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Articles 61 - 90 of 39060
Full-Text Articles in Biology
Data Curation And Integration For Cancer Cell Line Pharmacogenomics Analysis, Meric Kinali
Data Curation And Integration For Cancer Cell Line Pharmacogenomics Analysis, Meric Kinali
Graduate Masters Theses
Cancer cell lines are essential resources for connecting genomic and molecular features with drug response and identifying biomarkers. Therefore, large-scale cancer cell line resources have been growing, but this introduces challenges such as data standardization, consistent annotation, matching identifiers, cross-database integration, and a reproducible computational framework. CellMiner Cross Database (CellMinerCDB) integrates pharmacogenomic datasets from multiple resources and provides a standardized analysis of cell lines across datasets. This thesis examines cancer cell line cross-databases and their importance in pharmacogenomics, with a particular focus on CellMinerCDB. As part of this work, I developed an R package for the gCSI (Genentech Cell Line …
Infrared Detectability Of Whale Species And Behaviors To Enhance Automatic Detection For Real-Time Vessel Strike Avoidance, Laura J. Howes
Infrared Detectability Of Whale Species And Behaviors To Enhance Automatic Detection For Real-Time Vessel Strike Avoidance, Laura J. Howes
Graduate Masters Theses
Real-time detection of large whales at sea is critical for mitigating serious injury and mortality from ship strikes and other human activities such as seismic surveys, especially for endangered species such as the critically endangered North Atlantic Right Whale (Eubalaena glacialis). Traditional marine mammal observers are limited by environmental conditions and human factors, necessitating a robust, 24-hour solution. This study investigates the efficacy of a novel onboard detection tool infrared (IR) technology to detect whale blows and body parts. While IR is a promising advancement, its performance under varying sea conditions (e.g., fog, humidity) and its ability to …
Enhanced Osseointegration Of Functionally Graded Co˗Cr˗Mo˗Ti/Ha Implants: In Vitro And In Vivo Study In A Rabbit Model, Afrah M. Al Hussainey, Randa Kamel Hussain, Aseel Mustafa Abdul Majeed
Enhanced Osseointegration Of Functionally Graded Co˗Cr˗Mo˗Ti/Ha Implants: In Vitro And In Vivo Study In A Rabbit Model, Afrah M. Al Hussainey, Randa Kamel Hussain, Aseel Mustafa Abdul Majeed
Karbala International Journal of Modern Science
The present investigation aims to evaluate the effects of acid and laser surface treatments on the surface characteristics, biocompatibility, and osseointegration of functionally graded implants fabricated from a Co–Cr–Mo–Ti/HA alloy. The implant surfaces were modified using either an Nd: YAG laser or hydrochloric acid (HCl), while untreated implants served as controls. Atomic force microscopy (AFM) showed that the acid-treated surface exhibited the highest mean surface roughness (Sa) of 58.10 ± 0.24 nm compared to the laser-treated surface (42.64 ± 0.83 nm) and the untreated surface (37.73 ± 0.89 nm). The MTT assay also demonstrated a favourable cellular response on the …
Bryophyte Community Composition In A Second-Order Tropical Stream At The Luquillo Experimental Forest, Puerto Rico, Cecilia Sahnow, Jean P. González-Crespo, Amelia Merced
Bryophyte Community Composition In A Second-Order Tropical Stream At The Luquillo Experimental Forest, Puerto Rico, Cecilia Sahnow, Jean P. González-Crespo, Amelia Merced
Biology Faculty Publications and Presentations
Streams are important ecosystems that harbor a high diversity of plant species including bryophytes. Studies suggest streams can function as refugia and/or corridors that buffer against the effects of disturbances. In this study, we sampled five sites along a second-order tropical stream in the Luquillo Experimental Forest. We described the riparian bryophyte community composition in conjunction with the physical structure of the stream to understand what environmental factors influence bryophyte composition in the stream. We identified 56 bryophytes, 33 liverworts and 23 mosses; and we recorded cyanobacteria associated with over half of the species of bryophytes. Rocks were the most …
