Life Sciences Commons^™

Spider Biodiversity And Insecticide Sensitivity Across Active And Restored Cranberry Bogs On Nantucket, Tyler J. Kulak

Graduate Masters Theses

Spiders are one of the most diverse groups of organisms on the planet with over 53,000 species described as of 2026. They provide a suite of ecosystem services including their regulation of problematic pests in agricultural systems, appearing in high biomasses across a breadth of ecological niches. While beneficial as pest regulators, they are also susceptible to the same management techniques as pest organisms and are especially vulnerable to chemical control. Cranberry production in Massachusetts likely benefits from spider ecosystem services, but diversity research on spiders in these systems is limited. This study compares the diversity of spider populations from …

Urinary Collagen As An Indicator Of Prostate Fibrosis In Lower Urinary Tract Dysfunction, Claweens Quetant

Graduate Masters Theses

Lower urinary tract dysfunction (LUTD) is a progressive disorder that affects millions of men over the age of 50 years old. LUTD manifests as urgency, nocturia, urinary frequency, weak urinary stream, and incomplete bladder emptying (Egan, 2016). The current treatment for LUTD doesn’t always yield the desired results due to several issues. In this thesis, we aim to address the lack of suitable tools for detecting prostatic collagenization and to assess whether urine could serve as a substrate for detecting pro-fibrotic proteins associated with moderate-to-high AUASI scores. We used whole urine from 2 different cohorts, the Boston and the LURN …

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

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 …

Effect Of Partial Ablation Of Skeletal Dynamin Related Protein 1 On Mitochondrial Health, Inflammation, And Fibrosis In A Mouse Model Of Duchenne Muscular Dystrophy, Tessa L. Duzz

Graduate Masters Theses

Duchenne muscular dystrophy (DMD) is a progressive neuromuscular disorder characterized by muscle weakness, degeneration, fibrosis, and impaired muscle regeneration. Mitochondrial dysfunction is an early pathological feature of DMD and has been linked to excessive mitochondrial fission. Dynamin-related protein 1 (Drp1) is a central regulator of mitochondrial fission, a key process in regulating mitochondrial quality and function. Inhibition of Drp1-mediated mitochondrial fission has shown promise as a potential therapeutic target for alleviating pathology and dysfunction in dystrophic muscle. The objective of this study was to determine whether partial skeletal muscle-specific ablation of Drp1 could improve muscle pathology and mitochondrial health in …

Modeling Kinetics Of 5-Aminolevulinic Acid-Induced Protoporphyrin Ix Accumulation For Optimal Photodynamic Therapy, Priscilla Melebor

Graduate Masters Theses

Photodynamic therapy (PDT) is a minimally invasive treatment that uses light-activated photosensitizers to selectively destroy diseased tissue through the generation of reactive oxygen species. However, conventional in vitro models often fail to accurately reproduce the pharmacokinetics of photosensitizer accumulation and clearance observed in vivo. This study investigated protoporphyrin IX (PpIX) accumulation following 5-aminolevulinic acid (ALA) exposure under physiologically relevant conditions using two-dimensional (2D) monolayers and three-dimensional (3D) spheroids. By comparing continuous ALA exposure with transient exposure followed by ALA washout, this work provides a more biologically relevant framework for studying PpIX kinetics and optimizing photodynamic therapy.

Crosstalk Between Upr And Mitochondria: The Triad Of Er-Mitochondria Contacts, Ca²⁺, And Ros, Ester Zito, György Hajnóczky

Department of Pathology, Anatomy, and Cell Biology Faculty Papers

Endoplasmic reticulum (ER) stress is triggered by several cellular perturbations causing protein misfolding, and activates the unfolded protein response (UPR), an initially adaptive signaling network that aims to restore ER and cellular homeostasis. Growing evidence indicates that UPR signaling extends beyond ER proteostasis, influencing mitochondrial function and bioenergetics through ER-mitochondria contact sites (ERMCs). The CHOP-ERO1A-IP3R axis has a primary role in recruiting mitochondria to adaptive UPR. However, its sustained activation renders UPR signaling maladaptive, leading to mitochondrial dysfunction through both outer mitochondrial membrane permeabilization (OMMP) and mitochondrial permeability transition pore (mPTP) opening, ultimately contributing to irreversible cell injury and disease …

