Life Sciences Commons^™

Unpaired Virtual Histological Staining Of Tissue From Autofluorescence Using Regularized Cycle-Consistent Adversarial Networks, Zhesi Wen

Theses and Dissertations

We present a regularized CycleGAN with a Dense Residual U-Net to virtually stain autofluorescence images of tissue into H&E-like images. Our method outperforms standard architectures, reduces artifacts, and achieves superior FID scores, enabling efficient, label-free, and accurate digital pathology for unpaired datasets using multi-channel fluorescence inputs.

Examining Loss Of Imprint In F1 Hybrid Female Mice Due To X Chromosome Epimutation And The Implications For Autism, Arianna H. Roach

Honors Scholar Theses

Sex biases are prevalent among various neurodevelopmental disorders, with males experiencing them at higher frequencies or severities than females. This male bias is poorly understood, and our lab aims to elucidate this mechanism using our model of transgenerational epigenetic inheritance. Our lab identified the cluster of genes Xlr3b/4b/4c on the X chromosome that are imprinted in the female brain. Preliminary studies suggest that Xlr3 acts as a mediator molecule in our model. Xlr3 knockdown male mice exhibited significant meiocyte loss that can be attributed to Meiotic Sex Chromosome Inactivation. Their female offspring also displayed loss of imprinting of Xlr3 and …

The Interaction Between Physical Activity And Fruit And Vegetable Intake On Body Composition, Om S. Ghetia

Honors Scholar Theses

Objective: Fruit and Vegetable (FV) intake and Physical Activity (PA) are important lifestyle factors associated with body composition. This study assessed the combined impact of meeting FV intake and PA recommendations on body composition measures including body mass index (BMI), percent body fat (PBF), and waist circumference (WC) in adults aged 20–64 years from diverse backgrounds.

Design: A cross-sectional study conducted in Northeastern Connecticut.

Methods: A total of 124 participants completed a one-week dietary and PA record followed by anthropometric assessments. Participants were categorized into groups based on FV intake (≥400 g/day vs. < 400 g/day) and PA levels (≥600 MET-minutes/week vs. < 600 MET-minutes/week). Independent t-tests and chi-square tests were used to compare dietary intake, PA levels, and body composition outcomes across groups.

Results: Participants meeting FV recommendations had significantly …

The Role Of Elongin B In Drosophila Melanogaster Muscle Development, Madelyne Dayan

Student Theses and Dissertations

Muscle atrophy is a result of a number of muscle diseases, as well as aging, disuse, and infections. Muscles weakened in these ways exhibit a characteristic decrease in size, strength, and mobility. The similarities between muscle in humans and Drosophila allow for direct comparisons to be made in vertebrates from studying muscle in Drosophila. Differential gene expression has been shown to play an important role in embryonic muscle development in Drosophila melanogaster. A previous study identified Elongin B (EloB) to be involved in somatic muscle morphogenesis in Drosophila, with mutant embryos displaying severe muscle defects, including thin, mis-attached, and missing …

Know Thyself: A History Of Ancient Neuroscience, Alex Delano

Departmental Honors & Graduate Capstone Projects

Neuroscience is often described as one of the youngest bodies of science, but documented study of the brain begins as early as the Neolithic period. The ancient Mediterranean was a hub for science, mathematics, philosophy, and literature, all disciplines necessary for the study of the brain. Evidence of neurosurgical procedures like trepanation and craniotomy began in the Neolithic period and were practiced and improved upon throughout the ancient Mediterranean. The first detailed studies on brain anatomy were carried out in the 3^rd century BCE in Greece which created a necessary structure for future scientists to build on. While many …

