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Rewriting The Rules For Diagnostics: Implications Of Probability And Measure Theory For Sars-Cov-2 Testing, Paul Patrone, Anthony Kearsley 2022 National Institute of Standards and Technology

Rewriting The Rules For Diagnostics: Implications Of Probability And Measure Theory For Sars-Cov-2 Testing, Paul Patrone, Anthony Kearsley

Biology and Medicine Through Mathematics Conference

No abstract provided.


Factors Affecting Time To Recovery: A Covid-19 Survival Analysis, Fernanda Montoya 2022 Northern Illinois University

Factors Affecting Time To Recovery: A Covid-19 Survival Analysis, Fernanda Montoya

Honors Capstones

This project is focused on the recovery rates of patients diagnosed with COVID-19 after different clinical trial drug treatments. Data for the clinical trial studied was obtained from the National Institute of Allergy and Infectious Diseases for the primary purpose of a survival analysis on patient time to recovery under a placebo and therapeutic drug treatment. Specifically, patients in this clinical trial were randomly selected to receive remdesivir, an antiviral drug, in combination with a placebo or baricitinib, a janus kinase inhibitor drug. Cox PH models were used to identify how the different treatment drugs affect time to recovery and ...


Comparative Transcriptomic Study Between Cyanobacteria That Contain Chlorophyll D And Those That Lack Chlorophyll D, Fernanda Montoya 2022 Northern Illinois University

Comparative Transcriptomic Study Between Cyanobacteria That Contain Chlorophyll D And Those That Lack Chlorophyll D, Fernanda Montoya

Honors Capstones

All cyanobacteria, which perform oxygenic photosynthesis on Earth, contain the photosynthetic pigment chlorophyll a (Chl a) that absorbs light in the violet and red region of the visible spectrum. Cyanobacteria of the Acaryochloris species, however, contain the rare photosynthetic pigment chlorophyll d (Chl d) that absorbs light in the far-red region. Chl d’s ability to absorb light in this region allows it to avoid competing with other photosynthetic organisms for light. Creating a photosystem that uses Chl d in plants would be of great use for agricultural land optimization, but requires knowledge of the biosynthetic pathways of Chl d ...


Mathematical Modeling Suggests Cooperation Of Plant-Infecting Viruses, Joshua Miller, Vitaly V. Ganusov, Tessa Burch-Smith 2022 University of Tennessee, Knoxville

Mathematical Modeling Suggests Cooperation Of Plant-Infecting Viruses, Joshua Miller, Vitaly V. Ganusov, Tessa Burch-Smith

Chancellor’s Honors Program Projects

No abstract provided.


Examining Bacteriophage Reliance On The Tola Protein Of Escherichia Coli, Ellen Davis 2022 Bowling Green State University

Examining Bacteriophage Reliance On The Tola Protein Of Escherichia Coli, Ellen Davis

Honors Projects

With the ever-growing crisis of antibiotic resistant bacteria, bacteriophage provide an important potential alternative therapy to treat infections when antibiotics are ineffective. For this reason, it is important to understand the mechanisms bacteriophage use to enter their bacterial host cell. The cellular envelope of the gram-negative bacterium E. coli contains a protein system known as Tol-Pal, which utilizes energy from the Proton Motive Force to carry out several cellular functions, including some associated with cellular division and outer-membrane stability. Certain bacteriophage take advantage of the energy produced by this system to cross the bacterial cell membrane. One important protein of ...