Assessing The Evolving The Culture Of Biology Program Through The Lens Of The Teacher-Centered Systemic Reform Model, Diyala S. Shihadih, Elizabeth Runkel Baez, Mitra Asgari, Justin Berl, Adam J. Chouinard, Stephanie J. Gutzler, Kaleb K. Heinrich, Eden Riordan, Star W. Lee, Erin E. Shortlidge
Assessing The Evolving The Culture Of Biology Program Through The Lens Of The Teacher-Centered Systemic Reform Model, Diyala S. Shihadih, Elizabeth Runkel Baez, Mitra Asgari, Justin Berl, Adam J. Chouinard, Stephanie J. Gutzler, Kaleb K. Heinrich, Eden Riordan, Star W. Lee, Erin E. Shortlidge
Biology Faculty Publications and Presentations
There are persistent national calls to advance evidence-based instructional practices to increase the number of students graduating with science degrees. Evolving the Culture of Biology is a program designed to improve undergraduate education by prioritizing graduate teaching assistant teaching professional development (TA-TPD). Guided by the Teacher-Centered Systemic Reform (TCSR) model, this study examined how TA TPD practitioners’ (participants) attitudes, personal factors, institutional contexts, and instructional practices shape TA-TPD reform outcomes. Using a pre-program survey and end-of-year semi-structured interviews, we gained insight into participants’ experiences as they developed and implemented reformed TA-TPD. We investigated how TCSR components differentially influenced participant progress, …
Trophic Ecology Of A South Carolina Estuarine Predator Guild, Shane John Molander
Trophic Ecology Of A South Carolina Estuarine Predator Guild, Shane John Molander
Electronic Theses and Dissertations
Estuaries are among the world’s most productive ecosystems in the world and are characterized by the convergence of two distinct habitats, creating a mosaic of environmental conditions from inland rivers to the nearshore ocean. Many fishes occupy estuaries during various life stages for growth, reproduction, or foraging, and may reside in them seasonally. The co-occurrence of species, particularly upper-trophic level carnivores, can result in competitive interactions for prey resources within a shared environment. Identifying the degree of these interactions as well as understanding basal energy consumption can inform food web dynamics and how overlapping species use shared spaces. I used …
Insights Into Longevity And Virus-Driven Adaptation From Myotis Bat Genomes, Juan M. Vazquez, M. Elise Lauterbur, Saba Mottaghinia, Léa Gaucherand, Sarah Maesen, Michael Singer, Sarah Villa, Melanie Bucci, Devaughn Fraser, Genavieve Gray-Sandoval, Zeinab R. Haidar, Melissa Han, William Kohler, Tanya Lama, Et Al
Insights Into Longevity And Virus-Driven Adaptation From Myotis Bat Genomes, Juan M. Vazquez, M. Elise Lauterbur, Saba Mottaghinia, Léa Gaucherand, Sarah Maesen, Michael Singer, Sarah Villa, Melanie Bucci, Devaughn Fraser, Genavieve Gray-Sandoval, Zeinab R. Haidar, Melissa Han, William Kohler, Tanya Lama, Et Al
Biological Sciences: Faculty Publications
The genus Myotis is one of the largest clades of bats, and it exhibits some of the most extreme variation in lifespans among mammals, alongside unique adaptations to viral tolerance and immune defence1–3. Here, to study the evolution of these phenotypes, we generated cell lines and near-complete genome assemblies for eight closely related Myotis species. Using genome-wide screens of positive selection, analyses of structural variation and functional experiments in primary cells, we identify patterns of adaptation contributing to longevity, cancer resistance and viral interactions. We demonstrate distinct modes of adaptation to DNA and RNA viruses compared with all …
The Role Of Seed Mix Characteristics And Soil Amendments During Post-Agricultural Prairie Restoration, Valerie N. Thurston, Michaela J. Woods, Madelaine Gregory, Mary C. Lloyd, Ryan W. Mcewan
The Role Of Seed Mix Characteristics And Soil Amendments During Post-Agricultural Prairie Restoration, Valerie N. Thurston, Michaela J. Woods, Madelaine Gregory, Mary C. Lloyd, Ryan W. Mcewan
Biology Faculty Publications
Introduction: Prairie restoration on degraded lands may be influenced by seed mix characteristics, including species richness and legume establishment. Soil amendments may facilitate restoration; however, the practical usefulness of techniques such as applications of whole soil and leaf mulch remains relatively unclear.