Enhancing Food Safety: Detecting Pathogens In Bison, Vrinda Brahmbhatt

Honors Capstones

Bison herds are being reintroduced across Illinois for prairie conservation efforts and as an important food source, with bison meat gaining popularity as a healthier alternative to beef. However, bison can act as reservoirs of pathogens such as Shiga toxin-producing Escherichia coli (STEC) and antimicrobial resistance (AMR) genes, posing food safety and public health risks. Conservational and commercial herds are managed differently, which may influence the prevalence of STEC and associated AMR genes. To address concerns about potential AMR transmission from bison to humans via fecal-oral routes, we examined the prevalence of AMR in STEC isolates from both herd types. …

Developing A Trial Unique Sequencing Task For Mice, Yader Gomez, Lilly Hagos, Gage Pompa, Ariana Mitic, Orlando Montiel, Talha Soluoku

Undergraduate Research Symposium Posters

The hippocampus and the anterior cingulate cortex (ACC) play distinct yet complimentary roles in the performance of cognitively demanding tasks.

While rodent models cannot truly capture human cognition, there is a serious need to develop more cognitively demanding rodent tasks to better understand human cognition to develop new tools to fight neurodegeneration.

Sequencing tasks are some of the most difficult for rodents to perform and are notoriously difficult to train.

Cutting edge interactive touch screen technology allows us to test an endless array of sequences, in a sound-controlled enclosure featuring a simple behavioral response for the mice.

Study Aim: To …

Marine Heat Waves Effects On Rocky Intertidal Ecosystem Functioning, Skyler Peterson, S. Schneider, C.L. Webb, A. Leighton

Undergraduate Research Symposium Posters

Severe heat waves may cause long-term changes in marine ecosystems and are expected to increase in magnitude and frequency. Here we use surveys from six localities across a six-year interval (2013-2019) to investigate the effects of heat waves on the functional diversity of rocky intertidal ecosystems (Vancouver Island, Canada).

Functional diversity, the number and types of functions performed by organisms, influences ecosystem stability and health. To assess changes in functional diversity we used analyses of biological traits. Biological traits are measurable properties of organisms that describe their morphology, physiology, and behavior. We quantitatively assessed changes in functional diversity in response …

Competence Protein Comea And Oxidative Stress In Bacillus Subtilis Stationary Phase Mutagenesis, Angeline Roldan, Sam Schauf

Undergraduate Research Symposium Posters

Stationary Phase Mutagenesis is a process where a bacterium can accumulate mutations in the absence of cell division. This may occur via competent DNA uptake and oxidant DNA damage and repair. ComEA is a transmembrane protein in B. subtilis that is required for the transport of exogenous DNA into the cell. (Figure 1)

Exploring Mobility: Phylogenetic And Structural Analysis Of The Intein In The Helicase Of Mycobacteriophage Alice, Sandra Xu

Honors Scholar Theses

This paper investigates the intein insertion in the DNA helicase gene Alice_175 of the Mycobacterium phage Alice, exploring its evolutionary significance and potential propagation mechanisms. Using phylogenetic analysis, there is evidence for gene transfer as a driving force in intein dissemination in phage and bacterial genomes. Structural predictions of the Alice_175 intein that were generated through AlphaFold2 as well as a phylogeny generated using SeaView infer a timeline of the intein's invasion and reveal key features that may influence protein functionality and host adaptation. Additionally, protein database searches suggest that intein mobility in this gene may not rely on prophages, …

Preparation And Characterization Of Phthalocyanine Photocatalysts Supported On Mixed Metal Oxides, Malak Alsharhan

Seton Hall University Dissertations and Theses (ETDs)

This research explores the development of hybrid photocatalysts by combining GeO₂ doping of metal oxides with phthalocyanine functionalization to enhance the degradation of Methyl Orange (MO) dye under visible light. Four metal oxide supports, TiO₂, Al₂O₃, SiO₂, and ZrO₂, were tested in their pristine form, then modified with GeO₂ and further functionalized by solution adsorption using two types of zinc phthalocyanines: F₁₆PcZn and F₆₄PcZn.

