of Superficial Subcutaneous Fat Camper's And Scarpa's Fascia In A United States Cohort, David Z Chen, Aravinda Ganapathy, Yash Nayak, Christopher Mejias, Grace L Bishop, Vincent M Mellnick, David H Ballard

2020-Current year OA Pubs

Together, the Camper's and Scarpa's fasciae form the superficial fat layer of the abdominal wall. Though they have clinical and surgical relevance, little is known about their role in body composition across diverse patient populations. This study aimed to determine the relationship between patient characteristics, including sex and body mass index, and the distribution of Camper's and Scarpa's fascial layers in the abdominal wall. A total of 458 patients' abdominal CT examinations were segmented via CoreSlicer 1.0 to determine the surface area of each patient's Camper's, Scarpa's, and visceral fascia layers. The reproducibility of segmentation was corroborated by an inter-rater …

Using Audit And Feedback To Guide Tailored Implementations Of Measurement-Based Care In Community Mental Health: A Multiple Case Study, Mira D H Snider, Meredith R Boyd, Madison R Walker, Byron J Powell, Cara C Lewis

2020-Current year OA Pubs

BACKGROUND: Audit and feedback (A&F) is an implementation strategy that can facilitate implementation tailoring by identifying gaps between desired and actual clinical care. While there are several theory-based propositions on which A&F components lead to better implementation outcomes, many have not been empirically investigated, and there is limited guidance for stakeholders when applying A&F in practice. The current study aims to illustrate A&F procedures in six community mental health clinics, with an emphasis on reporting A&F components that are relevant to theories of how feedback elicits behavior change.

METHODS: Six clinics from a larger trial using a tailored approach to …

Socio-Economic Determinants Of Gender-Based Violence [Gbv]: Sdg Analytics On The Global Gbv Scenario With Special Reference To Technology Facilitated Gender-Based Violence And Adolescent Birth Rates, Chandra P. Daniel

NYMC Student Theses and Dissertations

Gender-based violence (GBV) is a multifaceted problem. The most rapidly increasing modern form of violence is the intertwined epidemic of ‘Technology Facilitated GBV’ [TF GBV] and sexual violence against women and girls. It was critical to investigate the global impact of this epidemic during COVID-19 since a disproportionate impact of violence was observed among women and girls in low and middle-income countries. A retrospective cross-sectional research design was adopted using linear regression analysis (univariate and multivariate) on SDG 5.2, a set of global indicators, to elicit the socioeconomic determinants of GBV. Phase-I results exposed the top-four socio-economic determinants …

Predicting Pediatric Tuberculosis: The Need For Age-Specific Host Biosignatures, Sara Suliman, Devan Jaganath, Andrew Dinardo

Faculty, Staff and Students Publications

No abstract provided.

Proteogenomic Data And Resources For Pan-Cancer Analysis, Yize Li, Yongchao Dou, Felipe Da Veiga Leprevost, Yifat Geffen, Anna P Calinawan, François Aguet, Yo Akiyama, Shankara Anand, Chet Birger, Song Cao, Rekha Chaudhary, Padmini Chilappagari, Marcin Cieslik, Antonio Colaprico, Daniel Cui Zhou, Corbin Day, Marcin J Domagalski, Myvizhi Esai Selvan, David Fenyö, Steven M Foltz, Alicia Francis, Tania Gonzalez-Robles, Zeynep H Gümüş, David Heiman, Michael Holck, Runyu Hong, Yingwei Hu, Eric J Jaehnig, Jiayi Ji, Wen Jiang, Lizabeth Katsnelson, Karen A Ketchum, Robert J Klein, Jonathan T Lei, Wen-Wei Liang, Yuxing Liao, Caleb M Lindgren, Weiping Ma, Lei Ma, Michael J Maccoss, Fernanda Martins Rodrigues, Wilson Mckerrow, Ngoc Nguyen, Robert Oldroyd, Alexander Pilozzi, Pietro Pugliese, Boris Reva, Paul Rudnick, Kelly V Ruggles, Dmitry Rykunov, Sara R Savage, Michael Schnaubelt, Tobias Schraink, Zhiao Shi, Deepak Singhal, Xiaoyu Song, Erik Storrs, Nadezhda V Terekhanova, Ratna R Thangudu, Mathangi Thiagarajan, Liang-Bo Wang, Joshua M Wang, Ying Wang, Bo Wen, Yige Wu, Matthew A Wyczalkowski, Yi Xin, Lijun Yao, Xinpei Yi, Hui Zhang, Qing Zhang, Maya Zuhl, Gad Getz, Li Ding, Alexey I Nesvizhskii, Pei Wang, Ana I Robles, Bing Zhang, Samuel H Payne