Objectives: We assessed whether increasing species richness and legume content in seed mixes enhances prairie restoration success and examined how soil amendments interact with seed mix composition to influence cover, species richness, diversity, and legume establishment.
Methods: We conducted a field experiment on a 12-ha post-agricultural site in Ohio, U.S.A. Twenty 50 × 50 m plots received one …
Hydrogels For Local Drug Delivery In Biofilm-Associated Periprosthetic Joint Infection: Current Progress And Future Directions, Karolina Kraus, Pawel Mikziński, Bindu Subhadra, Emil Paluch
Hydrogels For Local Drug Delivery In Biofilm-Associated Periprosthetic Joint Infection: Current Progress And Future Directions, Karolina Kraus, Pawel Mikziński, Bindu Subhadra, Emil Paluch
Faculty Publications - Biological Sciences
Periprosthetic joint infection (PJI) remains one of the most serious complications of arthroplasty, largely due to the formation of microbial biofilms on implant surfaces. Biofilm-associated infections exhibit increased tolerance to antimicrobial therapy and host immune responses, making eradication difficult and often requiring repeated surgical interventions. Consequently, there is a growing need for effective local therapeutic strategies capable of delivering high concentrations of antimicrobial agents directly to the site of infection while minimizing systemic toxicity. Hydrogels have emerged as promising drug delivery platforms for the management of biofilm-associated PJI. Their biocompatibility, injectability, high water content, and tunable physicochemical properties enable controlled …
Exploring Foundations Of Animal Host-Microbe Interactions In A Freshwater Sponge, Jacob S. Pawley
Exploring Foundations Of Animal Host-Microbe Interactions In A Freshwater Sponge, Jacob S. Pawley
Electronic Theses and Dissertations
The most ancient eukaryotic immune defense mechanisms evolved in unicellular species. Multicellular eukaryotes, however, expanded these mechanisms to meet challenges unique to multicellular life, including barrier formation, long-distance cell signaling, and coordinated responses that eliminate microbial threats while minimizing damage to the host. As such, animal immune signaling pathways are exceptionally intricate and diverse. Though, most of what is understood about animal host–microbe interactions stems from a small handful of model systems. Here, I evaluate host–microbe interactions and innate immunity in sponges using the highly tractable freshwater sponge, Ephydatia muelleri. I report the discovery of an external host-derived matrix …
Policy System Of Us Bioeconomy Based On “3ms” Framework, Jingyan Zhou, Nianping Tian, Xuehui Jin, Cuijuan Yin
Policy System Of Us Bioeconomy Based On “3ms” Framework, Jingyan Zhou, Nianping Tian, Xuehui Jin, Cuijuan Yin
Bulletin of Chinese Academy of Sciences (Chinese Version)
The United States is a dominant power in the global bioeconomy. An in-depth analysis of its policy system characteristics holds significant reference value for China to further formulate China’s bioeconomy strategy and drive the development of China’s bioeconomy. This study employs the “3Ms” policy analysis framework to conduct a comprehensive analysis of the US bioeconomy policy from three dimensions: macro strategy, meso architecture, and micro structure. The research reveals that the US bioeconomy policy demonstrates the following characteristics in the macro strategy: being systematic, comprehensive, and scientifically decision-making; in the meso architecture: forming government-congressional cooperation and multi-party collaboration; and in …
Analysis Of Early Menopause And Endometriosis Genetics Merit In Use Of Polygenic Risk Assessments For Prediction, Emily Solomon
