Digital Commons Network^™

Adaptive Evolution Shapes The Transmissibility Of West Nile Virus In New York State, Sean M. Bialosuknia

Electronic Theses & Dissertations (2024 - present)

Arthropod-borne viruses (arboviruses), which are maintained in nature in complex transmission cycles involving hematophagic invertebrates and their vertebrate hosts, are the cause of a significant and expanding global health burden. Defining arbovirus-host interactions is necessary if we are to understand the adaptive and epidemiological potential of arboviruses. The results presented with West Nile virus (WNV Flaviviridae: Orthoflavivirus), are a compilation of such studies. WNV is the most prevalent arboviral pathogen in the U.S. and the most geographically distributed arbovirus in the world. Despite the evolutionary potential of these RNA viruses, WNV and other arboviruses have experienced only limited …

The Inextricable Link Between Gendered Security And State Stability: Strategic Costs Of U.S. Humanitarian Retrenchment, Kirby Eh Kimball

CMC Senior Theses

This thesis examines the strategic consequences of the 2025 U.S. foreign aid freeze on gendered security in conflict-affected states, focusing on Sudan, Syria, and Ukraine. It argues that gendered security—the protection, empowerment, and rights of women and girls—is not a peripheral humanitarian concern but a foundational determinant of state stability, development, and democratic resilience. Through a qualitative comparative case study methodology, the research synthesizes empirical literature, United Nations reports, human rights documentation, and cross-national statistical analyses to demonstrate how the collapse of gender-focused humanitarian programs following the aid freeze will critically exacerbate conflict-related sexual violence (CRSV), weaken state institutions, and …

Embracing The Unmanageable: The Critique Of The Everyday And The Postwar Condition In Wallace Stevens’ And Robert Duncan’S Works Circa 1950, Kazuma Morita

Electronic Theses & Dissertations (2024 - present)

My thesis is designed as an investigation of the ethical and political implications of the everyday in postwar American poetry. While recent scholarship of everyday life studies has clarified the centrality of the everyday or the ordinary to modernism and postwar literature, it does not elaborate enough on the impact of the political condition on literary expressions of everyday life in post-1945 period. Given U.S. military’s infiltration into everyday life of people living inside and outside the country after World War II, it is an important task to spotlight the way American postwar poets tackled U.S. war culture through their …

Elucidating The Effects Of Environmental And Physiological Conditions On Stem Cell Regulation In Vivo, Nimmy John

Electronic Theses & Dissertations (2024 - present)

The Notch signaling pathway is a highly conserved intercellular signaling pathway that any dysregulation can lead to a variety of human diseases. These diseases are further exacerbated by various environmental, pathological and genetic conditions. Previous studies have shown that these conditions have been known to affect the Notch transcriptional response. However, the molecular mechanisms by which such conditions influence Notch signaling remained largely unknown. Moreover, most Notch studies have relied on in vitro systems and indirect reporters, which can miss the dynamic and contextual nature of Notch signaling. Here, we systematically analyzed the effects of these conditions with single molecule …

Postcolonial Notions Of Criminality In Jane Eyre And Wide Sargasso Sea, Hannah M. Karim

Electronic Theses & Dissertations (2024 - present)

This thesis will use Charlotte Brontë's Jane Eyre and Jean Rhys’s Wide Sargasso Sea to gain a greater understanding of the postcolonial notions of criminality that are sustained and reproduced through racialized purity rhetoric and hierarchy. I argue that the restriction of the definition of the human, within scientific, religious, and legal realms, functioned towards the colonial end of sustaining racial hierarchy. In terms of its means of functioning, I argue that its need to function discretely is a direct response to the abolishment of slavery and with it, the shifting social demand for an appearance of reason, moral righteousness, …

Diversity Within Species: Mechanisms, Evolution And Implications In Bacterial Disease, Kathryn R. Piper

Electronic Theses & Dissertations (2024 - present)

