Medical Biomathematics and Biometrics Commons^™

Computer-Aided Drug Discovery For Helicobacter Pylori, Nicole Ann Vita

Theses and Dissertations (ETD)

Helicobacter pylori is a high-priority drug-resistant pathogen and is currently the only bacteria considered to be a class I carcinogen and there is a critical need to identify novel chemical matter to treat H. pylori infections. Hp is responsible for greater than 60% of gastric cancer related deaths and 89% of all gastric cancer morbidities. In a previous study, our lab identified novel Hp thienopyrmidine inhibitors that target respiratory complex I, an essential enzyme in respiration. Respiratory complex I is a large asymmetric multidomain and membrane bound enzyme and due to these innate features, it is not practical for biophysical …

A Two-Layer Continuous-Capillary Oxygen Transport Model: Development And Application To Blood Flow Regulation In Resting Skeletal Muscle., Keith C. Afas

Electronic Thesis and Dissertation Repository

In skeletal muscle (SM), the microcirculation distributes blood flow to capillary networks to meet local oxygen (O₂) demand. Experiments using intra-vital video microscopy (IVVM) have quantified blood flow and O₂ supply in capillary networks, and using an O₂ exchange chamber have measured local changes in blood flow believed due to O₂-dependent regulation. However, IVVM is unable to simultaneously measure capillary O₂ supply and SM O₂ content, implying the need for theoretical models to understand how flow regulation and SM oxygenation interact. In this thesis, a novel blood-tissue O₂ transport model using …

Demographics Of Periprosthetic Joint Infection Rates, Katelynn Donnelly, Abigail Erwin, Andrew Chapple, Peter Krause, Vinod Dasa

Medical Research Day

Introduction: Risk factors for periprosthetic joint infections (PJIs) following total joint arthroplasties (TJAs) include patient demographics and comorbidities such as age, gender, obesity, rheumatoid arthritis, and diabetes. 1 However, there is insufficient research analyzing the number of PJIs in certain racial subsets of the population despite the presence of disparities due to race that still exists in orthopedics today. 2 The purpose of this study is to investigate if PJI rates differ by race, as well as other patient demographics. This may uncover valuable information on how race relates to PJIs which is frequently unaccounted for in other studies. This …

Lack Of Demographic Information In Tha/Tka Randomized Controlled Trial Publications, Katelynn Donnelly, Hannah Theriot, John Bourgeois, Andrew Chapple, Peter Krause, Vinod Dasa

Medical Research Day

Introduction: The impact of social determinants of health (SDOH) has been documented in orthopedic literature. However, there is a lack of data on the inclusion of these variables in orthopedic studies. Our aim was to investigate how many THA and TKA randomized controlled trials (RCTs) report SDOH variables such as race, ethnicity, insurance, income, and education within the manuscript. Methods: A literature review was conducted on a PubMed search for RCTs published from 2017-2019 in 4 major orthopedic journals which routinely publish on total joint arthroplasty: JBJS, Journal of Arthroplasty, CORR, and Osteoarthritis and Cartilage. The inclusion criteria, THA/TKA RCTs …

Demographics Of Periprosthetic Joint Infections Rates, Katelynn Donnelly, Abigail Erwin, Andrew Chapple, Peter Krause, Vinod Dasa

Medical Research Day

Introduction: Risk factors for periprosthetic joint infections (PJIs) following total joint arthroplasties (TJAs) include patient demographics and comorbidities such as age, gender, obesity, rheumatoid arthritis, and diabetes. However, there is insufficient research analyzing the number of PJIs in certain racial subsets of the population despite the presence of disparities due to race that still exists in orthopedics today. The purpose of this study is to investigate if PJI rates differ by race, as well as other patient demographics. This may uncover valuable information on how race relates to PJIs which is frequently unaccounted for in other studies. This study aims …

Neutrophil Dynamics Affect Mycobacterium Tuberculosis Granuloma Outcomes And Dissemination, Caitlin Hult, Joshua T. Mattila, Hannah P. Gideon, Jennifer J. Linderman, Denise E. Kischner

Math Faculty Publications

Neutrophil infiltration into tuberculous granulomas is often associated with higher bacteria loads and severe disease but the basis for this relationship is not well understood. To better elucidate the connection between neutrophils and pathology in primate systems, we paired data from experimental studies with our next generation computational model GranSim to identify neutrophil-related factors, including neutrophil recruitment, lifespan, and intracellular bacteria numbers, that drive granuloma-level outcomes. We predict mechanisms underlying spatial organization of neutrophils within granulomas and identify how neutrophils contribute to granuloma dissemination. We also performed virtual deletion and depletion of neutrophils within granulomas and found that neutrophils play …

