Life Sciences Commons^™

Knocking On Resistance’S Door: Investigating The Spread And Drivers Of Kdr Mutations In Northern California Culex Tarsalis, Esther Blankenship-Cutshall

University of the Pacific Theses and Dissertations

Vector-borne diseases are an increasingly relevant threat to public health as climate change alters the ecology of vector populations in relation to humans. One key to combating vector-borne disease is using pyrethroid insecticides against mosquito populations. However, wild mosquito populations have exhibited resistance to those key pyrethroids. One resistance mechanism under investigation is the altering of the voltage-gated sodium channel, which is associated with the genetic mutations known as kdr. The prevalence and history of kdr mutations has been investigated in some populations of Culex pipiens, however, it is unknown in northern California Culex tarsalis populations. This study aims to …

Associations Between Dietary Sodium And Potassium Intakes, Urinary Sodium And Potassium Excretion And Blood Pressure Among Adult Females In Oromia Region, Ethiopia, Fred Baffour Addo

Open Access Master's Theses

Introduction: Accurate assessment of sodium (Na) and potassium (K) intake is essential for population level monitoring of salt intake as part of global strategies to reduce salt consumption to control the increasing prevalence of high blood pressure (BP). Thus, a simple, cost-effective, and low-burden method is particularly valuable in resource-limited settings for population level monitoring of Na and K intake. This study aimed to compare the reliability of various methods of Na and K intake assessment, and their associations with blood pressure measurements.

Methods: This secondary analysis was based on a cross-sectional study of 100 non-pregnant women of …

Bird Watching In Chitral, Sehba Akhter

Institute for Educational Development Pakistan (IED-PK) Archives

This booklet comprises brief information about different species of thrush birds found in Chitral, identified by different researchers and field guides. The sources used include Helm Field Guide, Birds of Pakistan by Richard Grimmett, Tom Roberts, Tim Inskipp, and The Birds of Pakistan by T.J Roberts. This booklet aims to help the people of Chitral know about the birds they see every day.

Screening And Addressing Food Insecurity At Free Clinics: A Scoping Review, Gautam Ramanathan, William Zak, Daiwik Munjwani, Robert Fisher, Esther May Sarino, Mary J. Scourboutakos

Department of Medicine Faculty Publications

Food insecurity (FI) is highly prevalent amongst patients seeking care at free, student-run health clinics. This study sought to examine the existing literature of food insecurity screenings and interventions at free clinics across the U.S. In this review, we provide the rate of FI screenings, the prevalence of FI, demographic information of patients screened, and interventions and barriers faced by clinics while implementing interventions to improve FI. Studies included in this review needed to implement a FI screening and intervention program in a free clinic within the United States. Additionally, eligible studies could address additional social determinants of health or …

Isolation And Molecular Identification Of Pathogens Causing Sea Turtle Egg Fusariosis In Key Nesting Beaches In Costa Rica, Keilor E. Cordero-Umaña, Ruth Hernando-Martínez, María Martínez-Ríos, Jaime Restrepo, Roldán A. Valverde, Laura Martín-Torrijos, Pilar Santidrián Tomillo, Javier Diéguez-Uribeondo

School of Earth, Environmental, & Marine Sciences Faculty Publications

The global rise of fungal pathogens presents an emerging threat to biodiversity, with significant risks to species such as endangered sea turtles. The fungal disease known as sea turtle egg fusariosis (STEF) is associated with high embryo mortality rates and represents a substantial conservation challenge. This disease is caused by two fungal species, namely Fusarium falciforme (Ff) and Fusarium keratoplasticum (Fk), and their identification is essential for guiding future efforts to address potential fungal infections, particularly on important nesting beaches such as those in Costa Rica. In this study, we conducted fungal isolations from sea turtle eggshells …

Copula-Based Bayesian Model For Detecting Differential Gene Expression, Prasansha Liyanaarachchi, N. Rao Chaganty