Faculty, Staff and Students Publications

The National Cancer Institute's Clinical Proteomic Tumor Analysis Consortium (CPTAC) investigates tumors from a proteogenomic perspective, creating rich multi-omics datasets connecting genomic aberrations to cancer phenotypes. To facilitate pan-cancer investigations, we have generated harmonized genomic, transcriptomic, proteomic, and clinical data for >1000 tumors in 10 cohorts to create a cohesive and powerful dataset for scientific discovery. We outline efforts by the CPTAC pan-cancer working group in data harmonization, data dissemination, and computational resources for aiding biological discoveries. We also discuss challenges for multi-omics data integration and analysis, specifically the unique challenges of working with both nucleotide sequencing and mass spectrometry …

Successful Return To Sport And Daily Activities After Suture Augmentation Of Both The Anterior Talofibular Ligament And Calcaneofibular Ligament, S Ali Ghasemi, Jetha Tallapaneni, Benjamin C Murray, Clark Yin, James Raphael, Zachary Vaupel, Allan Grant, Paul Fortin

Department of Orthopaedic Surgery Faculty Papers

PURPOSE: To evaluate the return to sport and daily activities in addition to clinical outcomes after modification of the Brostöm repair, specifically using suture augmentation for concomitant fixation of both the anterior talofibular ligament and calcaneofibular ligament.

METHODS: Patients who had grade III ankle sprains and lateral ankle instability, all of whom failed supervised conservative management, were included. Patients underwent a modified Broström procedure consisting of suture augmentation for both the anterior talofibular ligament and calcaneofibular ligament. For clinical outcome evaluation, Foot and Ankle Ability Measure (FAAM) and Karlsson-Peterson Scoring System for Ankle Function questionnaires coupled with questions regarding time …

Exploring Chemovar-Specific Cannabis Extracts Quantification And Evaluation Of Cytotoxic Compounds For Targeting Glioblastoma Multiforme, Ashraf Duzan, Mufeed Basti, Travis Cesarone, Waldemar Debinski, Daniel Todd

HPD Articles

Glioblastoma Multiforme (GBM) represents one of the most aggressive and metastatic brain tumors, with a dismal success rate of less than three percent after five years, particularly in tumors with active immune checkpoints. This necessitates the development of targeted endogenous agents for precise GBM treatment. Previous experiments utilizing Chemovar Specific Cannabis Extractions (CSCEs), fractionated with polar solvents and quantified using Liquid and Gas Column Chromatography combined with Mass Spectrometry (LC/GCMS), have shown reduced viability and motility in human GBM cell lines. However, the complexity of the botanical substance has hindered the personalization of standard cannabis medicines for GBM due to …

Bimanual Movement Characteristics And Real-World Performance Following Hand-Arm Bimanual Intensive Therapy In Children With Unilateral Cerebral Palsy, Shailesh S. Gardas, Christine Lysaght, Amy Gross Mcmillan, Shailesh Kantak, John D. Willson, Charity G. Patterson, Swati M. Surkar

Department of Rehabilitation Medicine Faculty Papers

The purpose of this study was to quantify characteristics of bimanual movement intensity during 30 h of hand-arm bimanual intensive therapy (HABIT) and bimanual performance (activities and participation) in real-world settings using accelerometers in children with unilateral cerebral palsy (UCP). Twenty-five children with UCP participated in a 30 h HABIT program. Data were collected from bilateral wrist-worn accelerometers during 30 h of HABIT to quantify the movement intensity and three days pre- and post-HABIT to assess real-world performance gains. Movement intensity and performance gains were measured using six standard accelerometer-derived variables. Bimanual capacity (body function and activities) was assessed using …