A Novel Nonparametric Test For Heterogeneity Detection And Assessment Of Fluid Removal Among Crrt Patients In Icu, Shaowli Kabir 2022 University of Kentucky

A Novel Nonparametric Test For Heterogeneity Detection And Assessment Of Fluid Removal Among Crrt Patients In Icu, Shaowli Kabir

Theses and Dissertations--Epidemiology and Biostatistics

Over the past decade acute kidney injury (AKI) has been occurring among 20%-50% of patients admitted to the intensive care unit (ICU) in United States. Continuous renal replacement therapy (CRRT) has become a popular treatment method among these critically ill patients. But there are multiple complications in implementing this treatment, including discrepancies in practiced and prescribed fluid removal, possibly related to the heterogeneity among these patients. With mixture modeling there have been several techniques in detecting heterogeneity with their specific limitations. In this dissertation a novel nonparametric ‘d test’ will be used to detect heterogeneity among CRRT patients in ...


Empirically Adjusted Weighted Ordered P-Values Method, Wimarsha Jayanetti, Sinjini Sikdar, N. Rao Chaganty 2022 Old Dominion University

Empirically Adjusted Weighted Ordered P-Values Method, Wimarsha Jayanetti, Sinjini Sikdar, N. Rao Chaganty

College of Sciences Posters

Recent advancements in high-throughput technologies have enabled simultaneous inference of thousands of genes. With the abundance of public databases, it is now possible to rapidly access the results of several genomic studies, each of which includes the significance testing results of a large number of genes. Researchers frequently aggregate genomic data from multiple studies in the form of a meta-analysis. Most traditional meta-analysis methods aim at combining summary results to find signals in at least one of the studies. However, often the goal is to identify genes that are differentially expressed in a consistent pattern across multiple studies. Recently, a ...


Team Coordination Dynamics Of Winning Nba Teams, Alli Grunkemeyer, Joel H. Sommerfeld 2022 University of Nebraska at Omaha

Team Coordination Dynamics Of Winning Nba Teams, Alli Grunkemeyer, Joel H. Sommerfeld

Student Research and Creative Activity Fair

Predicting sports games outcomes is an endless pursuit shared by stakeholders ranging from fans to coaches to data scientists. We have begun investigating the value of positional data recorded during basketball gameplay with the goal of predicting outcomes from team dynamics as they emerge. We approached this problem by analyzing the “shape” of team movements on the court and investigated whether team dynamics in NBA games mimicked long-range correlated patterns observed in other team contexts. We analyzed 622 NBA games from an archival data set, including all area time series obtained for each of the four quarters. We fit a ...


Angiotensin Blockade Therapy And Survival In Pancreatic Cancer: A Population Study, Scott W Keith, Vittorio Maio, Hwyda A Arafat, Matthew Alcusky, Thomas Karagiannis, Carol Rabinowitz, Harish Lavu, Daniel Z. Louis 2022 Thomas Jefferson University

Angiotensin Blockade Therapy And Survival In Pancreatic Cancer: A Population Study, Scott W Keith, Vittorio Maio, Hwyda A Arafat, Matthew Alcusky, Thomas Karagiannis, Carol Rabinowitz, Harish Lavu, Daniel Z. Louis

College of Population Health Faculty Papers

Background: Pancreatic cancer (PC) is one of the most aggressive and challenging cancer types to effectively treat, ranking as the fourth-leading cause of cancer death in the United States. We investigated if exposures to angiotensin II receptor blockers (ARBs) or angiotensin I converting enzyme (ACE) inhibitors after PC diagnosis are associated with survival.

Methods: PC patients were identified by ICD-9 diagnosis and procedure codes among the 3.7 million adults living in the Emilia-Romagna Region from their administrative health care database containing patient data on demographics, hospital discharges, all-cause mortality, and outpatient pharmacy prescriptions. Cox modeling estimated covariate-adjusted mortality hazard ...