The Gram-positive bacterium Staphylococcus aureus and the Gram-negative bacterium Escherichia coli are ubiquitous commensal and opportunistic pathogens. In humans, S. aureus is commonly found on the skin and mucus membranes, and is known to cause infections in the skin, bloodstream and brain. E. coli is a normal part of the gut microbiota in humans and can cause intestinal and extraintestinal infections alike. S. aureus and E. coli pose global threats to public health, due to the high morbidity and mortality of invasive strains. The wide range of infections they cause in humans and other animals are exacerbated by the presence …

Aviation Cybersecurity And Third-Party Software Service Providers: Do Companies Like Crowdstrike Get A Free Pass To Create Cyber Vulnerabilities?, Claire Konerza

Journal of Air Law and Commerce

Commercial aviation has steadily become the busiest and most efficient means of travel across the world. In order to keep up with the increasing demands of its customers, the industry has undergone numerous digital and technological transformations in recent years. Collision avoidance systems have allowed for more planes in the skies, online ticket reservations have made booking a flight as simple as a few clicks, and in-flight wi-fi allows passengers to engage in both work and leisure at 30,000 feet. Overall, these innovations have increased safety, capacity, and convenience for both airlines and their customers. However, these transformations have also …

A Comprehensive Uhplc-Ms/Ms And Extraction Method Reveals Flavonoid Profile And Concentration Are Diverse In Spinach (Spinacia Oleracea L), Michael P Dzakovich, Elaine A Le, Alvin L Tak, Shaji K Chacko

Children’s Nutrition Research Center Staff Publications

INTRODUCTION: Spinach produces an array of unique flavonoids not commonly found in other fruits and vegetables. These molecules likely serve as defense agents against biotic and abiotic stress and may have health beneficial properties for humans. Current methods to analyze spinach flavonoids are incomplete and only capture a portion of this uncharacterized pathway. A comprehensive analysis method is needed to determine how genetics, environmental conditions, and other factors influence spinach flavonoid biosynthesis.

METHODS: We developed and validated a high-throughput extraction and ultra high-performance liquid chromatography tandem mass spectrometry (UHPLC-MS/MS) method to separate and quantify 39 spinach flavonoid species in 11.5 …

Comparing The Sensitivity And Specificity Of Novel Motor Assessments For Traumatic Brain Injury, Paula K. Johnson, Ariana M. Hedges-Muncy, Erin D. Bigler, Lorie Richards, Steven Knight Charles

Faculty Publications

Background: Portable technology that records movements with high accuracy provides potential for sensitive clinical movement tests for individuals who experienced a traumatic brain injury (TBI). Objective: (1)To present impairments assessed using markerless motion capture (MMC) and (2) to compare the sensitivity and specificity of the MMCmediated tests to each other and to common clinical tests. Design: Screening study, using as criterion standard the ability to classify participant with TBI versus control participant. Setting: Research laboratory. Participants: The study included 30 individuals with TBI and 101 control participants. Entry criteria included most recent head injury < 5 years old, no history of movement issues prior to injury, no movement-affecting medications, and sufficient cognitive ability to follow instructions. Interventions: Not applicable. Main Outcome Measures: Performance on MMC-mediated tests and existing clinical analogs. MMC-mediated tests included finger oscillation, simple reaction time, and visually guided movement tasks. For comparison, participants also completed the following clinical tests: Halstead–Reitan finger tapping, simple reaction time test, and Beery Visuomotor Integration test. Impairments were identified as test scores of participants with TBI that fell outside of the 95% interval of control participants’ test scores. Random forest analysis was used to calculate the sensitivity and specificity of MMC and clinical tests according to their ability to correctly classify participants with TBI and control participants. Results: MMC-mediated tests revealed impairments in more participants with TBI than clinical tests in all three TBI groups (mild, repeated, and moderate to severe). Similarly, MMC-mediated tests revealed a higher percentage of scores as impairments than clinical tests in all three groups with TBI. Furthermore, MMC-mediated tests proved more sensitive and more specific than clinical tests (70% versus 50% and 98% versus 93%, respectively). Conclusion: MMC-mediated tests are sensitive and specific (compared to traditional clinical tests) and have potential to fill a gap in clinical care of TBI.