Mathematics & Statistics Faculty Publications

Deoxyribonucleic acid, more commonly known as DNA, is a fundamental genetic material in all living organisms, containing thousands of genes, but only a subset exhibit differential expression and play a crucial role in diseases. Microarray technology has revolutionized the study of gene expression, with two primary types available for expression analysis: spotted cDNA arrays and oligonucleotide arrays. This research focuses on the statistical analysis of data from spotted cDNA microarrays. Numerous models have been developed to identify differentially expressed genes based on the red and green fluorescence intensities measured using these arrays. We propose a novel approach using a Gaussian …

Factors Affecting In-Hospital Mortality After Sudden Cardiac Arrest In The Emergency Department: A Retrospective Cohort Study, Erkan Boğa, Abdullah Algın

Mansoura Medical Journal

Giriş: Ani kalp hastalıkları (SCA), özellikle acil serviste (AS) yüksek hastane içi ölüm tutarları ve önemli bir tıbbi acil durumları. Prognostik bilgilerin belirlenmesi, sonuçların değiştirilmesi için çok önemlidir. Amaç: Acil serviste SCA'lı hastane içi ölümle sağlanan klinik ve demografik oranların belirlenmesi. Yöntemler: Bu retrospektif kohort çalışmaları Ocak 2023 ile Aralık 2024 arasında üçüncü basamaktaki bir hastanenin AS'sinde SCA'nın 345 yıl boyunca geçirdiği süre dahil edildi. Demografik özellikler, türü olmayan yayılma, durma özellikleri, resüsitasyon süresi, laboratuvar gelişimi ve patoloji durumuyla ilgili veriler toplandı. Bağımsız ölüm öngörmelerini belirlemek için lojistik regresyon kaydı. Sonuçlar: Hastane içi ölüm %38,3 idi. Çok değişkenli analiz, resüsitasyon …

Clinical And Radiological Outcomes Of Posterior Malleolar Fractures Fixation Through Posterolateral Approach: A Prospective Case Series Study, Mohammed Abdulrafei Farag, Ahmed Elsayed Elhawary, Ahmed Salah-Eldeen Zaghloul

Mansoura Medical Journal

Background: Posterior malleolar fractures are frequently associated with other malleolar injuries and significantly affect ankle stability through the posterior tibiofibular ligament. CT imaging is vital for preoperative classification, fragment size measurement, and syndesmotic evaluation. Objective: To assess clinical and radiological outcomes of posterior malleolar fractures treated using the posterolateral approach. Methods: This prospective case series included 20 skeletally mature patients treated between March 2022 and January 2024. Preoperative evaluation included radiographs and CT scans for classification, fragment size, articular step-off, and syndesmotic injury. Postoperative reduction and alignment were assessed with X-ray and CT. Functional outcomes were evaluated at ≥6 months …

The Relationship Between Nutrition Knowledge And Dietary Behavior Of Student-Athletes, Kerry A. Smith, Kathleen Fritch, James Rost, Amy Jo Riggs, Juliann Sergi Mcbrayer, Monika Krah

Georgia Educational Researcher

The purpose of this study was to examine the relationship between nutrition knowledge and dietary behavior while controlling for academic major, year, and gender among Division III student-athletes. Sufficient nutrition is essential for athletic performance, injury reduction, and overall health. However, student-athletes face unique challenges that can disrupt optimal nutrition, including poor nutrition knowledge and access to available resources. While several studies have examined the relationship between nutrition knowledge and dietary behavior, no known studies have addressed this among Division III student-athletes. This non-experimental correlational study examined dietary behavior using the Rapid Eating and Activity Assessment for Participants (REAP-S) and …

Practical Experimental Microbiology: Laboratory Manual, Rivka Levron

Open Touro Created

2025

Microbiology, especially the laboratory component, is a highly practical and useful course for students pursuing many career options. While a number of excellent microbiology laboratory manuals are available, many are more suitable for a full-year course in microbiology or for more advanced studies.