Decoding Clinical Biomarker Space Of Covid-19: Exploring Matrix Factorization-Based Feature Selection Methods, Farshad Saberi-Movahed, Mahyar Mohammadifard, Adel Mehrpooya, Mohammad Rezaei-Ravari, Kamal Berahmand, Mehrdad Rostami, Saeed Karami, Mohammad Najafzadeh, Davood Hajinezhad, Mina Jamshidi, Farshid Abedi, Mahtab Mohammadifard, Elnaz Farbod, Farinaz Safavi, Mohammadreza Dorvash, Shahrzad Vahedi, Mahdi Eftekhari, Farid Saberi-Movahed, Iman Tavassoly

Publications and Research

One of the most critical challenges in managing complex diseases like COVID-19 is to establish an intelligent triage system that can optimize the clinical decision-making at the time of a global pandemic. The clinical presentation and patients’ characteristics are usually utilized to identify those patients who need more critical care. However, the clinical evidence shows an unmet need to determine more accurate and optimal clinical biomarkers to triage patients under a condition like the COVID-19 crisis. Here we have presented a machine learning approach to find a group of clinical indicators from the blood tests of a set of COVID-19 …

The Effect Of Using Bolometric Exercises On Enhancing Explosive Strength Among Female Students Of The Faculty Of Physical Education At Yarmouk University, Mohammed A. Mqableh, Sulaiman M. Qazaqzeh, Bassam M. Khalifa, Sumayeh M. Ekhwelah

Journal of the Association of Arab Universities for Research in Higher Education (مجلة اتحاد الجامعات العربية (للبحوث في التعليم العالي

The Effect of Using bolometric Exercises on Enhancing Explosive Strength among Female Students of the Faculty of Physical Education at Yarmouk University. The study purpose was to identify the effect of bolometric exercises on improving the explosive force of female students in the Faculty of Physical Education at Yarmouk University. The researchers used the experimental method. The sample consisted of 22 students in the course of preparation and physical fitness for the first semester of the academic year (2018-2019) and the sample was chosen by randomly. The researchers designed a training program that includes training exercises, consisting of (18) training …

Covid19 Disease Map, A Computational Knowledge Repository Of Virus–Host Interaction Mechanisms, Marek Ostaszewski, Tomáš Helikar, Bhanwar Lal Puniya, A Host Of Co-Authors, Covid-19 Disease Map Community

Biochemistry -- Faculty Publications

We need to effectively combine the knowledge from surging literature with complex datasets to propose mechanistic models of SARS-CoV-2 infection, improving data interpretation and predicting key targets of intervention. Here, we describe a large-scale community effort to build an open access, interoperable and computable repository of COVID-19 molecular mechanisms. The COVID-19 Disease Map (C19DMap) is a graphical, interactive representation of disease-relevant molecular mechanisms linking many knowledge sources. Notably, it is a computational resource for graph-based analyses and disease modelling. To this end, we established a framework of tools, platforms and guidelines necessary for a multifaceted community of biocurators, domain experts, …

Testing The Effect Of Acetaminophen Overdose On The Liver And The Role Of Biomarkers To Predict Death Or Survival, Christine Brasic

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

A Differential Geometry-Based Machine Learning Algorithm For The Brain Age Problem, Justin Asher, Khoa Tan Dang, Maxwell Masters

The Journal of Purdue Undergraduate Research

No abstract provided.

Automatic Recognition, Segmentation, And Sex Assignment Of Nocturnal Asthmatic Coughs And Cough Epochs In Smartphone Audio Recordings: Observational Field Study, Filipe Barata, Peter Tinschert, Frank Rassouli, Claudia Steurer-Stey, Elgar Fleisch, Milo Puhan, Martin Brutsche, David Kotz, Tobias Kowatsch

Dartmouth Scholarship

Background: Asthma is one of the most prevalent chronic respiratory diseases. Despite increased investment in treatment, little progress has been made in the early recognition and treatment of asthma exacerbations over the last decade. Nocturnal cough monitoring may provide an opportunity to identify patients at risk for imminent exacerbations. Recently developed approaches enable smartphone-based cough monitoring. These approaches, however, have not undergone longitudinal overnight testing nor have they been specifically evaluated in the context of asthma. Also, the problem of distinguishing partner coughs from patient coughs when two or more people are sleeping in the same room using contact-free audio …