The degradation of MO was monitored using UV-Vis spectroscopy, and kinetic models were applied to evaluate the reaction rates. The results showed that the bare oxides exhibited little to no photocatalytic performance. GeO₂ doping …

Genomic Characterization Of High-Grade Serous Ovarian Carcinoma Reveals Distinct Somatic Features In Black Individuals, Katherine A Lawson-Michod, Jeffrey R Marks, Lindsay J Collin, David A Nix, Natalie R Davidson, Chad D Huff, Yao Yu, Aaron Atkinson, Courtney E Johnson, Lucas A Salas, Lauren C Peres, Casey S Greene, Joellen M Schildkraut, Jennifer A Doherty

Faculty, Staff and Student Publications

Black individuals experience worse survival after a diagnosis of high-grade serous ovarian carcinoma (HGSC) than White individuals and are underrepresented in ovarian cancer research. To date, the understanding of the molecular and genomic heterogeneity of HGSC is based primarily on the evaluation of tumors from White individuals. In the present study, we performed whole-exome sequencing on HGSC samples from 211 Black patients to identify significantly mutated genes and characterize mutational signatures, assessing their distributions by gene expression subtypes. The occurrence and frequency of somatic mutations and signatures by self-reported race were compared with historic data from The Cancer Genome Atlas …

Longitudinal Profiling Of Circulating Tumor Dna Reveals The Evolutionary Dynamics Of Metastatic Prostate Cancer During Serial Therapy, Yuehui Zhao, Naveen Ramesh, Ping Xu, Emi Sei, Min Hu, Shanshan Bai, Patricia Troncoso, Ana M Aparicio, Christopher J Logothetis, Paul G Corn, Nicholas E Navin, Amado J Zurita

Faculty, Staff and Student Publications

Treatment decisions in metastatic castration-resistant prostate cancer are mostly guided by clinical variables, but efforts to molecularly monitor the disease remain hampered by challenges in acquiring tumor tissue repeatedly. In this study, we simultaneously profiled the genome copy number and exome in longitudinal plasma circulating tumor DNA (ctDNA) acquired before, during, and upon progression to serial treatments with androgen signaling inhibitors and taxane chemotherapy from 60 patients with metastatic castration-resistant prostate cancer (2-10 samples per patient). The genomic data were used to delineate the clonal substructure and evolutionary dynamics of each patient, and an evolutionary dynamic index was developed to …

Efficacy And Safety Of Larotrectinib In Patients With Trk Fusion Gastrointestinal Cancer, Changsong Qi, Lin Shen, Thierry Andre, Hyun Cheol Chung, Timothy L Cannon, Elena Garralda, Antoine Italiano, Damian T Rieke, Tianshu Liu, Domnita-Ileana Burcoveanu, Natascha Neu, Chiara E Mussi, Rui-Hua Xu, David S Hong, Alexander Drilon, Jordan Berlin

Faculty, Staff and Student Publications

Background: Larotrectinib is the first-in-class, highly selective TRK inhibitor with demonstrated efficacy in various TRK fusion solid tumours. We report the efficacy and safety of larotrectinib in patients with TRK fusion gastrointestinal (GI) cancer.

Methods: Patients with TRK fusion GI cancer from NAVIGATE (NCT02576431) were included. Response was independent review committee (IRC)-assessed per RECIST v1.1.

Results: As of July 2023, 44 patients were enrolled. Tumour types included colorectal (CRC; n = 26), pancreatic (n = 7), cholangiocarcinoma (n = 4), gastric (n = 3), and one each of appendiceal, duodenal, oesophageal and hepatic cancers. Of the 26 patients …

A History Of Omics Discoveries Reveals The Correlates And Mechanisms Of Loading-Induced Hypertrophy In Adult Skeletal Muscle. 2024 Camps Young Investigator Award Invited Review, Toby L. Chambers, Kevin A. Murach