Microbiology Experimental Laboratory Manual is comprehensive in teaching students basic microbiological techniques, i.e., how to grow and stain bacteria, how to identify bacteria and fungi, and means of identifying different species of bacteria microscopically. Further experiments enable students to identify the most effective soap/detergent from those readily available; to discover which spices have the most anti-bacterial …

Swatting Flies: Biting Insects As Non-Invasive Samplers For Mammalian Population Genomics, Anubhab Khan, Ryan Carter, Chengetai D. Mpamhanga, Daniel Masiga, Manun Channumsin, Marc Ciosi, Oliva Manangwa, Furaha Mramba, Umer Zeeshan Ijaz, Harriet Auty, Barbara K. Mable

All Peer-Reviewed Publications

Advances in next-generation sequencing have allowed the use of DNA obtained from unusual sources for wildlife studies. However, these samples have been used predominantly to sequence mitochondrial DNA for species identification while population genetics analyses have been rare. Since next-generation sequencing allows indiscriminate detection of all DNA fragments in a sample, technically it should be possible to sequence whole genomes of animals from environmental samples. Here we used a blood-feeding insect, tsetse fly, to target whole genome sequences of wild animals. Using pools of flies, we compared the ability to recover genomic data from hosts using the short-read sequencing (Illumina) …

Aflatoxin Prevalence And Association With Maize Grain Physical And Nutritional Qualities In The Informal Markets In Meru County, Kenya, C. Cherotich, M. W. Okoth, Abong’ Go, S. W. Kariuki, E. R. Omuse

All Peer-Reviewed Publications

In Kenya, aflatoxin contamination in maize remains a persistent issue, with potential negative impacts on both public health and economic growth. Aflatoxins are toxic secondary metabolites produced by certain mold species, primarily Aspergillus flavus. The extent of Aspergillus fungal invasion in maize grains and the resulting increase in aflatoxin levels is heavily influenced by pre-and post-harvest practices. Before harvest, factors such as insect damage and exposure to warm, humid conditions increase the crop's susceptibility to Aspergillus infection and subsequent aflatoxin formation. Post-harvest, additional risks arise when kernels are damaged by pests like rats or when they are stored in unfavorable …

Bakterielle Schutzmechanismen Gegen Hypochlorige Säure, Jan-Ulrik Dahl

Faculty Publications – Biological Sciences

Reactive chlorine species (RCS) are highly bactericidal and produced in large amounts during host defense to kill invading pathogens. More recent studies have investigated how bacteria respond to and defend RCS, which appear to elicit more multifaceted responses compared to reactive oxygen species. A comprehensive understanding of bacterial RCS responses has clear potential to devise strategies that increase the sensitivity of bacterial pathogens to host defenses without harming commensals.

Host-Associated Beneficial Gut Microbiota Boosts Induced Immunity And Limits Immune Deployment Costs In Bumblebees, Austin C. Calhoun, Teni Shosanya, Brenna K. Long, Jade K. Rehberger, Ben M. Sadd

Faculty Publications – Biological Sciences

1. Ecological immunology posits that variation in host resistance to infection may be attributed partly to the ecological and evolutionary costs of immunity. While the deployment of immune defence is necessary to combat pathogenic infection, hosts pay energetic and other costs for activation.
2. Host-associated beneficial microbiota have been shown to affect multiple host traits, including immunity, but how interactions with these microbial communities may mitigate the costs of immune activation remains an open question. For apid bees, including eusocial bumblebees, core members of the adult gut microbiota contribute to a variety of fitness-relevant traits and provide a key ecological and evolutionary …

Physiological Conditions Of Barn Owl (Tyto Furcata) Nestlings As Indicators Of Habitat Quality Within The Wine-Growing Region Of Napa Valley, Christian Cortez

Cal Poly Humboldt theses and projects

The global environmental impacts of increasing agricultural demand a transition to sustainable farming practices, including the use of integrated pest management to decrease reliance on harmful pesticides. Vineyard managers in Napa Valley, California, have implemented this strategy by establishing nest boxes that attract barn owls (Tyto furcata) which, in turn, provide an ecosystem service by removing rodent pests. Studies in this system have found uncultivated landcover to be positively associated with distributional and demographic measures of habitat quality for barn owls, but individual measures have not been thoroughly explored. I examined three physiological conditions of barn owl nestlings …