Impact Of Order Set Use On Stroke Care, Bilal Nadeem, Edward Waseleski, Meryem Maras-Casey, Sabih Alam, Adnan Faruqui, Michael Gutierrez, Maruthsakhi Molugu, Christina Oricompil, Ashar Mahmood, Katherine Torralba, Fatima Agha, Nour Tlimat, Olu Oyesanmi, Irina Davis, Salman Muddassir, Nikolay Mitzov

West Florida Division Virtual Research Day 2020

• A case control study on stroke patients was recently completed for a quality improvement (QI) investigation.
• The objective was to determine if the use of either Hemorrhagic or Ischemic Stroke Order Set had an effect on the length of stay (LOS) or adherence to current stroke guideline recommendations

A Mathematical Model To Explore The Potential Of Combinations Of Adt And Immunotherapies, Johnna Barnaby

Biology and Medicine Through Mathematics Conference

No abstract provided.

452— Potential Impacts Of Basic Reproduction Number On The Covid-19 Epidemic, Marisa Presutto

GREAT Day

The basic reproduction number (R₀) of a disease can be thought of as the number of cases that one case will directly generate if the rest of the population is susceptible to infection. The R₀ of COVID-19 has recently become clearer; toward the beginning of the outbreak, the Imperial College Group estimated it to be somewhere between 1.5 and 3.5 (Imai et al. 2020), but they have now assumed a value of 2.4 (Ferguson et al. 2020). Using the Watts-Strogatz small-world model, I examined the effects of different R₀ values within the original range on the …

Mathematical Model Of Atm Activation And Chromatin Relaxation By Ionizing Radiation, Yongfeng Li, Francis A. Cucinotta

Healthcare Administration & Policy Faculty Publications

International Journal of Molecular Sciences

Quantifying The Heterogeneity Of The Immunoglobulin G N-Glycome In An Ageing Australian Population: The Busselton Healthy Ageing Study, Alyce Russell

Theses: Doctorates and Masters

The use of immunoglobulin G N-glycomics to study chronic non-communicable disorders and other complex phenotypes emerged following the Human Genome Project. The consortium discovered that most phenotypes were too complex to be explained by genetics alone. Thus, the biological importance of epigenetics was recognised; heritable modifications to gene expression rather than the genome itself. Nglycosylation is a form of epigenetic regulation known as a post-translational modification. It stabilises the immunoglobulin G structure and alters downstream responses elicited by the antibody and is extensively studied as a candidate biomarker in the post-genomic era.

The N-glycosylation of immunoglobulin G itself is complex, …

Connectivity Differences Between Gulf War Illness (Gwi) Phenotypes During A Test Of Attention, Tomas Clarke, Jessie Jamieson, Patrick Malone, Rakib U. Rayhan, Stuart Washington, John W. Vanmeter, James N. Baraniuk

Faculty Publications, Department of Mathematics

One quarter of veterans returning from the 1990–1991 Persian Gulf War have developed Gulf War Illness (GWI) with chronic pain, fatigue, cognitive and gastrointestinal dysfunction. Exertion leads to characteristic, delayed onset exacerbations that are not relieved by sleep. We have modeled exertional exhaustion by comparing magnetic resonance images from before and after submaximal exercise. One third of the 27 GWI participants had brain stem atrophy and developed postural tachycardia after exercise (START: Stress Test Activated Reversible Tachycardia). The remainder activated basal ganglia and anterior insulae during a cognitive task (STOPP: Stress Test Originated Phantom Perception). Here, the role of attention …

Deepcon-Pre: Improved Protein Contact Map Prediction Using Inverse Covariance And Deep Residual Networks, Nachammai Palaniappan

Theses

As with most domains where machine learning methods are applied, correct feature engineering is critical when developing deep learning algorithms for solving the protein folding problem. Unlike the domains such as computer vision and natural language processing, feature engineering is not rigorously studied towards solving the protein folding problem. A recent research has highlighted that input features known as precision matrix are most informative for predicting inter-residue contact map, the key for building three-dimensional models. In this work, we study the significance of the precision matrix feature when very deep residual networks are trained. Using a standard dataset of 3456 …

Mathematics Saves Lives: Models And Signals Enabling Medicine And Biology, Raina Robeva

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.