Health, Human Performance and Recreation Faculty Publications and Presentations

Since the early 2000s, omics approaches to study skeletal muscle hypertrophy consequent to loading (e.g., resistance exercise) have expanded dramatically. Beginning with genomics and transcriptomics, there are now omics datasets from hypertrophying skeletal muscle spanning methylomics, proteomics, and phosphoproteomics, with further integration of single cell/nucleus-specific omics, among others. The purpose of this review is to explore the history of leveraging omics to enable understanding and discovery with respect to loading-induced hypertrophy in adult skeletal muscle. We elaborate on key historical and contemporary studies and findings, highlight specific examples where omics discoveries led to a mechanistic understanding of skeletal muscle growth, …

Using Satellite Tracking And Stable Isotopes To Characterize The Movements, Core-Use Areas, And Distribution Of Loggerhead And Green Turtles Nesting In South Florida, Usa: Internesting, Foraging, And Migration, Glenn D. Goodwin

All HCAS Student Capstones, Theses, and Dissertations

The movements of animals in response to environmental variation influence the fitness of individuals and drive major ecological processes, while also varying their exposure level to anthropogenic risks. Understanding the movements and spatial distribution of imperiled species is critical for developing effective conservation strategies. This can be difficult for wide ranging and highly migratory species, such as sea turtles. Throughout their adult life stages, the females of most sea turtle species spend the majority of their time in their foraging areas for multiyear intervals between nesting periods. These foraging areas are typically widely dispersed and variable within nesting populations. To …

New Mexico Cooper's Hawk Demographic Study: 2024 Annual Report, Brian A. Millsap Dr., Jay Gedir, Chris Vennum, Fitsum Abadi, Kristin Madden, Kirsten Mcdonnell, Emily Bjerre, Hillary White, Ted Swem, Michael Stewart

New Mexico Cooper’s Hawk: Publications

The 2024 Annual Report for a long-term (2011 -  present) demographic study of Cooper's hawks (Astur cooperii) in Albuquerque, New Mexico.

Parsing Heterogeneity In Depression, Kayla Hannon

Arts & Sciences Graduate Student Theses and Dissertations

Depression is a highly prevalent mental health disorder that often requires treatment. While current treatments are effective for a large portion of patients generally, the exact medication that works for any specific person is unclear, leading to large delays in symptom remittance if at all. This hurdle has motivated substantial efforts to identify markers of depression that might predict treatment outcomes. However, large sources of heterogeneity in depression have stymied progress on identifying robust and replicable neuroimaging markers. Parsing this heterogeneity is crucial but mired with challenges. My dissertation work has elucidated several key barriers in parsing the heterogeneity of …

Role Of The Small Intestinal Microbiota In The Pathogenesis Of Environmental Enteric Dysfunction In Undernourished Children And Mothers, Clara Kao

Arts & Sciences Graduate Student Theses and Dissertations

Undernutrition in women and its propagation in their children remains a major global health challenge. Worldwide, one in five children under five years of age manifests undernutrition as impaired linear growth, or stunting. Stunting, defined as having a length-for-age z-score (LAZ) <-2, is associated with poor developmental outcomes, including impaired neurodevelopment and immune responses. Furthermore, stunting and its long-term sequelae persist across generations, contributing to an intergenerational cycle of undernutrition. Existing nutritional interventions fail to substantially improve stunting, highlighting the need to (i) better understand other factors contributing to stunting and (ii) focus clinical efforts towards treating maternal undernutrition. Environmental enteric dysfunction (EED) is a subclinical inflammatory enteropathy of the small intestine proposed to contribute to stunting. EED is diagnosed histologically by blunted intestinal villi, epithelial barrier disruption and an immunoinflammatory infiltrate in the lamina propria. However, the pathophysiology of EED remains poorly defined. Furthermore, the small intestinal microbiota remains understudied due to difficulties in sampling. Evidence that the small intestinal microbiota contributes to EED pathogenesis comes in part from our collaborative work with colleagues at icddr,b (the International Centre for Diarrhoeal Disease Research, Bangladesh) who oversaw the Bangladesh EED (BEED) study. In this study children, aged 12-18 months residing in an urban slum in the Mirpur district of Dhaka who failed a nutritional intervention for their stunting, underwent esophago-gastroduodenoscopy (EGD) to obtain duodenal mucosal biopsies, aspirates of duodenal luminal fluid and plasma samples. A set of 14 bacteria taxa (defined by 16S rRNA amplicon sequencing) were identified in the duodenal microbiota of >80% of children with EED. Moreover, the absolute abundances of these ‘core taxa’ were positively correlated with duodenal mucosal and systemic inflammation in study participants and negatively correlated with linear growth. Our lab showed that introduction of a consortium of bacteria cultured from these duodenal aspirates, including these core taxa, produced small intestinal inflammation in young adult gnotobiotic, providing …