Benthic Community Structure Changes In Northern California Following A Marine Heatwave, Franklin D. Moitoza

Cal Poly Humboldt theses and projects

In 2014, an unprecedented ecosystem shift impacted the rocky reef communities of northern coastal California following a rapid succession of severe disturbance events. Rocky reef communities shifted from kelp forests to large scale urchin barrens due to the demise of the sunflower sea star (Pycnopodia helianthoides), an unprecedented marine heatwave event (MHW) and increased purple sea urchin densities. This “perfect storm” caused a decrease in benthic species richness and led to a change in community structure due to intense sea urchin grazing. Here I examine the richness of the benthic community across four survey sites over an 8-year time …

Just Keep Swimming: Outmigration Survival Of Upper Klamath Basin Juvenile Chinook Salmon, James M. Whelan

Cal Poly Humboldt theses and projects

The removal of four impassable hydroelectric dams on the Klamath River provides salmonids with the opportunity to recolonize their historic range in the upper Klamath River watershed. However, successful reestablishment of salmon populations requires juvenile salmon born in Oregon's upper tributaries to safely migrate downstream through the river's upper reaches. This stretch of the Klamath River, immediately downstream of Upper Klamath Lake, presents multiple migration challenges, including two flow-control dams not scheduled for removal (Link River Dam and Keno Dam), significant water diversions, and water quality issues. To evaluate these challenges, I conducted experimental releases of radio-tagged juvenile Chinook salmon …

Exploring The Placebo Effect On The Cortisol Stress Response, Povheng Yam

Cal Poly Humboldt theses and projects

The placebo effect is well-studied on pain perception and is often observed to have a pain-reducing effect in patients. A few studies suggest that the placebo effect can influence physiological changes in people. To date, not many studies have examined the placebo effect on stress; thus, the current study explored the placebo effect on participants’ cortisol stress response and self-reported stress while undergoing a modified acute stress task, the Sing-a-Song Stress Test (SSST). The current study includes 44 participants (22 in the control group and 22 in the treatment group). A deceptive stress-reducing tincture (filled with water) was used as …

Facilitating On-Task Behavior In Physical Education For Learners With Asd Through Special Interest Modified Materials: Antecedent-Based Intervention, Gary Smith

Cal Poly Humboldt theses and projects

Children with Autism Spectrum Disorder (ASD) are affected in the areas of social skills, communication, and restrictive and repetitive behaviors that can lead to barriers in accessing physical education (PE). School-based PE helps children learn how to develop the knowledge, skills, and confidence to live physically active lifestyles. The purpose of this current study is to implement an antecedent based intervention using special interest materials to increase on task and engagement in learners with ASD in PE activities. The intervention showed modest to minimal improvements in on-task behavior and performance for two of the three participants, with high variability and …

Modeling Forest Stewardship In Goukdi’N: An Assessment Of Carbon, Wildlife Habitat, And Fire Resilience In A University Forest, Benjamin Stock

Cal Poly Humboldt theses and projects

This thesis presents a forest management plan for Goukdi’n (also known as the Jacoby Creek Forest University Tract), a coast redwood–tanoak–Douglas-fir forest within the ancestral homelands of the Wiyot Tribe. This project addresses the need for a forest stewardship approach that supports ecological resilience, cultural values, and long-term forest health in a landscape shaped by industrial logging, fire exclusion, and decades of under-management. To evaluate potential management pathways, forest growth modeling was conducted using the USFS Forest Vegetation Simulator (FVS) to compare three management prescriptions focused on carbon storage, fire resilience, and structural heterogeneity and a no-action alternative. Model outputs …

Variation In The Timing And Duration Of Rough-Skinned Newt (Taricha Granulosa) Larval Period In The Center Of Their Geographic Range (Humboldt County, California), Emmery R. Parker