A Reflection-Spectroscopy Measured Skin Carotenoid Score Strongly Correlates With Plasma Concentrations Of All Major Dietary Carotenoid Species Except For Lycopene, Qiang Wu, Cheryl Webb Cherry, Stephanie Jilcott Pitts, Melissa N Laska, Neal Craft, Nancy E Moran

Children’s Nutrition Research Center Staff Publications

Skin carotenoids can be measured non-invasively using spectroscopy methods to provide a biomarker of total dietary carotenoid and carotenoid-rich fruit and vegetable intake. However, the degree to which skin carotenoid biomarkers reflect intakes of specific carotenoids must be determined for specific devices. Previously, findings were mixed regarding the correlation between reflection spectroscopy (RS)-assessed skin carotenoids and individual plasma carotenoid concentrations. The current study expands on prior analyses to examine the cross-sectional associations between adult RS-assessed skin carotenoids and individual carotenoid species intakes and plasma concentrations, controlling for potential covariates. We hypothesized that RS-assessed skin carotenoid scores would strongly correlate with …

Fingerprints Of Injustice: The Truth Behind Artificial Intelligence And Algorithmic-Driven Evidence,, Aubrey Butler

Chapman Law Review

Artificial intelligence (AI) has steadily grown in prominence, reaching into nearly every aspect of daily life, and the legal system is not immune from its influence. As various forms of machine evidence have been admitted in court, there has been an accompanying rise in concerns from researchers, judges, and defense attorneys as to the trustworthiness and reliability of this new category of evidence.

Though AI and machine evidence takes various forms, this Note focuses on some of the most prominent programs being used in courtrooms today, namely the probabilistic genotyping software TrueAllele and the recidivism rate prediction software COMPAS. The …

Dual Inhibitor Of Mdm2 And Nfat1 For Experimental Therapy Of Breast Cancer: In Vitro And In Vivo Anticancer Activities And Newly Discovered Effects On Cancer Metabolic Pathways, Wei Wang, Marlene Aguilar, Sayantap Datta, Abigail Alley, Meheret Tadesse, Xinshi Wang, Xia Gao, Ruiwen Zhang

Faculty, Staff and Students Publications

INTRODUCTION: The oncogene MDM2 has garnered attention not only for its role in cancer as a negative regulator of the tumor suppressor p53 but also for its p53-independent oncogenic activities. MDM2 also involves metabolic reprogramming, such as serine metabolism, respiration, mitochondrial functions, the folate cycle, and redox balance. Traditional MDM2 inhibitors blocking the protein-protein binding between MDM2 and p53 have shown limited clinical success in various stages of clinical trials, most likely due to low efficacy, drug toxicity, and drug resistance, highlighting the need for a novel, p53-independent strategy to inhibit MDM2. The present study investigated the antitumor effects of …

A Scoping Review Of The Social Determinants Of Pediatric And Adolescent Obesity, Deepali K Ernest, Elizabeth A Onugha, Bipin Singh, Shreela V Sharma, Jayna M Dave

Faculty, Staff and Student Publications

Context: Social determinants of health (SDOH) play a large role in pediatric and adolescent metabolic health worldwide.

Objective: The study is aimed at exploring key SDOH related to childhood obesity, worldwide.

Methods: Primary research articles from PubMed, Embase, and Medline databases published between 2013 and 2023, had a study population of 0-19-year-olds, and examined the association between WHO-defined SDOH and childhood obesity were included. Non-English papers and those outside WHO-defined SDOHs were excluded. Two reviewers independently performed a blinded screening of titles and abstracts, followed by a full-text assessment of selected articles.