The Correlation Between Medication Adherence, Blood Glucose Levels, And Quality Of Life In Patients With Type 2 Diabetes Mellitus At Ciamis Regional Hospital, Amyla Putri Nurul Nazmi, Nur Rahayuningsih, Lusi N

Pharmacology and Clinical Pharmacy Research

Type 2 diabetes mellitus is a chronic condition requiring continuous treatment, including patient adherence to prescribed medication. This study aimed to explore the relationship between medication adherence, blood glucose levels, and quality of life in patients with type 2 diabetes mellitus at Ciamis Regional Hospital, conducted from January to March 2025, the research employed a quantitative, prospective cross-sectional design involving 49 hospitalized patients. Data included blood glucose levels (RPG, FPG, 2hPG), medication adherence measured using the Medication Adherence Report Scale (MARS-5), and quality of life assessed via the Diabetes Quality of Life-Brief Clinical Inventory (DQOL-BCI). The chi-square test was used …

The Phytochemical Content And Antibacterial Activity Of Purified Extract Of Mangifera Indica L. Against Gram Positive Pathogen, Dewi Andini Kunti Mulangsri, Masduki Faqih, Sugar Arifin, Mutiara Trie Sieya Agustin

Pharmacology and Clinical Pharmacy Research

The purified extract of arum manis mango leaves contained flavonoid compounds by TLC methods and antibacterial activity against Gram-positive and negative pathogens. This research aimed to identify and determine the phytochemical content (mangiferin and flavonoids content) and antibacterial activity against other Gram-positive pathogens. Purification of ethanol extract of arum manis mango leaves by liquid-liquid fraction method. Determination of total flavonoid content and identification of mangiferin used respectively by aluminum chloride and Thin Layer Chromatography method. The disk diffusion method was used to assay antibacterial activity against S. epidermidis, and B. subtilis bacteria with the concentration of the sample such …

Cost Effectiveness Analysis Of Psychopharmaca Therapy Combination Compared With Psychopharmaca Therapy And Ect Combination In Schizoaffective Inpatients At The Rsj Provinsi Jawa Barat, Yasmin Fadillah, Sani Asmi Ramdani Lestari, Ardilla Kemala Dewi

Pharmacology and Clinical Pharmacy Research

Mental disorders constitute an economic burden on health, estimated at USD 2.5 trillion in 2010 and expected to increase to USD 6 trillion by 2030. Treatment of schizoaffective disorder involves a combination of medication and psychotherapy. Pharmacoeconomics is an important consideration in drug selection. This study aims to determine the cost-effectiveness of psychopharmaca therapy combination compared with psychopharmaca therapy and ECT combination in schizoaffective inpatients at the RSJ Provinsi Jawa Barat. Data collection was conducted retrospectively from patient medical records for the period December 2023–December 2024. Total costs, based on a health perspective, include psychopharmaca drug costs, inpatient care costs, …

Evaluation Of Antibiotic Use Using The Gyssens Method On Clinical Outcomes In Ischemic Stroke Patients, Juniarto Mende, Graciano A. Maturbongs, Yohana K. A. Mbulang

Pharmacology and Clinical Pharmacy Research

Ischemic stroke is a health problem that causes death and neurovascular disability worldwide. The inflammatory response due to infection can increase ischemic stroke and increase brain damage through changes in blood pressure, coagulation, immune response, and endothelial function. This study aims to evaluate the rationality of antibiotic use on clinical outcomes in ischemic stroke patients. This study used a cross-sectional design. Retrospective data were taken from the medical records of Jayapura Regional Hospital for the period January 1, 2023, to May 31, 2025. The study subjects were all patients who suffered ischemic stroke and received antibiotics. Evaluation of the rationality …