Microbial Community And Water Quality Assessment Of Crassostrea Virginica Habitats In Southeast Florida, Stacy Brown

All HCAS Student Capstones, Theses, and Dissertations

Eastern oysters (Crassostrea virginica) are essential habitat-forming species that contribute significantly to coastal water quality due to their filter-feeding behavior. Unlike other coastal regions in the Gulf of Mexico and Northeastern United States, oysters are not commercially managed in Southeast Florida and as a result sparse data exists on locations of the Eastern oyster habitat. Similarly, the benefits of oyster reefs to water quality are also not fully documented in Southeast Florida. Although beneficial and often referred to as keystone habitat building species, populations of C. virginica are not currently listed as protected species so little work has …

Table Of Contents And Front Matter, Bjur Staff

Butler Journal of Undergraduate Research

No abstract provided.

Rising Use Of Immune Checkpoint Inhibitors And The Escalating Burden Of Gastrointestinal And Hepatic Toxicities: A Nine-Year Analysis, Donghyun Ko, Do Han Kim Md, Pedro Palacios Argueta Md, Wilhelm S. Basegoda Md, Jose A. Porres, Francis F. Fadi, Jana G. Hashash, Francis A. Farraye, Paul T. Kroner Md

Posters

The advent of immune checkpoint inhibitors (ICIs), including programmed death 1 (PD-1), PD-L1, and cytotoxic T-lymphocyte-associated antigen 4 (CTLA-4) inhibitors, has revolutionized cancer therapeutics, markedly improving survival in various malignancies. However, their expanding utilization has been paralleled by the emergence of immune-related adverse events (irAEs), particularly gastrointestinal (GI) and hepatic toxicities, which pose significant challenges in clinical practice. These toxicities can manifest as a spectrum of conditions, from mild transient symptoms to severe, life-threatening complications, necessitating a better understanding of their prevalence and trends. This study aims to evaluate the temporal changes in ICI use and associated GI and hepatic …

The Effect Of Boom Leveling On Spray Dispersion, Miguel Bustamante, Juan F. Vivanco, Travis A. Burgers

Mechanical Engineering Faculty Publications

Automatic boom height systems reduce the variability of agricultural sprayer boom height. When a boom is not at its target height, this can lead to uneven spray dispersion from the nozzles. Boom heights and sprayer position were previously measured in time for three commercially-available boom leveling systems for three test runs for at least three speeds over each of a mild, medium and rough terrain course. A computational model was created to use measured spray dispersion from a nozzle, measured boom heights in time, and measured sprayer position in time to calculate a spray coverage map. The model was used …

Autonomous Agricultural Equipment Evaluation For Broad-Acre Crop Production, Sofia Bahmutsky, Ashutosh Singh, Travis A. Burgers, Roy Maki

Mechanical Engineering Faculty Publications

No abstract provided.