Chronic Lower Back Pain Among Women In India: Evidence-Based Approach To Risk Factors And Interventions, Aelita Matosova

Master's Projects and Capstones

Chronic lower back pain (CLBP) is a prevalent issue worldwide, affecting about 1.71 billion people, with a significant proportion being women. CLBP is a major health concern in India, particularly among women, which were 80% reported experiencing this condition. Several factors, such as personal beliefs, sociocultural norms, restricted healthcare access, repetitive movements, and psychological aspects, contribute to this high prevalence leading to severe health and economic implications, including reduced work productivity and income. Although there have been several reports on prevalence and risk factors of CLBP, to our knowledge, there has not been enough work focusing on evidence-based interventions to …

Seeking Patient-Centered Care Through Bedside Handoff In The Postpartum Unit, Evelyn Ndaki

Master's Projects and Capstones

Problem: Patient discontent with nurse compassion and attentiveness prompted the implementation of standardized bedside shift handoff (BSH) for nurses in the postpartum unit of a Northern California teaching hospital.

Context: Pandemic stressors led to nurse practices not reflecting patient-centered care. Bedside handoff offers an opportunity to improve patient-centered nurse behaviors.

Intervention: To standardize BSH, a modified SBAR (Situation, Background, Assessment, Recommendation) tool was implemented.

Measures: The Hospital Consumer Assessment of Healthcare Providers and Systems (HCAHPS) question on “Nurses kept you informed” was tracked, and nurse satisfaction with the handoff process was measured with a pre- and post-implementation survey.

Results: Final …

The Implementation Of A Career-Readiness Program For Youth In A Group/Foster Care Setting, Brianie Clarke, Brianie Clarke

Department of Occupational Therapy Entry-Level Capstone Projects

The transition from high school to any form of postsecondary education is often a challenging experience in and of itself. For individuals who are a part of the foster care system, it is increasingly difficult to traverse this transition due to decreased access to resources and support. Throughout this capstone experience at the group home, A Kid's Place, I created a career readiness program that focused on gauging what each individuals’ interests are, curating a realistic career pathway/plan that would aid in the accomplishment of their goals, and created resourceful materials that would prepare participants to begin their own postsecondary …

Environmental And Occupational Health Risks: Educating Undergraduate (Adn-Bsn) Nursing Students For Safer Practice, Dorinda A. Mercado

Doctor of Nursing Practice (DNP) Projects

Background: Globally, adverse health effects, including deaths and disabilities, occur from living or working in unhealthy domains where exposure to environmental and occupational hazards exists. A multitude of these hazards are present in clinical settings in the healthcare environment where nurses care for patients and risk ongoing exposures to toxic substances.

Problem: Environmental and occupational health education is rarely included in the standard undergraduate nursing curriculum, contributing to a deficit among nurses in environmental health awareness and knowledge.

Methods: The study design was a pre/post evaluation of a single cohort (n=32) of undergraduate nursing students to assess environmental and occupational …

Variant Characterization Of A Representative Large Pedigree Suggests “Variant Risk Clusters” Convey Varying Predisposition Of Risk To Lynch Syndrome, Mouadh Barbirou, Amanda A. Miller, Amel Mezlini, Balkiss Bouhaouala-Zahar, Peter J. Tonellato

Department of Medical Oncology Faculty Papers

Recently, worldwide incidences of young adult aggressive colorectal cancer (CRC) have rapidly increased. Of these incidences diagnosed as familial Lynch syndrome (LS) CRC, outcomes are extremely poor. In this study, we seek novel familial germline variants from a large pedigree Tunisian family with 12 LS-affected individuals to identify putative germline variants associated with varying risk of LS. Whole-genome sequencing analysis was performed to identify known and novel germline variants shared between affected and non-affected pedigree members. SNPs, indels, and structural variants (SVs) were computationally identified, and their oncological influence was predicted using the Genetic Association of Complex Diseases and Disorders, …

The Directional Effect Of Target Position On Spatial Selective Auditory Attention, Heesung Park

