Life Sciences Commons^™

Key Regulatory Roles Of Prdm1 In Human Nk-Cell Differentiation And Activation, Xuxiang Liu, Yunfei Shi, Jibin Zhang, Kunal Shetty, Krystie Chew, Can Küçük, Qiang Gong, Esra Esmeray, Haiqing Li, Ru Chen, Sheng Pan, Katarzyna Dąbrowska, Roger E Moore, Krystine Garcia-Mansfield, Patrick Pirrotte, Jinhui Wang, Yuping Li, Gehong Dong, Logan Lee, Timothy W Mckeithan, Javeed Iqbal, Wing C Chan

Faculty, Staff and Student Publications

PRDM1, encoding a transcription factor (TF), regulates plasma cell and CD8+ T-cell terminal differentiation and Th2 lineage specification, while its role in human NK-cell differentiation and homeostasis is largely unknown. Here, we employed a multi-omics approach to dissect the transcriptional control of PRDM1 on human NK-cells. PRDM1 is important in NK-cell terminal differentiation based on gene expression profiling and its targeting of key regulators in the process. PRDM1-deleted NK-cells displayed a less mature phenotype simulating the CD56bright NK-cell population accompanied by upregulation of stem-like gene signatures. PRDM1-bound genes were enriched in T/NK-cell receptor signaling, activation, and NK-cell effector …

Grading Melanocytic Dysplasia: Updated Histopathologic Criteria, Christopher R Shea, Victor G Prieto, Catherine M Shachaf, Scott R Florell

Faculty, Staff and Student Publications

Dr. Martin C. Mihm, Jr.'s innovative work on the dysplastic nevus achieved a milestone in his chapter in the World Health Organisation Classification of Skin Tumours (WHO-C). WHO-C presents a dichotomous classification (high-grade versus low-grade dysplastic nevi) and a quantitative metric to assess melanocytic nuclear enlargement. The Duke classification is a related approach that provides mostly quantitative histopathologic criteria for dysplastic nevi and gives due weight to architectural features as well as cytology. This paper proposes and illustrates updated criteria for scoring and grading melanocytic dysplasia, incorporating some of the definitions and categories of WHO-C, while refining the quantitative and …

Evaluation Of Organ-Specific Relative Biological Effectiveness Of Proton Therapy Using Radiation-Induced Pneumonitis As An Endpoint, Li Liao, Ting Xu, Mei Chen, Tingshi Su, Narayan Sahoo, Xiaorong Zhu, Steven J Frank, Quynh-Nhu Nguyen, Zhongxing Liao, Xiaodong Zhang

Faculty, Staff and Student Publications

Background and purpose: Proton therapy has become widely used for non-small cell lung cancer (NSCLC) due to its ability to spare normal tissue. However, the commonly assumed relative biological effectiveness (RBE) of 1.1 may underestimate the therapy's true biological effects on lung, potentially leading to a higher than expected incidence of radiation-induced pneumonitis (RP). In this retrospective study, we evaluated the variability of organ-specific RBE of proton therapy using RP grade 2 or higher (RP2+) as an endpoint.

Materials and methods: Data from 270 NSCLC patients across two clinical trials were analyzed, with 134 given photon therapy and 136 given …

Trial Interviews To Explore Glycogen Storage Disease Type Ia Patient Experiences Following Gene Therapy, Diane M Turner-Bowker, Jessica Butler, Shayna Egan, David A Weinstein, David F Rodriguez-Buritica, Ayesha Ahmad, María-Luz Couce, Rebecca Riba-Wolman, John J Mitchell, Christina Theodore-Oklota

Faculty, Staff and Student Publications

Background: Glycogen storage disease type Ia (GSDIa) is a rare, inherited, autosomal recessive deficiency of glucose-6-phosphatase (G6Pase), an enzyme necessary in glycogenolysis and gluconeogenesis. To maintain normal blood glucose levels and ensure survival, individuals living with GSDIa must frequently consume complex carbohydrates (eg, uncooked cornstarch). Dietary management can result in chronic complications and significant patient burden. DTX401 (pariglasgene brecaparvovec) is an investigational adeno-associated virus serotype 8 vector (AAV8)-based gene therapy designed to restore endogenous glucose production.