Results: Of the 703 initial articles, 22 duplicates …

Mapping Epidermal And Dermal Cellular Senescence In Human Skin Aging, Grace T Yu, Clarisse Ganier, David B Allison, Tamara Tchkonia, Sundeep Khosla, James L Kirkland, Magnus D Lynch, Saranya P Wyles

Children’s Nutrition Research Center Staff Publications

Single-cell RNA sequencing and spatial transcriptomics enable unprecedented insight into cellular and molecular pathways implicated in human skin aging and regeneration. Senescent cells are individual cells that are irreversibly cell cycle arrested and can accumulate across the human lifespan due to cell-intrinsic and -extrinsic stressors. With an atlas of single-cell RNA-sequencing and spatial transcriptomics, epidermal and dermal senescence and its effects were investigated, with a focus on melanocytes and fibroblasts. Photoaging due to ultraviolet light exposure was associated with higher burdens of senescent cells, a sign of biological aging, compared to chronological aging. A skin-specific cellular senescence gene set, termed …

Fecal Glucocorticoid Metabolite And T3 Profiles Of Orphaned Elephants Differ From Non-Orphaned Elephants In Zambia, Daniella E Chusyd, Janine L Brown, Steve Paris, Nicole Boisseau, Webster Mwaanga, Moses Kasongo, Lisa Olivier, Stephanie L Dickinson, Bailey Ortyl, Tessa Steiniche, Steven N Austad, David B Allison, Michael D Wasserman

Children’s Nutrition Research Center Staff Publications

Background: Elephants provide valuable insight into how early-life adverse events (ELAEs) associate with animal health and welfare because they can live to advanced ages, display extensive cognitive and memory capabilities, and rely heavily on social bonds. Although it is known that African savanna elephants that experienced ELAEs, such as being orphaned due to human activities, have altered behavioral outcomes, little is known regarding the physiological consequences associated with those stressors.

Methods: We compared fecal glucocorticoid (fGCM) and thyroid (fT3) metabolites as well as body condition scores (BCS) in rescued and rehabilitated orphaned (early-dry season: n = 20; late-dry season: n …

Regulatory B Cells, The Key Regulator To Induce Immune Tolerance In Organ Transplantation, Jinfeng Liao, Yixin Yang, Jisong Li, Zheng Liu, Siyuan Song, Yu Zeng, Yi Wang

Children’s Nutrition Research Center Staff Publications

In solid organ transplantation, especially renal transplantation, for the induction of immune tolerance, accumulating evidence has revealed that Regulatory B cells (Breg) play a crucial role in stimulating immune tolerance, alleviating immune responses, and improving graft survival. We describe the heterogeneous nature of Bregs, focusing on their defining surface markers and regulatory functions. Meanwhile, the major cytokine secretion function and the correlation between Breg and Treg or other immune checkpoints to balance the immune responses are addressed. Furthermore, we summarized the intrinsic and extrinsic pathways or costimulatory stimuli for the differentiation from naïve B cells. More importantly, we summarized the …

Establishing Standardized Transthoracic Echocardiography Reference Ranges For Mouse Models: Insights Into The Impact Of Anesthesia, Sex, And Age, Manuela A Oestereicher, Christopher S Ward, Elida Schneltzer, Susan Marschall, Helmut Fuchs, Valerie Gailus-Durner, Ghina Bou About, Mohammed Selloum, Hamid Meziane, Michelle Stewart, Lydia Teboul, Clare Norris, Dale Pimm, Marina Kan, Federico López Gómez, Robert Wilson, Mayra Monroy, Sheraz Pasha, Eva Zabrodska, Jan Prochazka, David Pajuelo Reguera, Zuzana Nichtova, Yann Herault, Sara Wells, Helen Parkinson, Jason D Heaney, Radislav Sedlacek, Xiang Gao, Martin Hrabe De Angelis, Nadine Spielmann

Faculty, Staff and Students Publications

Introduction: Mouse models play a critical role in cardiology research, offering valuable insights into the molecular mechanisms, genetics, and potential treatments for cardiovascular diseases. However, the ability to transfer findings in mice between studies is limited by the absence of standardized protocols and valid reference values for the assessment of normal cardiac function in mice. This study aims to establish comprehensive transthoracic echocardiography (TTE) reference ranges for mice, particularly focusing on C57BL/6N wild-type controls.