Analysis Of Early Menopause And Endometriosis Genetics Merit In Use Of Polygenic Risk Assessments For Prediction, Emily Solomon
Graduate Student Dissertations, Theses, Capstones, and Portfolios
Endometriosis and Early Menopause are reproductive conditions that are under research in women's health. Both conditions impact a woman’s quality of life through severity of symptoms and associated risk factors and are influenced by genetic, hormonal and environmental elements. Both conditions have extensive and growing genetic knowledge that is being used to calculate either an increased or decreased risk of condition development. The array of genetic data shows promises in predicting risk for both conditions, as well as certain symptoms, to contribute to a personalized predictive tool to guide management of care. Endometriosis benefits from a potential polygenic risk assessment …
The Influence Of Circadian Rhythm Disruption And Apoe4 On The Prognosis And Progression Of Alzheimer’S Disease, Kayla Bradby
The Influence Of Circadian Rhythm Disruption And Apoe4 On The Prognosis And Progression Of Alzheimer’S Disease, Kayla Bradby
Graduate Student Dissertations, Theses, Capstones, and Portfolios
Alzheimer’s disease is characterized by cognitive decline and memory loss and is the most common form of dementia. Genetic factors such as apolipoprotein E have been significantly associated with AD development and progression, most specifically the APOE4 isoform. Emerging evidence has shown that when the body’s circadian rhythm, the 24-hour dark/light cycle, is disrupted, the potential to develop a neurodegenerative disease such as AD increases. The purpose of this literature review is to examine the relationship between AD, circadian rhythm, and the APOE isoforms. This review puts a particular emphasis on the APOE4 isoform, as it has been shown to …
Complete Genome Sequence Of Strain Dk8, A Thermoacidophilic Archaeon From Lassen Volcanic National Park, Jonathan Abshier, Kenneth Stedman
Complete Genome Sequence Of Strain Dk8, A Thermoacidophilic Archaeon From Lassen Volcanic National Park, Jonathan Abshier, Kenneth Stedman
Biology Faculty Publications and Presentations
Here, we report the genome sequence of strain DK8, a thermoacidophilic archaeal isolate from the Devil's Kitchen geothermal area of Lassen Volcanic National Park, California, USA. The genome is 2,783,064 bp, with a guanine-cytosine content of 35.02%. Strain DK8 is most closely related to L.S.2.15.
Dissecting Tumor Evolution And Immune Composition In Prc2 Loss (H3k27me3 Loss) Vs Retained Mpnst, Kuangying Yang
Dissecting Tumor Evolution And Immune Composition In Prc2 Loss (H3k27me3 Loss) Vs Retained Mpnst, Kuangying Yang
Arts & Sciences Graduate Student Theses and Dissertations
Malignant peripheral nerve sheath tumors (MPNSTs) are aggressive sarcomas that arise sporadically or in the setting of neurofibromatosis type 1 (NF1). Although benign plexiform neurofibromas (PNs) are common in NF1, only a subset undergo malignant transformation, and the molecular events that define high-risk progression remain incompletely understood. A major axis of biological heterogeneity in MPNST is loss of Polycomb Repressive Complex 2 (PRC2), commonly detected through loss of H3K27me3 and frequently mediated by alterations in SUZ12 or EED. This dissertation integrates three manuscript-based studies to define genomic resources, tumor-intrinsic vulnerabilities, and immune microenvironmental remodeling in NF1-associated peripheral nerve sheath tumors, …
Expression Profiling And Bioinformatic Characterization Of Depalmitoylation-Associated Genes During Sh-Sy5y Neuronal Differentiation, Ayesha Lodhi
Seton Hall University Dissertations and Theses (ETDs)