Marginal Proportional Hazards Models For Clustered Interval-Censored Data With Time-Dependent Covariates, Kaitlyn Cook, Wenbin Lu, Rui Wang 2022 Harvard University

Marginal Proportional Hazards Models For Clustered Interval-Censored Data With Time-Dependent Covariates, Kaitlyn Cook, Wenbin Lu, Rui Wang

Harvard University Biostatistics Working Paper Series

The Botswana Combination Prevention Project was a cluster-randomized HIV prevention trial whose follow-up period coincided with Botswana’s national adoption of a universal test-and-treat strategy for HIV management. Of interest is whether, and to what extent, this change in policy (i) modified the observed preventative effects of the study intervention and (ii) was associated with a reduction in the population-level incidence of HIV in Botswana. To address these questions, we propose a stratified proportional hazards model for clustered interval-censored data with time-dependent covariates and develop a composite expectation maximization algorithm that facilitates estimation of model parameters without placing parametric assumptions ...


On Assessing Survival Benefit Of Immunotherapy Using Long-Term Restricted Mean Survival Time, Miki Horiguchi, Lu Tian, Hajime Uno 2022 Dana-Farber Cancer Institute

On Assessing Survival Benefit Of Immunotherapy Using Long-Term Restricted Mean Survival Time, Miki Horiguchi, Lu Tian, Hajime Uno

Harvard University Biostatistics Working Paper Series

The pattern of the difference between two survival curves we often observe in randomized clinical trials for evaluating immunotherapy is not proportional hazards; the treatment effect typically appears several months after the initiation of the treatment (i.e., delayed difference pattern). The commonly used logrank test and hazard ratio estimation approach will be suboptimal concerning testing and estimation for those trials. The long-term restricted mean survival time (LT-RMST) approach is a promising alternative for detecting the treatment effect that potentially appears later in the study. A challenge in employing the LT-RMST approach is that it must specify a lower end ...


Upregulation Of Cd36, A Fatty Acid Translocase, Promotes Colorectal Cancer Metastasis By Increasing Mmp28 And Decreasing E-Cadherin Expression, James Drury, Piotr G. Rychahou, Courtney O. Kelson, Mariah E. Geisen, Yuanyuan Wu, Daheng He, Chi Wang, Eun Y. Lee, B. Mark Evers, Yekaterina Y. Zaytseva 2022 University of Kentucky

Upregulation Of Cd36, A Fatty Acid Translocase, Promotes Colorectal Cancer Metastasis By Increasing Mmp28 And Decreasing E-Cadherin Expression, James Drury, Piotr G. Rychahou, Courtney O. Kelson, Mariah E. Geisen, Yuanyuan Wu, Daheng He, Chi Wang, Eun Y. Lee, B. Mark Evers, Yekaterina Y. Zaytseva

Surgery Faculty Publications

Altered fatty acid metabolism continues to be an attractive target for therapeutic intervention in cancer. We previously found that colorectal cancer (CRC) cells with a higher metastatic potential express a higher level of fatty acid translocase (CD36). However, the role of CD36 in CRC metastasis has not been studied. Here, we demonstrate that high expression of CD36 promotes invasion of CRC cells. Consistently, CD36 promoted lung metastasis in the tail vein model and GI metastasis in the cecum injection model. RNA-Seq analysis of CRC cells with altered expression of CD36 revealed an association between high expression of CD36 and upregulation ...


Nonlinear Mixed-Effects Models For Hiv Viral Load Trajectories Before And After Antiretroviral Therapy Interruption, Incorporating Left Censoring, Sihaoyu Gao, Lang Wu, Tingting Yu, Roger Kouyos, Huldrych F. Gunthard, Rui Wang 2022 University of British Columbia

Nonlinear Mixed-Effects Models For Hiv Viral Load Trajectories Before And After Antiretroviral Therapy Interruption, Incorporating Left Censoring, Sihaoyu Gao, Lang Wu, Tingting Yu, Roger Kouyos, Huldrych F. Gunthard, Rui Wang

Harvard University Biostatistics Working Paper Series

Characterizing features of the viral rebound trajectories and identifying host, virological, and immunological factors that are predictive of the viral rebound trajectories are central to HIV cure research. In this paper, we investigate if key features of HIV viral decay and CD4 trajectories during antiretroviral therapy (ART) are associated with characteristics of HIV viral rebound following ART interruption. Nonlinear mixed effect (NLME) models are used to model viral load trajectories before and following ART interruption, incorporating left censoring due to lower detection limits of viral load assays. A stochastic approximation EM (SAEM) algorithm is used for parameter estimation and inference ...