Objectives: Patient experience interviews were conducted as part of an open-label, phase 1/2 dose-escalation trial (NCT03517085) evaluating the safety and efficacy of …

Dietetic Guidance For Nutritional Management Of People With Phenylketonuria Receiving Sepiapterin, Anita Macdonald, Kirsten Ahring, Alexa Bledsoe, Hiroki Fujimoto, Sara Giorda, Christian Kogelmann, Jessica Kopesky, Laura Nagy, Sara O'Neill, Alex Pinto, Soraia Poloni, Paige Roberts, Annemiek M J Van Wegberg, Suzanne Hollander

Faculty, Staff and Student Publications

Background/objectives: Phenylketonuria (PKU) is an autosomal recessive inborn error of metabolism. If untreated, elevated blood phenylalanine (Phe) levels lead to neurological and behavioral impairments. Phe levels can be managed through a lifelong Phe-restricted diet; however, this can be challenging to maintain. Sepiapterin is an adjunct therapy for PKU that has shown efficacy in reducing blood Phe levels in both tetrahydrobiopterin (BH4)-responsive and BH4-non-responsive people with PKU in clinical trials. Practical guidance is needed for dietitians and other healthcare professionals supporting the dietary management of people with PKU who are initiating or receiving sepiapterin.

Methods: A group of international dietitians participated …

The Effect Of The Affordable Care Act Medicaid Expansion On The Risk Of Hospital Closure And Adolescent Hpv Immunization In Rural Counties, Juliette Des Rosiers

Scripps Senior Theses

From 2005 to 2025, over 200 rural hospitals shut their doors, often citing increased operational costs, staffing shortages, low patient volume, regulatory barriers, financial challenges exacerbated by the COVID-19 pandemic, and uncompensated care as common contributors to the closures. Rural patients are often referred by their primary care physician to a hospital for regular immunizations, since smaller clinics have less capacity to provide immunizations due to a shortage of pediatricians and limited vaccine stock. A crucial vaccine that is not required by schools and underutilized in rural areas is that against human papillomavirus (HPV), a virus that infects cutaneous and …

Micrornas Regulated By Pregnancy Target Antiviral And Cancer Immunity Overlapping With The Hiv Interactome, Paula F. T. Cezar-De-Mello, Jonathan M. Dreyfuss, Pai-Lien Chen, Hidemi Yamamoto, Xiaoming Gao, Hui Pan, Charles Morrison, Gustavo F. Doncel, Robert L. Barbieri, Raina N. Fichorova

CONRAD Publications

Innate immunity predictors of HIV-1 risk and pathogenesis vary with reproductive hormones, pregnancy, and lactation, yet the underlying mechanisms remain unclear. We hypothesized that pregnancy-associated physiological adaptations alter systemic microRNA (miRNA) expression, thereby regulating immunity, pathogenesis and susceptibility to infection. We analyzed 174 serum samples from 88 participants in a longitudinal cohort from Uganda and Zimbabwe across pre-pregnancy (PP), pregnancy (P), and postpartum breastfeeding (BF). Cell-free peripheral blood miRNAs (n = 2083) were profiled using HTG EdgeSeq. Pregnancy-specific miRNAs were identified by intersecting differentially expressed (DE) miRNAs from P vs. PP and P vs. BF comparisons. miRNA targets and pathways …

Coordinated Whole-Body Dynamic Pressing And Reaction Inhibition — Impact Of High-Intensity Intermittent Exercise And Dehydration, Modesto A. Lebron

Graduate Studies Theses and Dissertations 2026

Dynamic whole-body pressing movements are an imperative aspect of various sport and occupational settings, requiring motor coordination to kinetically sequence from lower- to upper-extremities. Recently, exercises such as the jammer arm punch press (JPP) have increased in popularity, promoted as an exercise to improve strength and force transfer. While the JPP has observed increased practical utility, its use in research is limited potentially due to difficulties with quantifying exercise intensity. One method to quantify exercise intensity is the assessment of velocity, serving as the basis for velocity-based training. For optimization, this strategy requires an understanding of velocity ranges and their …

Effects Of Short-Term Exposure To Environmentally Relevant Pesticides Mixture On Morphological Alterations, Oxidative-Nitrative Stress Biomarkers, Cellular Apoptosis, And Antioxidant Expression In Kidneys Of Goldfish, Esmirna Cantu, Md Saydur Rahman