Retrospective Analysis Of Antimicrobial Resistance Patterns In Gram-Positive And Gram-Negative Blood Isolates, Helman Kurniadi, Timbul Partogi Haposan Simorangkir, Ros Sumarny, Fitria Heldiana

Pharmacology and Clinical Pharmacy Research

Bloodstream infections are an important cause of morbidity and mortality, while antimicrobial resistance limits treatment options. This retrospective study evaluated bacterial distribution and antimicrobial susceptibility in blood cultures at RSPAD Gatot Soebroto, Jakarta, using microbiology and medical record data from January-December 2019. Clinically significant isolates were included, while duplicates and contaminants were excluded. Identification and susceptibility testing followed standard procedures and CLSI 2019 guidelines. Data were analyzed descriptively. Among 482 isolates, 246 (51.0%) were Gram-positive and 236 (49.0%) were Gram-negative. The Gram-positive isolates were mainly coagulase-negative staphylococci, including Staphylococcus epidermidis (62, 25.2%), S. hominis (61, 24.8%), and S. haemolyticus (50, …

Analysis Of Pharmacotherapy And Non-Pharmacotherapy Burden From The Ina-Cbgs Package For Cesarean Section Surgery At The Regional General Hospital Dr. Soedarso In 2023, Ananda Rizky Awwaliyah, Nurmainah Nurmainah, Ridha Ulfah

Pharmacology and Clinical Pharmacy Research

The prevalence of cesarean sections has been increasing each year. Previous studies show that the cost of medications and medical supplies for cesarean patients accounts for one-third of the total care costs. In the era of National Health Insurance (NHI), medications and medical supplies are considered operational expenses for hospitals rather than sources of income. This condition requires proper medication management and the use of medical supplies. This study aims to analyze the percentage of pharmacotherapy and non-pharmacotherapy, including the types and quantities of medications as well as disposable medical supplies used on patients undergoing cesarean section procedures at the …

Alexithymia In Substance Use Disorders: A Scoping Review Of Therapeutic Approaches, Pratami Diah Herliani, Shelly Iskandar, Angela Vera Herman Efendi

Pharmacology and Clinical Pharmacy Research

Alexithymia, defined as the inability to recognize and express emotions, has a high prevalence (40–50%) among individuals with substance use disorders (SUD), particularly alcohol use disorder, and is associated with poorer clinical outcomes. Despite this, comprehensive mapping of psychotherapeutic interventions targeting this condition within the SUD population remains limited. This study aimed to systematically map the therapeutic approaches investigated to address alexithymia among individuals with substance use disorders and to summarize the reported outcomes. A scoping review was conducted in accordance with the PRISMA-ScR guidelines using systematic literature searches in the PubMed and Scopus databases. Relevant studies were screened based …

Genomic Based Environmental Health Assessment: Vieques, Puerto Rico, Valeria Hernandez Talavera

Graduate Doctoral Dissertations

From 1941 to 2003, the United States Navy and North Atlantic Treaty Organization (NATO) used Vieques, Puerto Rico, for military training, which led to long-term pollution from metals, organic chemicals, explosives, and per- and polyfluoroalkyl substances (PFAS). While earlier research found these contaminants in the environment and in living organisms, their combined effects on local ecosystems remain poorly understood.

This dissertation used a Genomic-Based Environmental Health Assessment (GEHA) framework to study the ecological risks from past military pollution in Vieques. The approach combined sediment toxicity tests, chemical analysis, gene expression studies, microbial community analysis, and community-based research. The four main …

Innovating A Crustacean Embryo Toxicity (Cet) Assay For Screening Environmental Contaminants, Irina A. Polunina-Proulx

Graduate Doctoral Dissertations

Environmental pollutants can disrupt normal developmental processes, leading to neurobehavioral and developmental abnormalities. Toxicity tests are important for evaluating environmental contaminants; however, standard assays are often time- and cost-intensive and typically require large numbers of vertebrate animals. These limitations highlight the need to reduce reliance on vertebrate testing and to develop New Approach Methodologies that provide comparable results while improving efficiency and cost-effectiveness. This research utilizes a novel screening assay to evaluate developmental toxicity using Hyalella azteca. H. azteca is a freshwater amphipod widely used as a model organism for sediment toxicity in ecotoxicology, yet its embryos have been minimally …