Palmitoylation is a reversible post-translational modification involving covalent attachment of palmitoyl groups to cysteine residues. Till date, 23 members of this family have been identified in mammals, located in Golgi apparatus and endoplasmic reticulum and nearly 40% of synaptic proteins are estimated undergo palmitoylation. These proteins include vesicle fusion proteins (SNARE), signaling molecules, ion channels and neurotransmitter receptors such as gamma-aminobutyric acidreceptors, kainate receptors and glutamate receptors. While its role in neuronal function has been widely recognized, comparatively little is known about how depalmitoylation-associated enzymes are regulated during neuronal differentiation. The present study aimed to characterize changes in depalmitoylation-associated gene …
Host-Pathogen Dynamics Underpinning Staphylococcus Aureus Growth During Intracellular Osteoclast Infection, Luke D. O'Connor
Host-Pathogen Dynamics Underpinning Staphylococcus Aureus Growth During Intracellular Osteoclast Infection, Luke D. O'Connor
WUSM Theses and Dissertations – All Programs
Bone infection is most commonly caused by the gram-positive bacterium Staphylococcus aureus. It has myriad ways in which it can circumvent or subvert killing by the host or antibiotics. Intracellular infection is one such niche that is protective from immune and antibiotic attack. In 2019, Krauss and colleagues discovered that infected osteoclasts (OCs) allow S. aureus to replicate intracellularly. There they found that the ability of S. aureus to grow inside the cell was tied to OC differentiation. The magnitude of overnight bacterial expansion positively correlated with OC maturity and duration cultured with the osteoclastogenic factor RANK ligand (RANKL). Bacterial …
Profiling Arbutin As A Potent Cholinesterase And Gsk-3Β Inhibitor And Evaluating Its Cytotoxicity In Sh-Sy5y Cells For Alzheimer’S Disease Therapy, Shirin Tarbiat, Tuğba Bal, Deni̇z Gülmez
Profiling Arbutin As A Potent Cholinesterase And Gsk-3Β Inhibitor And Evaluating Its Cytotoxicity In Sh-Sy5y Cells For Alzheimer’S Disease Therapy, Shirin Tarbiat, Tuğba Bal, Deni̇z Gülmez
Turkish Journal of Biology
Background/aim: Alzheimer’s disease (AD) is a neurodegenerative disorder linked to cognitive decline and memory loss, marked by hyperphosphorylated tau tangles and decreased acetylcholine levels, which are affected by acetylcholinesterase (AChE) and butyrylcholinesterase (BuChE) activity. Glycogen synthase kinase-3 beta (GSK-3β) also plays a role in AD through abnormal activation. In this study, the potential of β-arbutin to inhibit cholinesterases and GSK-3β was investigated, utilizing in vitro assays, cytotoxicity analysis, and molecular docking simulations to explore its therapeutic implications.
Materials and methods: Ellman’s technique was used to test the inhibitory effects of arbutin on cholinesterase enzymes. An ATP-Glo luminescent assay kit was …
Probiotic Intervention In Colorectal Cancer: The Cytotoxic And Apoptotic Potential Of Lactobacillus Cell-Free Supernatants, Bahar Yilmaz, Berna Erdal
Probiotic Intervention In Colorectal Cancer: The Cytotoxic And Apoptotic Potential Of Lactobacillus Cell-Free Supernatants, Bahar Yilmaz, Berna Erdal
Turkish Journal of Biology
Background/aim: Failures in the treatment of colorectal cancer (CRC) have increased scientific interest in the potential of the bioactive compounds contained in cell-free supernatants (CFSs) obtained from probiotic bacteria for cancer treatment. The aim in this study was to investigate the effects of CFSs obtained from Lactobacillus delbrueckii subsp. bulgaricus (L. bulgaricus) and Lactobacillus paracasei subsp. paracasei (L. paracasei) on colorectal cancer cell lines (HT-29 and Caco-2) and a healthy colon epithelial cell line (CCD841 CoN).