Methods: The study, which includes data from over 15,000 mice through the International Mouse Phenotyping Consortium (IMPC), highlights how variables such as sex, age, body weight, …

General Kernel Machine Methods For Multi-Omics Integration And Genome-Wide Association Testing With Related Individuals, Amarise Little, Ni Zhao, Anna Mikhaylova, Angela Zhang, Wodan Ling, Florian Thibord, Andrew D Johnson, Laura M Raffield, Joanne E Curran, John Blangero, Jeffrey R O'Connell, Huichun Xu, Jerome I Rotter, Stephen S Rich, Kenneth M Rice, Ming-Huei Chen, Alexander Reiner, Charles Kooperberg, Thao Vu, Lifang Hou, Myriam Fornage, Ruth J F Loos, Eimear Kenny, Rasika Mathias, Lewis Becker, Albert V Smith, Eric Boerwinkle, Bing Yu, Timothy Thornton, Michael C Wu

Faculty, Staff and Student Publications

Integrating multi-omics data may help researchers understand the genetic underpinnings of complex traits and diseases. However, the best ways to integrate multi-omics data and use them to address pressing scientific questions remain a challenge. One important and topical problem is how to assess the aggregate effect of multiple genomic data types (e.g. genotypes and gene expression levels) on a phenotype, particularly while accommodating routine issues, such as having related subjects' data in analyses. In this paper, we extend an existing composite kernel machine regression model to integrate two multi-omics data types, while accommodating for general correlation structures amongst outcomes. Due …

Refinement Of A Published Gene-Physical Activity Interaction Impacting Hdl-Cholesterol: Role Of Sex And Lipoprotein Subfractions, Kenneth E Westerman, Tuomas O Kilpeläinen, Magdalena Sevilla-Gonzalez, Margery A Connelly, Alexis C Wood, Michael Y Tsai, Kent D Taylor, Stephen S Rich, Jerome I Rotter, James D Otvos, Amy R Bentley, Samia Mora, Hugues Aschard, D C Rao, Charles Gu, Daniel I Chasman, Alisa K Manning

Faculty, Staff and Students Publications

Large-scale gene-environment interaction (GxE) discovery efforts often involve analytical compromises for the sake of data harmonization and statistical power. Refinement of exposures, covariates, outcomes, and population subsets may be helpful to establish often-elusive replication and evaluate potential clinical utility. Here, we used additional datasets, an expanded set of statistical models, and interrogation of lipoprotein metabolism via nuclear magnetic resonance (NMR)-based lipoprotein subfractions to refine a previously discovered GxE modifying the relationship between physical activity (PA) and HDL-cholesterol (HDL-C). We explored this GxE in the Women’s Genome Health Study (WGHS; N=23,294; the strongest cohort-specific signal in the original meta-analysis), the UK …

Pathological Changes In Soft Tissues Associated With Radiographically Normal Impacted Teeth: A Critical Update And Meta-Analysis, Adesh S. Manchanda M.D.S., Ramandeep S. Narang M.D.S., Komaldeep Kaur Sandhu B.D.S

The New York State Dental Journal

The purpose of the study was to conduct a retrospective analysis of histopathological diagnosis of all pericoronal tissues associated with impacted teeth and to correlate it with a hypothetical classification of pericoronal follicular space to improve our clinical management of treating impacted teeth. Materials and Method. The study was carried out in the Department of Oral and Maxillofacial Pathology at Sri Guru Ram Das Institute of Dental Sciences, Amritsar. Data revealed that during a 12-year period, 1,268 patients reported with a pericoronal follicular space associated with the crown of an unerupted tooth, which was subsequently submitted for histopathological evaluation. Panoramic …

Naïve Bayes Based Android Adaptive User Authenticationprototype For Young Internet Of Medical Things Users, Prudence Munyaradzi Mavhemwa Mavhemwa, Marco Zennaro, Philibert Nsengiyumva, Frederic Nzanywayingoma

All Rsif Scholars' Publications

The increasing use of the Internet of Medical Things (IoMT) in healthcare highlights privacy and security concerns surroundingsensitive health data. This research focuses on enhancing the security and usability of IoMT for young users through arobust, adaptive continuous authentication model using physiological biometrics on Android devices and heart rate data fromsmartwatches. By integrating user behavior, environmental context, and health conditions, the model dynamically determinesrisk, trust, and authorization decisions. Machine learning techniques analyse data related to devices, networks, locations, anduser habits while considering demographics like age and medical conditions to assign suitable authenticators. The model balancesaccuracy and usability, favouring correct positive …