Cal Poly Humboldt theses and projects

Rough-skinned newts (Taricha granulosa) occur along the Pacific coast of the U.S. from central California to southwestern Alaska at elevations from zero to 2,800 m. Across that range, the timing and duration of various life history events (i.e., hatching, metamorphosis, breeding, and oviposition) are largely unknown, although general trends have been observed in a few locales. Larval life stages are particularly important for determining amphibian population persistence, but there have been no formal studies describing the larval period of rough-skinned newts. Using minnow-trap and dip net surveys at nine lentic sites in northern Humboldt County, California (elevations 400 …

Examining The Effects Of Songbird Nest Boxes And Habitat On Avian And Arthropod Communities In A Vineyard Ecosystem, Eleanor Macdonald

Cal Poly Humboldt theses and projects

Agricultural expansion threatens biodiversity, but integrating insectivorous birds into vineyard ecosystems may support both conservation and ecosystem services. We tested how nest boxes and habitat composition influence avian and arthropod communities in Napa Valley vineyards using a before-after, control-impact experiment across 20 sites. During the 2023-2024 breeding seasons we conducted avian point counts, sampled key pest and beneficial arthropods, and collected fecal samples from adult and nestling tree swallows (Tachycineta bicolor) and western bluebirds (Sialia mexicana) to detect vineyard pest DNA. Nest boxes significantly increased swallow and bluebird abundance within one year; swallow responses were strongest …

Heterogeneous Clustering Of Multiomics Data For Breast Cancer Subgroup Classification And Detection, Joseph Pateras, Musaddiq Lodi, Pratip Rana, Preetam Ghosh

Computer Science Faculty Publications

The rapid growth of diverse -omics datasets has made multiomics data integration crucial in cancer research. This study adapts the expectation–maximization routine for the joint latent variable modeling of multiomics patient profiles. By combining this approach with traditional biological feature selection methods, this study optimizes latent distribution, enabling efficient patient clustering from well-studied cancer types with reduced computational expense. The proposed optimization subroutines enhance survival analysis and improve runtime performance. This article presents a framework for distinguishing cancer subtypes and identifying potential biomarkers for breast cancer. Key insights into individual subtype expression and function were obtained through differentially expressed gene …

A Data-Driven Sliding-Window Pairwise Comparative Approach For The Estimation Of Transmission Fitness Of Sars-Cov-2 Variants And The Construction Of The Evolution Fitness Landscape, Md Jubair Pantho, Richard Annan, Landen Alexander Bauder, Sophia Huang, Letu Qingge, Hong Qin

Computer Science Faculty Publications

Estimating the transmission fitness of SARS-CoV-2 variants and understanding their evolutionary fitness trends are important for epidemiological forecasting. Existing methods are often constrained by their parametric natures and do not satisfactorily align with the observations during COVID-19. Here, we introduce a sliding-window data-driven pairwise comparison method, the differential population growth rate (DPGR) that uses viral strains as internal controls to mitigate sampling biases. DPGR is applicable in time windows in which the logarithmic ratio of two variant subpopulations is approximately linear. We apply DPGR to genomic surveillance data and focus on variants of concern (VOCs) in multiple countries and regions. …

Cath-Ddg: Towards Robust Mutation Effect Prediction On Protein-Protein Interactions Out Of Cath Homologous Superfamily, Guanglei Yu, Xuehua Bi, Teng Ma, Yaohang Li, Jianxin Wang

Computer Science Faculty Publications

Motivation: Protein-protein interactions (PPIs) are fundamental aspects in understanding biological processes. Accurately predicting the effects of mutations on PPIs remains a critical requirement for drug design and disease mechanistic studies. Recently, deep learning models using protein 3D structures have become predominant for predicting mutation effects. However, significant challenges remain in practical applications, in part due to the considerable disparity in generalization capabilities between easy and hard mutations. Specifically, a hard mutation is defined as one with its maximum TM-score < 0.6 when compared to the training set. Additionally, compared to physics-based approaches, deep learning models may overestimate performance due to potential data leakage.