The Association Between Rapid Growth In Children Under The Age Of Five And Adolescent Obesity, Ratu Ayu Dewi Sartika, Fadila Wirawan, Iche Andriyani Liberty, Nurul Husna Mohd Shukri, Siti Arifah Pujonarti, Edy Purwanto, Munaya Fauziah

Kesmas

Early-life nutrition is a critical predictor of long-term health, yet the association between rapid early-childhood growth and adolescent obesity, particularly in relation to the “double burden of malnutrition,” remains under-researched in Indonesia. This study aimed to analyze the association between rapid growth and adolescent obesity. Data were obtained from the 1997, 2000, and 2014 waves of the Indonesian Family Life Survey (IFLS). This study included 641 children (aged 0–23 months at baseline) with complete anthropometric measurements across all three waves. Rapid growth was defined as an increase in z-scores of >0.67 in weight-for-age (WAZ), height-for-age (HAZ), or weight-for-height (WHZ) between …

Environmental Perspective For System Dynamics Modeling Of Stunting Mitigation To Achieve The Sustainable Development Goals In West Sumatra, Indonesia, Elsa Yuniarti, Nabila Azzahra, Yulhendri Yulhendri, Heldi Heldi, Mery Delvina, Saskia Putri Azeli

Kesmas

This study developed a system dynamics model to simulate stunting reduction in West Sumatra Province, Indonesia, by integrating infant and toddler health, maternal health, and environmental determinants. Secondary data from 2020–2024 on low birth weight, immunization, malnutrition, exclusive breastfeeding, maternal chronic energy deficiency, iron and folic acid supplement distribution, sanitation, and safe drinking water access were compiled from West Sumatra Provincial Health Office and Statistics Indonesia, and validated through consultation with five stakeholder institutions. Causal Loop Diagrams mapped feedback relationships among determinants and were translated into Stock Flow Diagrams using Powersim Studio 10. The model was validated through structural verification, …

Transcriptomic Architecture Of Metabolic Dysfunction-Associated Steatotic Liver Disease (Masld) Risk In Mexican Americans, Satish Kumar, Miriam Aceves, Lorena Guerra, Jose C. Granados, Earl Novilla, Felicia Juarez, Tolulope Oluwadairo, Ana C. Leandro, Marcelo Leandro, Juan M. Peralta, Sarah Williams-Blangero, John Blangero, Joanne E. Curran

Human Genetics Publications

Hispanics of Mexican American descent in South Texas show a very high prevalence of MASLD, with some studies reporting rates as high as 50% in adults. However, assessment of genetic risk factors underlying this prevalence is complicated by a high co-occurrence of other metabolic disorders and variable endogenous and exogenous environmental risk factors. To map the transcriptomic architecture of MASLD hepatic steatosis risk, we conducted an epidemiological-scale investigation using human induced pluripotent stem cell (iPSC)-derived hepatocyte cultures from 193 participants in our longitudinal South Texas Family Study (STFS). iPSC-based models offer greater power to map genetic risk factors by experimentally …

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 …

Outcome Evaluation Of Percutaneous Coronary Intervention Vs Medical Therapy Alone In Patients With Chronic Coronary Syndrome, Hsien-Yuan Chang, Hsin-Yu Fang, Mu-Shiang Huang, You-Zhen Chen, Di-Yung Chen, Edward Chia-Cheng Lai, Jung-Der Wang, Yi-Heng Li, Li-Jung Elizabeth Ku

Journal of Food and Drug Analysis

This study provides real-world evidence by comparing the long-term clinical outcomes of percutaneous coronary intervention (PCI) versus medical therapy alone in patients with chronic coronary syndrome (CCS) diagnosed non-invasively, given the lack of evidence in this population. This retrospective cohort study (2013-2018) utilized data from a medical center’s Cardiovascular Disease Databank, which was linked to national mortality records in Taiwan. Propensity score matching (PSM) and stabilized inverse probability of treatment weighting (IPTW) were applied to adjust for baseline differences between the PCI and medication-only groups. Major adverse cardiovascular events (MACE), including all-cause mortality, non-fatal myocardial infarction (MI), and revascularization, were …