Dissertations, 2020-current

Spatial selective auditory attention plays a crucial role in listening in a mixture of competing speech sounds. Previous neuroimaging studies have reported alpha band neural activity modulated by auditory attention, along with the alpha lateralization corresponding to attentional focus. A greater cortical representation of the attended speech envelope compared to the ignored speech envelope was also found, a phenomenon known as 'neural speech tracking’. However, little is known about the neural activities when attentional focus is directed on speech sounds from behind the listener, even though understanding speech from behind is a common and essential aspect of daily life. The …

Perceptions Of Mental Health Among Pakistani Women With Micro-Finance Loans: An Interpretive Descriptive Study, Farhana Irfan Madhani, Catherine Tompkins, Susan Jack, Carolyn Byrne

The Qualitative Report

Mental health has gained significant recognition and importance as a crucial aspect of overall well-being. An individual's mental health is influenced by the intersection of individual, social, cultural, and systematic sources of stress and resilience. It is important to include subjective conceptualizations of mental health and well-being to develop culturally sensitive approaches to mental health promotion. This qualitative study aimed to understand how urban-dwelling women living in Pakistan who are micro-finance loan recipients conceptualize the meaning of mental health. Using interpretive description methodology, data were collected and analyzed through in-depth, semi-structured interviews conducted in Urdu with a purposeful sample of …

Lvpt: Lazy Velocity Pseudotime Inference Method, Shuainan Mao, Jiajia Liu, Weiling Zhao, Xiaobo Zhou

Faculty, Staff and Student Publications

The emergence of RNA velocity has enriched our understanding of the dynamic transcriptional landscape within individual cells. In light of this breakthrough, we embarked on integrating RNA velocity with cellular pseudotime inference, aiming to improve the prediction of cell orders along biological trajectories beyond existing methods. Here, we developed LVPT, a novel method for pseudotime and trajectory inference. LVPT introduces a lazy probability to indicate the probability that the cell stays in the original state and calculates the transition matrix based on RNA velocity to provide the probability and direction of cell differentiation. LVPT shows better and comparable performance of …

Hepatitis A Virus And Hepatitis E Virus As Food- And Waterborne Pathogens—Transmission Routes And Methods For Detection In Food, Katalin Nemes, Sofia Persson, Magnus Simonsson

Faculty, Staff and Student Publications

Foodborne viruses are an important threat to food safety and public health. Globally, there are approximately 5 million cases of acute viral hepatitis due to hepatitis A virus (HAV) and hepatitis E virus (HEV) every year. HAV is responsible for numerous food-related viral outbreaks worldwide, while HEV is an emerging pathogen with a global health burden. The reported HEV cases in Europe have increased tenfold in the last 20 years due to its zoonotic transmission through the consumption of infected meat or meat products. HEV is considered the most common cause of acute viral hepatitis worldwide currently. This review focuses …

Simplifying Qualitative Case Study Research Methodology: A Step-By-Step Guide Using A Palliative Care Example, Elizabeth M. Miller Mrs, Joanne E. Porter Professor, Michael S. Barbagallo Dr

The Qualitative Report

Qualitative case study research can be a helpful methodology when conducting health research. However, it can be overlooked or dismissed as a possible methodological choice due to different epistemological positionings by case study theorists and often confusing and contradictory definitions and terminology. Much has been written about case studies, but it takes time to wade through volumes of often philosophically and methodologically dense material to locate a theorist who presents case study research at a depth the novice researcher can understand. Case study research literature may offer a condensed summary of processes but often needs more theoretical detail. Therefore, discerning …

Characterizing Cancer Metabolism From Bulk And Single-Cell Rna-Seq Data Using Metaflux, Yuefan Huang, Vakul Mohanty, Merve Dede, Kyle Tsai, May Daher, Li Li, Katayoun Rezvani, Ken Chen

Faculty, Staff and Student Publications

Cells often alter metabolic strategies under nutrient-deprived conditions to support their survival and growth. Characterizing metabolic reprogramming in the tumor microenvironment (TME) is of emerging importance in cancer research and patient care. However, recent technologies only measure a subset of metabolites and cannot provide in situ measurements. Computational methods such as flux balance analysis (FBA) have been developed to estimate metabolic flux from bulk RNA-seq data and can potentially be extended to single-cell RNA-seq (scRNA-seq) data. However, it is unclear how reliable current methods are, particularly in TME characterization. Here, we present a computational framework METAFlux (METAbolic Flux balance analysis) …