Synthesizing Knowledge About Tree Diversity, Density, And Distribution In The Savanna Woodlands Of Sudan, Ahmed M.M. Hasoba, Ahmed A.H. Siddig, Kornel Czimber, Ali Omer, Nasradeen A.H. Gadallah, Mohamed M.A. Adam, Audrey Barker Plotkin

All Rsif Scholars' Publications

Savanna ecosystems comprise a complex and diverse biome, marked by the balanced cohabitation of trees and shrubs alongside a rich assembly of herbaceous flora, particularly grasses. In Sudan, savanna ecosystems provide invaluable services that sustain the livelihoods of millions of people. Here, we synthesized the existing knowledge about tree density, diversity, and distribution in the savanna woodlands of Sudan to assess tree diversity, evaluate tree conservation status on the basis of tree abundance and distribution according to IUCN guidelines, and map tree diversity and density in savanna woodlands. The research process started with an extensive search for relevant literature across …

Conserving Carbon Stocks Under Climate Change: Importance Of Trees Outside Forests In Agricultural Landscapes Of Mongala Province, Democratic Republic Of Congo, Jean Pierre Azenge Bokoy, Aboubacar‑Oumar Zon, Jean Pierre Pitchou Meniko, Jérôme Ebuy, Justin N’Dja Kassi, Paxie W. Chirwa

All Rsif Scholars' Publications

This study aimed to evaluate the role of trees outside forests on agricultural land (TOF‑AL) in preserving the initial aboveground biomass (AGB) of forests within the agricultural landscape of Mongala province in the Democratic Republic of Congo. In 2024, tree inventories were conducted over four months in the forests and agricultural lands of Mongala province to analyse AGB. The effects of artisanal logging and charcoal production activities on the AGB conservation rate were considered. This study indicates that 78.3% of the trees encountered in agricultural lands were large‑diameter trees (diameter at breast height (DBH) ≥ 60 cm). In forest areas, …

Effect Of Aflasafe Tz01® On Aflatoxin Reduction And Emerging Challenges With Fusarium Mycotoxins In Maize From Rural Tanzania, Sambwe Fundikira, Martin Kimanya, Rashid Suleiman, Marthe De Boevre, Kokeb Tesfamariam Kokeb Tesfamariam, Sarah De Saeger

All Rsif Scholars' Publications

Aflatoxins are carcinogenic secondary metabolites produced by Aspergillus species and are common contaminants of many crops including maize. Atoxigenic Aspergillus flavus strains, formulated as biocontrol products such as Aflasafe® TZ01, that comprises a mixture of four native atoxigenic strains, are used as pre-harvest agents to suppress toxigenic strains and reduce aflatoxin levels. This study assessed the intended and potential unintended impacts of Aflasafe® TZ01 on mycotoxin contamination in maize. A total of 158 samples 79 from treated and 79 from untreated fields were collected from Chemba and Kiteto districts in Tanzania. Multi-mycotoxin analysis was conducted using liquid chromatography coupled with …

Molecular Evidence Of Brucella Abortus Circulating In Cattle, Goats, And Humans In Central Equatoria State, South Sudan, Emmanuel Philip Lasuba Lita, Ernatus M. Mkupas, Erneo B. Och, Gerald Misinzo, Henriette Van Heerden, Robab Katani, Jacques Godfroid, Coletha Mathew

All Rsif Scholars' Publications

Brucellosis is a neglected zoonotic disease in most developing countries, including South Sudan. Precise identification of Brucella species is crucial for addressing public health and epidemiological concerns associated with brucellosis. The study aimed to identify Brucella species using real-time polymerase chain reaction (qPCR) from seropositive samples that were acquired from an earlier investigation. A total of 143 genomic DNA samples were extracted from brucellosis Rose Bengal plate test (RBPT) seropositive samples from humans (n=7), cattle (n=103) and goats (n=33). The samples were collected from Terekeka and Juba counties, Central Equatoria State (CES), South Sudan. The qPCR targeting the Brucella-specific IS711 …