Addressing Ascertainment Bias In The Study Of Cardiovascular Disease Burden In Opioid Use Disorders - Application Of Natural Language Processing Of Electronic Health Records, Jade Huang Singleton 2022 University of Kentucky

Addressing Ascertainment Bias In The Study Of Cardiovascular Disease Burden In Opioid Use Disorders - Application Of Natural Language Processing Of Electronic Health Records, Jade Huang Singleton

Theses and Dissertations--Epidemiology and Biostatistics

In the United States, the prevalence of long-term exposure to opioid drugs, for both medically and nonmedically indicated purposes, has increased considerably since the mid-1990’s. Concerns have emerged about the potential health effects of opioid use. There is also growing interest in other possible connections with opioid use including cardiovascular disease. Electronic health records (EHR) contain information about patient care in the form of structured codes and unstructured notes. Natural language processing (NLP) provides a tool for processing unstructured textual data in EHR clinical notes and extracts useful information for research with structured formats. The purpose of this dissertation ...


Estimating Weighted Panel Sizes For Primary Care Providers: An Assessment Of Clustering And Novel Methods Of Panel Size Estimation On Electronic Medical Records, Martin A. Lavallee 2022 Virginia Commonwealth University

Estimating Weighted Panel Sizes For Primary Care Providers: An Assessment Of Clustering And Novel Methods Of Panel Size Estimation On Electronic Medical Records, Martin A. Lavallee

Theses and Dissertations

Primary Care is on the frontlines of healthcare, thus they see the most diverse set of patients. In order to achieve high functioning primary care, a practice must establish empanelment, the pairing of patients to providers. Enumeration of empanelment, or estimating panel sizes, helps ensure that the demands of the patients demand the supply of providers and optimize the balance of primary care resources to improve quality of care. Further we can adjust panel sizes by using patient-level data on healthcare utilization and complexity extracted from the electronic medial record to determine the amount of care or burden of work ...


Finding The Best Predictors For Foot Traffic In Us Seafood Restaurants, Isabel Paige Beaulieu 2022 University of New Hampshire

Finding The Best Predictors For Foot Traffic In Us Seafood Restaurants, Isabel Paige Beaulieu

Honors Theses and Capstones

COVID-19 caused state and nation-wide lockdowns, which altered human foot traffic, especially in restaurants. The seafood sector in particular suffered greatly as there was an increase in illegal fishing, it is made up of perishable goods, it is seasonal in some places, and imports and exports were slowed. Foot traffic data is useful for business owners to have to know how much to order, how many employees to schedule, etc. One issue is that the data is very expensive, hard to get, and not available until months after it is recorded. Our goal is to not only find covariates that ...


Genetic Contributors Of Incident Stroke In 10,700 African Americans With Hypertension: A Meta-Analysis From The Genetics Of Hypertension Associated Treatments And Reasons For Geographic And Racial Differences In Stroke Studies, Nicole D. Armstrong, Vinodh Srinivasasainagendra, Amit Patki, Rikki M. Tanner, Bertha A. Hidalgo, Hemant K. Tiwari, Nita A. Limdi, Ethan M. Lange, Leslie A. Lange, Donna K. Arnett, Marguerite R. Irvin 2021 University of Alabama at Birmingham

Genetic Contributors Of Incident Stroke In 10,700 African Americans With Hypertension: A Meta-Analysis From The Genetics Of Hypertension Associated Treatments And Reasons For Geographic And Racial Differences In Stroke Studies, Nicole D. Armstrong, Vinodh Srinivasasainagendra, Amit Patki, Rikki M. Tanner, Bertha A. Hidalgo, Hemant K. Tiwari, Nita A. Limdi, Ethan M. Lange, Leslie A. Lange, Donna K. Arnett, Marguerite R. Irvin

Epidemiology Faculty Publications

Background: African Americans (AAs) suffer a higher stroke burden due to hypertension. Identifying genetic contributors to stroke among AAs with hypertension is critical to understanding the genetic basis of the disease, as well as detecting at-risk individuals.