Materials and methods: Cytotoxic effects on the cell lines were determined by MTT assay. In line with the IC50 values obtained, morphological changes were …
Antiatopic Dermatitis Activity Of Lissachatina Fulica Mucin: Network Pharmacology Analysis And Experimental Validation, Atin Supiyani, Wasmen Manalu, Lina Noviyanti Sutardi, Mawar Subangkit, Andriyanto Andriyanto
Antiatopic Dermatitis Activity Of Lissachatina Fulica Mucin: Network Pharmacology Analysis And Experimental Validation, Atin Supiyani, Wasmen Manalu, Lina Noviyanti Sutardi, Mawar Subangkit, Andriyanto Andriyanto
Turkish Journal of Biology
Background/aim: Lissachatina fulica mucin (LFM) has been used as a nutraceutical, therapeutic agent, and cosmetic ingredient. The bioactivity of mucin depends on bioactive compounds whose composition is strongly influenced by the snail’s diet. This study investigated the bioactive compounds in L. fulica mucin as potential therapeutic agents for atopic dermatitis (AD).
Materials and methods: LFM was collected from snails fed long beans and melon rinds for 4 weeks, freeze-dried, and analyzed using liquid chromatography–mass spectrometry followed by network pharmacology (NP) analysis to identify its bioactive compounds. A total of 60 BALB/c mice were sensitized on the dorsal skin with 1% …
The N-Terminal, Wd40, And C-Terminal Domains Of Wdr-31 Control Ciliary Localization And Cooperate With Elmod/Rp2 Gaps To Maintain Membrane Compartmentalization, Sebi̇ha Çevi̇k, Fatma Güzel
The N-Terminal, Wd40, And C-Terminal Domains Of Wdr-31 Control Ciliary Localization And Cooperate With Elmod/Rp2 Gaps To Maintain Membrane Compartmentalization, Sebi̇ha Çevi̇k, Fatma Güzel
Turkish Journal of Biology
Background/aim: WD40 repeats are found in many ciliary proteins. Although the WD40 repeat-containing WD repeat-containing protein 31 (WDR-31) is known to regulate ciliary protein trafficking and morphology, the specific contributions of its N-terminal, WD40, and C-terminal domains to protein localization and ciliary gate integrity remain unclear. Aim of this study is to dissect the functional roles of WDR-31 domains by investigating their contributions to ciliary localization, ciliary protein trafficking, and gate integrity.
Materials and methods: Using CRISPR/Cas9 technology, we generated Caenorhabditis elegans strains with in-frame deletions that removed the N-terminus (WDR-31(ΔN)), WD40 (WDR-31(ΔWD)), and C-terminus (WDR-31(ΔC)). We next examined the …
Discovery And Functional Characterization Of Novel Programmed Death-Ligand 1 Monoclonal Antibodies, Nurşah Ersezen, Mai̇de Şeker, Arzu Aysan, Durmuş Akdoğan, Mehmet Ender Avci, Asli Kurden Pekmezci̇, Si̇bel Kalyoncu Uzunlar, Mehmet İnan, Tamer Yağci
Discovery And Functional Characterization Of Novel Programmed Death-Ligand 1 Monoclonal Antibodies, Nurşah Ersezen, Mai̇de Şeker, Arzu Aysan, Durmuş Akdoğan, Mehmet Ender Avci, Asli Kurden Pekmezci̇, Si̇bel Kalyoncu Uzunlar, Mehmet İnan, Tamer Yağci
Turkish Journal of Biology
Background/aim: Targeted therapies with monoclonal antibodies provide cancer patients with better prognosis and diseasefree survival. The blockade of immune checkpoints, including programmed cell death protein-1 (PD-1) and its ligand PD-L1, with monoclonal antibodies may boost immune responses against tumors and is regarded as an effective strategy in cancer immunotherapy. We describe the generation of anti-PD-L1 monoclonal antibodies with high affinity and specificity, and we assess their potential for therapeutic use in cancer.
