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Medical Biomathematics and Biometrics Commons

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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 2021 North Carolina State University

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 2021 جامعة اليرموك

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 2021 University of Luxembourg

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 2020 University of Wisconsin-Whitewater

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 2020 Purdue University Fort Wayne

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 2020 ETH Zurich

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 2020 HCA Healthcare

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 2020 Shippensburg University of Pennsylvania

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 2020 SUNY Geneseo

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 ...


Mathematical Model Of Atm Activation And Chromatin Relaxation By Ionizing Radiation, Yongfeng Li, Francis A. Cucinotta 2020 USRA

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 2020 Edith Cowan University

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 2019 Georgetown University

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 ...


Deepcon-Pre: Improved Protein Contact Map Prediction Using Inverse Covariance And Deep Residual Networks, Nachammai Palaniappan 2019 University of Missouri-St. Louis

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 2019 Randolph-Macon College

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

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.


Transient Dynamics Of Infection Transmission In An Intensive Care Unit, Christopher Short, Matthew S. Mietchen, Eric T. Lofgren 2019 WSU

Transient Dynamics Of Infection Transmission In An Intensive Care Unit, Christopher Short, Matthew S. Mietchen, Eric T. Lofgren

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.


Not Just Either/Or: Discrete And Continuous Models Play Nicely Together In A Model Of Hospital Infection, Lester Caudill, Barry Lawson 2019 University of Richmond

Not Just Either/Or: Discrete And Continuous Models Play Nicely Together In A Model Of Hospital Infection, Lester Caudill, Barry Lawson

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.


An Analysis Of The Rajasthan Public Health System’S Response To The 2019 Dengue Insurgence, Luke Bryan 2019 SIT Study Abroad

An Analysis Of The Rajasthan Public Health System’S Response To The 2019 Dengue Insurgence, Luke Bryan

Independent Study Project (ISP) Collection

Dengue virus is in a pandemic status and is a major public health issue in the modern world. The mosquito-borne disease is largely prevalent in Asia and specifically India, where more than half of the states are considered to have complete presence of the dengue virus. The intricate infrastructure of the Indian public health system looks for dengue cases at all levels and reports to the integrated disease surveillance programme (IDSP).

Analyses of the IDSP and trends of dengue cases was done in response to dengue outbreaks throughout the state. Geographic information system (GIS) maps were created to evaluate a ...


Seeing Eye To Eye: A Machine Learning Approach To Automated Saccade Analysis, Maigh Attre 2019 University of Connecticut

Seeing Eye To Eye: A Machine Learning Approach To Automated Saccade Analysis, Maigh Attre

Honors Scholar Theses

Abnormal ocular motility is a common manifestation of many underlying pathologies particularly those that are neurological. Dynamics of saccades, when the eye rapidly changes its point of fixation, have been characterized for many neurological disorders including concussions, traumatic brain injuries (TBI), and Parkinson’s disease. However, widespread saccade analysis for diagnostic and research purposes requires the recognition of certain eye movement parameters. Key information such as velocity and duration must be determined from data based on a wide set of patients’ characteristics that may range in eye shapes and iris, hair and skin pigmentation [36]. Previous work on saccade analysis ...


Parameter Estimation And Optimal Design Techniques To Analyze A Mathematical Model In Wound Healing, Nigar Karimli 2019 Western Kentucky University

Parameter Estimation And Optimal Design Techniques To Analyze A Mathematical Model In Wound Healing, Nigar Karimli

Masters Theses & Specialist Projects

For this project, we use a modified version of a previously developed mathematical model, which describes the relationships among matrix metalloproteinases (MMPs), their tissue inhibitors (TIMPs), and extracellular matrix (ECM). Our ultimate goal is to quantify and understand differences in parameter estimates between patients in order to predict future responses and individualize treatment for each patient. By analyzing parameter confidence intervals and confidence and prediction intervals for the state variables, we develop a parameter space reduction algorithm that results in better future response predictions for each individual patient. Moreover, use of another subset selection method, namely Structured Covariance Analysis, that ...


Supervised Dimension Reduction For Large-Scale "Omics" Data With Censored Survival Outcomes Under Possible Non-Proportional Hazards, Lauren Spirko-Burns, Karthik Devarajan 2019 Temple University

Supervised Dimension Reduction For Large-Scale "Omics" Data With Censored Survival Outcomes Under Possible Non-Proportional Hazards, Lauren Spirko-Burns, Karthik Devarajan

COBRA Preprint Series

The past two decades have witnessed significant advances in high-throughput ``omics" technologies such as genomics, proteomics, metabolomics, transcriptomics and radiomics. These technologies have enabled simultaneous measurement of the expression levels of tens of thousands of features from individual patient samples and have generated enormous amounts of data that require analysis and interpretation. One specific area of interest has been in studying the relationship between these features and patient outcomes, such as overall and recurrence-free survival, with the goal of developing a predictive ``omics" profile. Large-scale studies often suffer from the presence of a large fraction of censored observations and potential ...


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