Methods: In a population comprising over 10,700 AAs treated for hypertension from the Genetics of Hypertension Associated Treatments (GenHAT) and Reasons for Geographic and Racial Differences in Stroke (REGARDS) studies, we performed an inverse variance-weighted meta-analysis of incident stroke. Additionally, we tested the predictive accuracy of a polygenic risk score (PRS) derived from a European ancestral population in both GenHAT and REGARDS ...


Smoking, Alcohol Consumption, And Depression In Association With Incidence Of Type 2 Diabetes Among Mexican Americans In Starr County, Texas, Gabriela Rubannelsonkumar 2021 St. Mary's University

Smoking, Alcohol Consumption, And Depression In Association With Incidence Of Type 2 Diabetes Among Mexican Americans In Starr County, Texas, Gabriela Rubannelsonkumar

St. Mary's University Honors Theses and Projects

Previous studies on conditions like obesity, hypertension, and type 2 diabetes mellitus (T2DM) have explored the correlations between them and various other human conditions, including aortic stiffness, left ventricular hypertrophy and sleep apnea, as they predict possibilities of developing certain diseases in Mexican Americans. This study aims to observe the correlation between lifestyle decisions that could relate to the onset of the depression in normal, prediabetic, and diabetic individuals. These include smoking habits and alcohol consumption. Many papers have previously conducted research on these lifestyle habits as they relate to obesity, hypertension, diabetes, however, have done so in a singular ...


The Efficacy Of Plant-Based Dietary Program In Patients With Diabetes: A Pilot Study, Reuben Adatorwovor, Nisha Sharma, Dakota McCoy, Sharon Wasserstrom, Matthew Robinson, Jacquelyn Nyenhuis, Sowmya Suryanarayanan 2021 University of Kentucky

The Efficacy Of Plant-Based Dietary Program In Patients With Diabetes: A Pilot Study, Reuben Adatorwovor, Nisha Sharma, Dakota Mccoy, Sharon Wasserstrom, Matthew Robinson, Jacquelyn Nyenhuis, Sowmya Suryanarayanan

Biostatistics Faculty Publications

Dietary choices play a key role in insulin sensitivity among diabetes patients. An 8-week pilot study was conducted to evaluate whether a mostly plant-based dietary program will lead to improvement in biochemical markers in adults with diabetes. The dietary program included educational presentations, weekly cooking demonstrations and small group discussions. A sample of thirty-two adults with diabetes (types 1 and 2) were recruited and seventeen (53%) completed the study. Matched-pair tests and Fishers exact tests were used to compare the changes in means and proportion of the participants’ responses. There were changes in HbA1c, lipids, CRP (mg/L), cholesterol (mg ...


A Copula Model Approach To Identify The Differential Gene Expression, Prasansha Liyanaarachchi 2021 Old Dominion University

A Copula Model Approach To Identify The Differential Gene Expression, Prasansha Liyanaarachchi

Mathematics & Statistics Theses & Dissertations

Deoxyribonucleic acid, more commonly known as DNA, is a complex double helix-shaped molecule present in all living organisms and hosts thousands of genes. However, only a few genes exhibit differential expression and play a vital role in a particular disease such as breast cancer. Microarray technology is one of the modern technologies developed to study these gene expressions. There are two major microarray technologies available for expression analysis: Spotted cDNA array and oligonucleotide array. The focus of our research is the statistical analysis of data that arises from the spotted cDNA microarray. Numerous models have been proposed in the literature ...


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