Materials and methods: Hybridomas were selected for PD-L1 specificity and cross-reactivity with other immune checkpoint proteins and PD-L1 orthologs using indirect ELISA. Immunofluorescence and Western blotting assays were …
Palmnet: Confidence-Calibrated Edge-Cloud Ai For Field Diagnosis Of Date Palm Diseases, Muntadher Kareem, Raed Majeed
Palmnet: Confidence-Calibrated Edge-Cloud Ai For Field Diagnosis Of Date Palm Diseases, Muntadher Kareem, Raed Majeed
Karbala International Journal of Modern Science
Date palm (Phoenix dactylifera L.) is a cornerstone crop for Iraq and the wider MENA region, yet reliable in-field diagnosis of leaf disorders remains slow, labour-intensive, and constrained by a limited pool of agronomists. This paper presents PalmNet, a full-stack diagnostic system that classifies nine leaf conditions through a calibrated edge-cloud framework. The system is developed and evaluated on a public dataset of 3,089 field images spanning the nine classes, using a 70/15/15 stratified split. A ShuffleNetV2 student network, distilled from a ConvNeXt-Tiny teacher, is deployed on two complementary edge endpoints: a Raspberry Pi Zero 2 W field station …
Beyond Autophagic Dysregulation: Vma21 Deficiency Reveals Altered Vesicle Trafficking And Broadens The Pathogenic Framework Of X-Linked Myopathy With Excessive Autophagy, Christian Suarez
Arts & Sciences Graduate Student Theses and Dissertations
Maintenance of protein homeostasis is essential for cellular function and depends on the coordinated regulation of protein synthesis and degradation. The major intracellular pathways responsible for protein degradation are the ubiquitin-proteasome system (UPS) and autophagy. Disruption of these processes has been implicated in a broad range of diseases, including neuromuscular disorders. X-linked myopathy with excessive autophagy (XMEA) is a rare vacuolar myopathy caused by mutations in VMA21, which encodes an assembly chaperone required for proper assembly of the vacuolar H⁺-ATPase (V-ATPase), the primary proton pump responsible for acidifying intracellular compartments, including lysosomes. Although impaired lysosomal acidification and autophagic dysregulation have …
The Gut-Bladder Axis: How Symbiont Microbes Alter Urinary Tract Infections, Benjamin S. Olson
The Gut-Bladder Axis: How Symbiont Microbes Alter Urinary Tract Infections, Benjamin S. Olson
Arts & Sciences Graduate Student Theses and Dissertations
Urinary tract infections (UTIs) are among the most common bacterial infections worldwide. Consequently, they are one of the leading indications for antibiotic prescription. Despite the typically successful treatment of an acute UTI, recurrent infections are exceedingly common, particularly among women. Nearly a quarter of otherwise healthy women will suffer recurrent UTIs (rUTI) after a primary UTI; why these select individuals are continually afflicted is unkown. There are no successful therapeutics to treat rUTI representing a gap not just in the medical toolkit but in our understanding of why rUTI is so prevalent. There are many hypotheses for the risk factors …
Integrative Evidence For Cryptic Diversity In The Thomomys Mazama Species Complex: Phylogenetics, Cranial Morphometrics, And Ecological Niche Modeling, Jessica Kate St. Michael
Integrative Evidence For Cryptic Diversity In The Thomomys Mazama Species Complex: Phylogenetics, Cranial Morphometrics, And Ecological Niche Modeling, Jessica Kate St. Michael
Dissertations and Theses
The population genetic structure and geographic distribution of the pocket gopher genus Thomomys Wied-Neuwied, 1839, lends itself to speciation events. Conserved morphology, ecological specialization, and high rates of molecular evolution may increase the probability of allopatric speciation, thereby contributing to the presence of morphologically cryptic taxa. In light of these patterns of evolution, we assessed genetic divergence and phylogenetic relationships, cranial morphometric differentiation, and ecological divergence among taxa in the Thomomys mazama species complex to test the hypothesis that T. mazama is a single species. Species delimitation analysis using Bayesian Poisson Tree Processes (bPTP) and data from the mitochondrial cytochrome …