From Insect Cognition To Sentience: Exploring The Edge, Catherine Macri, Martin Giurfa

Animal Sentience

What does The Edge of Sentience tell us about insect sentience and consciousness? In this commentary, we reflect on Jonathan Birch’s framework for defining and scientifically investigating sentience in animals. We discuss the methodological challenges of studying subjective experience in evolutionary distant species, and consider trace conditioning, affective states, and neural architectures as potential windows into consciousness in insects. We argue that uncertainty, whether concerning definitions or methodology, should not prevent experimental investigation; rather it should motivate new approaches and experimental designs for exploring the diversity of conscious experience.

American Plum Borer In Utah Orchards (Euzophera Semifuneralis), Emilie Demard, Marion Murray, Claudia Nischwitz

All Current Publications

This fact sheet provides information on American plum borer in Utah orchards, also known as APB. This pest primarily damages fruit trees. APB moths were detected in traps in 2026, but to date, no tree damage has been found. This fact sheet discusses hosts, identification, and management methods.

Mitochondrial Trna-Derived Fragments As Candidate Metastasis-Modifying Rna, Katy L. Swancutt, R. Mckinnon Walsh, Sydney Quijano, Emily Schueddig, Devin C. Koestler, Adam D. Scheid, Tony Vanden Bush, Yi Jing, Isidore Rigoutsos, Danny R. Welch

Computational Medicine Center Faculty Papers

UNLABELLED: How mitochondrial DNA (mtDNA) polymorphisms influence complex phenotypes remains poorly understood. Using mitochondrial-nuclear exchange mice, we previously showed that mtDNA single-nucleotide polymorphisms (SNP) modify metastasis, cardiovascular disease, and epigenetic marks independently of metabolic differences. The only mtDNA SNP correlating with these phenotypes resides in the gene encoding mitochondrial transfer RNA (tRNA)-arginine [mt-tRNAArg (UCG), mt-TR], suggesting a role for non-protein-coding loci. In this study, we identify and preliminarily characterize previously undescribed tRNA-derived fragments (tRF) generated from mt-TRs. Northern blotting revealed distinct tRF that are differentially expressed among mtDNA SNPs, between lung and liver, and between sexes. Surprisingly, small RNA sequencing …

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 …

Visualizing 25 Years Of Change In The Glades Oak Savanna, Zoe Fieberg

Summer Research Showcase

Oak savannas represent one of the most threatened ecosystems in Minnesota due to changing land use management, particularly absence of fire (Davis, 2001). Frequent burns kill fire-sensitive mesophytic tree species, reducing the dominance of woody understory and allowing for restoration of the oak savanna environment. The GLADES (Grid for Landscape Analysis and Demographic Study) site was established in 1988 in East Bethel, Minnesota to study the effect of frequent burning on oak savanna restoration. Through the use of standardized methods of photography, we compared canopy differences across GLADES between 2001 and 2026. Preliminary observations revealed increased canopy density and reduced …

Utah Vegetable Production Guide (5th Edition), Nick Volesky, Marion Murray, Amelia Olds, Bridger Carey

All Current Publications

This guide, written by a collection of Utah State University (USU) Extension faculty and specialists, provides information on general Utah vegetable production, soil, nutrient, and water management, integrated pest management practices, and pesticides. The included chapters cover various vegetable crops, including brassicas, cucurbits, leafy greens, potatoes, legumes, onions, root crops, sweet corn, and solanaceous crops.

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, …

Oregon State Rank Assessment For Schweinitz's Cyperus (Cyperus Schweinitzii), Nora Dunkirk

Institute for Natural Resources Publications

Oregon state conservation status assessment for Schweinitz's cyperus (Cyperus schweinitzii) using NatureServe methodology, 2026.

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 …