The Relationship Between Food Allergies And Intolerances And The Development Of Disordered Eating Patterns, Lucy M. Scholma

Human Nutrition and Hospitality Management Undergraduate Honors Theses

Food allergies and food intolerances are becoming an increasingly more prevalent issue in the Unites States. To mitigate adverse reactions, these individuals often eliminate food or food groups from their diets and the ramifications of these lifestyle changes may result in disordered eating patterns. In regard to food allergies and intolerances and eating disorders, it is reasonable to suggest that the overlapping lifestyle choices and physical, social, and emotional ramifications may lead to a correlation between the two phenomena. This study explores the relationship between food allergic and food intolerant individuals and disordered eating habits among college students. Survey results …

Excess Fructose In High-Fructose Corn Syrup Reduces Cell Viability & Promotes Nitric Oxide Release In Raw 264.7 Macrophages, Renzo F. Galarza, Edward L. Villegas

Research and Creativity Symposium

High-fructose corn syrup (HFCS) is an artificial sweetener that contains slightly higher concentrations of fructose compared to standard sucrose. It has been linked to an increased risk of obesity, type 2 diabetes, cardiovascular disease, and fatty liver disease. While both HFCS and sucrose are widely used sweeteners, growing evidence suggests they may differ in their inflammatory potential. We sought to understand the effects of elevated fructose on RAW 264.7 macrophages. To investigate these effects, we treated the cells with either a sucrose solution or a
solution designed to mimic high-fructose corn syrup. Lipopolysaccharide (LPS) stimulation was used to model innate …

Fisheries Research Report No. 351: Ecological Risk Assessment For The Western Australian Southern Nearshore Fish Resource, Kimberley A. Smith, Brett Crisafulli, Amber Quinn, Bianca Brooks, Gabby E. Mitsopoulos, Daniel Yeoh

Fisheries Research Reports

On 3 December 2024, the Department of Primary Industries and Regional Development (DPIRD, the Department) convened an ecological risk assessment (ERA) of the fisheries that access the Southern Nearshore Fish Resource (Resource). This Resource comprises a range of temperate fish species including Australian herring, Australian salmon, whiting, garfish, tailor and sandy sprat.

This document contains the results of the ERA as well as the background information used to support the ERA risk scoring process. This includes an overview of the Western Australian commercial, recreational and charter fisheries that access the Resource.

Impacts Of German Yellowjacket (Vespula Germanica) Removal On Pollinator Communities In Western New York, Jonathan M. Promowicz

Biology Theses

Invasive social insects can restructure native arthropod communities through predation and competition. Vespula germanica (German yellowjacket) is a globally invasive wasp species that dominates vespid assemblages across urban and suburban landscapes. This study tested the hypothesis that reducing V. germanica using protein-based fipronil baits would increase native pollinator abundance, species richness and native vespid abundance. Vespula germanica was experimentally suppressed at suburban and urban sites. Pollinator abundance and richness increased with V. germanica baiting. Native vespids had mixed results from baiting with suburban sites increasing in overall abundance and urban sites decreasing. These results indicate that suppressing dominant invasive wasps …

Evaluating The Health Of The Latah Creek Tributary And Its Impact On The Health Of The Spokane River By Aquatic Macroinvertebrate Analysis, Andee West, Ian Townley

CURCI Student Research

Research question: How does the Latah Creek tributary impact water quality of the Spokane River, monitoring the riverbanks and macroinvertebrate families?

Does Limb Specialization In Track And Field Introduce Asymmetry In Dynamic Stability?, Aaron X. Jones

Master's Theses

Time to stabilization (TTS) represents the time it takes for a person to become still after a hop landing. Lower times suggest greater dynamic stability. Whereas leg dominance (preference) does not seem to have a significant impact on TTS performance in the general healthy populations, limb specialization in sport may introduce asymmetry. This study compares TTS following forward hops in healthy male controls (N = 19) to varsity DIII Track & Field athletes (N = 20). Groups were equal for height, but the athlete group’s average limb length (106.7 ± 5.5 cm) was greater than the control group (101.5 ± …