Parental Thermal Environment Affects Offspring Resilience To Winter And Spring Weather Anomalies, Ruzhuo Chen, Mariel Dunn, Caroline A. Curtis, Mariana Abarca
Parental Thermal Environment Affects Offspring Resilience To Winter And Spring Weather Anomalies, Ruzhuo Chen, Mariel Dunn, Caroline A. Curtis, Mariana Abarca
Biological Sciences: Faculty Publications
Recent increases in the frequency and intensity of thermal anomalies can result in recurrent stressful weather events. Among annual insects, this phenomenon may expose parents and offspring to a succession of different weather anomalies (e.g. summer heatwaves and late spring frosts). Parental stress can alter offspring physiology and performance, potentially affecting their tolerance of environmental variation. We investigated the transgenerational effects of thermal anomalies on a univoltine wetland butterfly. We induced parental thermal stress by exposing pupae to a constant temperature, ranging from stressfully cold to stressfully hot (10 ◦C, 26 ◦C, 28 ◦C, 32 ◦C), for three days. Offspring …
Escherichia Coli Concentrations In Sand And Water At Tributary-Influenced Lake Michigan Beaches, Josie Elaine Kuhlman
Escherichia Coli Concentrations In Sand And Water At Tributary-Influenced Lake Michigan Beaches, Josie Elaine Kuhlman
Masters Theses
Contamination of public recreational water and sand is a human health concern, creating a management challenge for public health officials. Past research has shown that Escherichia coli can persist in sediment and can be washed into recreational water. Currently, beach monitoring practices only utilize E. coli concentrations in water samples to determine beach safety and do not consider potential exposure to sediment/sand concentrations. In this study, I investigated the relationship between E. coli concentrations in water and sand samples, which will aid public health officials in making more informed decisions about beach closures. I utilized culture-based measurements of E. coli …
Adaptive Phishing Url Detection Using Hybrid Fuzzy C-Means Clustering And Xgboost, Muntadher Mohammed Kareem, Rawaa I. Farhan
Adaptive Phishing Url Detection Using Hybrid Fuzzy C-Means Clustering And Xgboost, Muntadher Mohammed Kareem, Rawaa I. Farhan
Karbala International Journal of Modern Science
Phishing attacks continue to evolve in sophistication, rendering static detection methods increasingly ineffective. Existing URL-based approaches suffer from limited adaptability to emerging phishing patterns, mislabeled training data, and insufficient validation protocols. This paper proposes a hybrid phishing URL detection system that integrates Fuzzy C-Means (FCM) clustering with XGBoost classification, enhanced by a novel Micro Adaptive Feature Extractor (MAFE). The system employs a multi-stage pipeline: feature engineering generating 36 statistical and interaction features, MAFE producing 15 adaptive features through class-aware dynamic weighting, micro-pattern detection, and entropy analysis, and FCM with K=2 clusters providing soft membership features to XGBoost. A two-pass confidence-based …
Ai-Enhanced Fluorescein Angiography Detection Of Diabetes-Induced Silent Retinal Capillary Dropout And Rna-Seq Identification Of Pre-Symptomatic Biomarkers, Yiyan Peng, Huishi Toh, Dennis Clegg, Peng Jiiang
Ai-Enhanced Fluorescein Angiography Detection Of Diabetes-Induced Silent Retinal Capillary Dropout And Rna-Seq Identification Of Pre-Symptomatic Biomarkers, Yiyan Peng, Huishi Toh, Dennis Clegg, Peng Jiiang
Biological, Geological, and Environmental Faculty Publications
Objective: Retinal capillary dropout, characterized by acellular capillaries or "ghost vessels," is an early pathological sign of diabetic retinopathy (DR) that remains undetectable through standard clinical imaging techniques until visible morphological changes, such as microaneurysms or hemorrhages, occur. This study aims to develop a non-destructive artificial intelligence (AI)-based method using fluorescein angiography (FA) images to detect early-stage, silent retinal capillary dropout.
Methods: We utilized 94 FA images and corresponding destructive retinal capillary density measurements obtained through retinal trypsin digestion from 51 Nile rats. Early capillary dropout was defined as having an acellular capillary density of >= 18 counts per mm2. …