Synthesis, Stability, And Lumiinesent Properties Of Nayf₄:Yb³⁺, Er³⁺ Upconversion Rare-Earth Nanoparticles, Moshira Ibrahim

Graduate Thesis and Dissertation post-2024

Upconversion nanoparticles (UCNPs), particularly those based on Sodium Ytterium Floride ( NaYF₄) doped with Lanthanide ions, have emerged as promising multifunctional materials owing to their exceptional capacity to convert near-infrared (NIR) light into visible or ultraviolet light through multiphoton excitation processes. Their remarkable resistance to photobleaching, minimal toxicity, and customizable emission characteristics render them ideal candidates for applications in both environmental monitoring and biomedical fields. This thesis investigates the synthesis, structural characterization, and functional performance of NaYF₄:Yb³⁺,Er³⁺ upconversion nanoparticles s, with a focus on its applicability in fog. In response to the limitations of conventional fog detection technologies under low-visibility …

Computational Methods For Population Genetic Inference Using Identity By Descent And Local Ancestry, Yuan Wei

Graduate Thesis and Dissertation post-2024

Identity by descent (IBD) and local ancestry are essential for population genetic inference, such as understanding genealogical relationships and demographic history through genomic data. With the availability of large and high-resolution datasets, new opportunities and computational challenges are brought for efficient and accurate methods to infer IBD segments and local ancestry. This dissertation presents three computational methods designed to assist in population genetic inference. First, RaPID-Query is introduced to efficiently query IBD segments for individual haplotypes over a large genotype dataset. This method is based on the positional Burrows-Wheeler transform (PBWT) algorithm and utilizes a random projection approach. RaPID-Query is …

Algorithms And Benchmarking For Parallel Identity-By-Descent Segment Detection, Kecong Tang

Graduate Thesis and Dissertation post-2024

As genomic biobank initiatives continue to grow, the availability of large-scale genotype datasets, encompassing hundreds of thousands to millions of individuals, has transformed genetic research and biomedical discovery. However, the sheer volume of this data presents major computational barriers. Efficient and scalable methods are urgently needed to process and extract meaningful signals from biobank-scale data using modern multi-core architectures. One central task in this domain is the detection of identity-by-descent (IBD) segments, which underpins a range of applications including genealogical inference, disease mapping, phasing, and population structure analysis.

This dissertation addresses these challenges by presenting a sequence of contributions that …

A Numerical Assessment Of Shock-Raindrop Interaction: An Investigation Of Cavitation Dynamics Driven By Internal Pressure Wave Focusing, Reed Forehand

Graduate Thesis and Dissertation post-2024

This dissertation investigates the formation and evolution of cavitation within liquid droplets subjected to shock wave interactions, with emphasis on internal pressure wave focusing as a fragmentation mechanism. A numerical framework is developed in which high-resolution Volume-of-Fluid (VoF) simulations resolve shock transmission into spherical, cylindrical, and cubic water droplets across a range of flow conditions. The resulting pressure histories at droplet centers are extracted and post-processed using the Rayleigh–Plesset equation to model the dynamics of spherical vapor bubbles.

The modeling framework is validated against established benchmarks, including canonical shock tube behavior, shock-droplet interaction studies, and experimental cavitation observations. A series …

Removal Of Long- And Short-Chain Per- And Polyfluoroalkyl Substances From Surface Water Using Green Sorption Media–Nanofiltration Hybrid Processes, Md Touhidul Islam

Graduate Thesis and Dissertation post-2024

Per- and polyfluoroalkyl substances (PFAS) are a class of persistent environmental contaminants that pose significant risks to human health and aquatic ecosystems. This dissertation addresses the removal of both long- and short-chain PFAS from surface water through an integrated approach that combines green sorption media (GSM) with nanofiltration (NF). The research comprises laboratory-scale and field-scale studies designed to evaluate the effectiveness of novel recycled-material-based GSM formulations—namely, CPS and ZIPGEM—as pretreatment options to mitigate membrane fouling and enhance PFAS removal during NF. The study also investigates the adsorption mechanisms under varying water chemistry conditions, including pH, ammonia, and divalent cation concentrations. …