Results: We propose new training/test splits that mitigate data leakage according to the CATH homologous superfamily. Under the constraints of physical …

Integrated Roadside Vegetation Management Technical Manual [2025], Kristine Nemec, Josh Brandt, Kirk Henderson, Jim Uthe

Faculty Book Gallery

The objective of this publication is to provide basic technical support for new and existing Iowa county roadside programs. This manual is also intended to provide guidance to policymakers and engineers interested in adopting or expanding integrated roadside vegetation management in county rights-of-way.

Foundation Models In Bioinformatics, Fei Guo, Renchu Guan, Yaohang Li, Qi Liu, Xiaowo Wang, Can Yang, Jianxin Wang

Computer Science Faculty Publications

With the adoption of foundation models (FMs), artificial intelligence (AI) has become increasingly significant in bioinformatics and has successfully addressed many historical challenges, such as pre-training frameworks, model evaluation and interpretability. FMs demonstrate notable proficiency in managing large-scale, unlabeled datasets, because experimental procedures are costly and labor intensive. In various downstream tasks, FMs have consistently achieved noteworthy results, demonstrating high levels of accuracy in representing biological entities. A new era in computational biology has been ushered in by the application of FMs, focusing on both general and specific biological issues. In this review, we introduce recent advancements in bioinformatics FMs …

Benchmarking Batch-Effect Correction Methods Towards The Construction Of A Triple-Negative Breast Cancer Cell Atlas, Peter Scheible, Amy H. Tang, Jing He, Jiangwen Sun

Computer Science Faculty Publications

Triple-negative breast cancer (TNBC) requires detailed cellular mapping given its aggressive nature, immense tumor heterogeneity and genetic diversity. We integrated 156,794 cells from six scRNA-seq datasets—including tumors, metastases, and cell lines—to build a TNBC scRNA cell atlas, focusing on batch effect mitigation while maintaining biological and molecular details. Preprocessing f ilters noise, normalizes data, and leverages PCA for integration readiness. We utilized scANVI, a semi-supervised tool, to align datasets, preserving TNBC’s complex tumor heterogeneity via marker annotations [1]. UMAPs demonstrate biological clustering in integrated data, contrasted with datasetdriven unintegrated patterns. Assessments verifying effective batch correction. This method aligns with NASA’s …

A Survey On Deep Learning For Drug-Target Binding Prediction: Models, Benchmarks, Evaluation, And Case Studies, Kusal Debnath, Pratip Rana, Preetam Ghosh

Computer Science Faculty Publications

Conventional drug discovery is expensive, time-consuming, and prone to failure. Artificial intelligence has become a potent substitute over the last decade, providing strong answers to challenging biological issues in this field. Among these difficulties, drug-target binding (DTB) is a key component of drug discovery techniques. In this context, drug-target affinity and drug–target interaction are complementary and essential frameworks that work together to improve our comprehension of DTB dynamics. In this work, we thoroughly analyze the most recent deep learning models, popular benchmark datasets, and assessment metrics for DTB prediction. We look at the paradigm shift in the development of drug …

Deepssetracer 2.0: Improved Deep Learning Model Performance For Protein Secondary Structure Segmentation From Cryo-Em Maps, Bryan Hawickhorst, Thu Nguyen, Willy Wriggers, Jiangwen Sun, Jing He

Computer Science Faculty Publications

DeepSSETracer is a method for segmenting protein secondary structure from medium-resolution (5-10Å) cryogenic electron microscopy (cryo-EM) density maps. We conducted experiments and ablation studies to examine the effects of normalization methods, max-pooling, activation functions, and loss calculation region on DeepSSETracer. By combining multiple technical improvements, the performance of the new version, DeepSSETracer 2.0, was significantly enhanced compared to DeepSSETracer 1.1. On a set of 77 test cases, the weighted average per-voxel F1 score increased from 62.1% to 70.3% for helix detection, and from 47.8% to 62.5% for β-sheet detection. While each of the five modifications in the network enhanced the …