School of Earth, Environmental, & Marine Sciences Faculty Publications

Chemical stressors are pervasive, affecting both terrestrial and aquatic environments. The continual influx of these toxins is damaging ecosystems and the organisms that inhabit them. The abundance of environmental toxins makes aquatic habitats inhospitable for aquatic life. These chemical stressors consistently disrupt the life processes of aquatic organisms, particularly their physiological functions. This study examined on the effects of environmentally relevant pesticides mixture (low-dose and high-dose: S-metolachlor: 2.4 go/L, 12 μg/L; linuron: 2.0 μg/L, 10 μg/L; isoproturon: 1.2 μg/L, 6.0 μg/L; tebucanozole: 1.2 μg/L, 6.0 μg/L; aclonifen: 0.8 μg/L, 4.0 μg/L; atrazine: 0.4 μg/L, 2.0 μg/L; pendimethalin: 0.4 μg/L, 2.0 …

Biomarkers Of Foraging And Reproduction In Captive Adult Female Hawksbill Sea Turtles (Eretmochelys Imbricata), Joslyn Blessing Kent, Kari Renee Dawson, Shingo Fukada, Masae Makabe, Isao Kawazu, Ken Maeda, Roldán A. Valverde

School of Earth, Environmental, & Marine Sciences Faculty Publications

Hawksbill sea turtles (Eretmochelys imbricata) are listed as critically endangered by the International Union for the Conservation of Nature (IUCN). To implement best conservation practices for this species, its biology should be well understood. Attempting to characterize the foraging physiology of free-ranging hawksbill sea turtles is complicated by the fact that sampling is typically limited to nesting females during the reproductive season. Without data from non-reproductive periods, it is difficult to determine whether observed physiological values reflect baseline conditions or are specific to the energetically demanding nesting season. Accordingly, in this study, we described the physiology of foraging in …

Pilot Study On The Use Of Multimorbidity Index In Patients Receiving Home Parenteral Nutrition, Michael M. Rothkopf, Mohan Pant, Zachary Rothkopf, Rebecca Brown Rdn, Jaime Haselhorst Rdn, Debbie L. Stevenson Rdn, Andrew Depalma Mba, Michael Saracco

Epidemiology, Biostatistics, & Environmental Health Faculty Publications

Background

Home parenteral nutrition (HPN) patients often have multiple comorbidities. A validated multimorbidity index (MMI) could help determine resource needs and risks with HPN. We evaluated MMI scoring to determine if it predicted HPN resource use and outcomes.

Methods

We performed a secondary analysis of 60 HPN patients from a previous study based on Cumulative Illness Rating Scale (CIRS) scoring. We examined three variables: PN formula changes, hospitalizations, and hospital length of stay (LOS). Density plots were produced to select a CIRS score cutoff value. Spearman correlations among the three variables of interest were computed. The data were then subjected …

A Critical Perspective On The Society Of Environmental Toxicology And Chemistry's Adherence To Founding Principles— Opportunities For The Future, Barnett A. Rattner, Annegaaike Leopold, Carys L. Mitchelmore, Glenn W. Suter, Mark S. Johnson, Adriana C. Bejarano, Lawrence A. Kapustka, Niranjana Krishnan, Derek C. G. Muir, Beatrice O. Opeolu, Martha Georgina Orozco-Medina, April Reed, Bruce W. Vigon, Adam R. Wronski

Epidemiology, Biostatistics, & Environmental Health Faculty Publications

The Society of Environmental Toxicology and Chemistry (SETAC) is a global organization whose mission is the advancement of environmental science and management through collaboration, leadership, communication and education. On SETAC's 45th anniversary, the following question was raised: Are the 1979 founding principles of SETAC, multidisciplinary approaches to solving environmental problems, multisector engagement and scientific objectivity, still useful, adequate and effective in fulfilling its mission? In a special session held at the 45th Annual Meeting in Fort Worth, Texas, United States, a critical evaluation of the founding principles was initiated by reviewing SETAC's history and ongoing activities, and recommendations were made …

Vitamin D Status During Pregnancy Modulates The Effect Of Pre-Pregnancy Obesity On Gestational Diabetes Mellitus Risk: A Birth Cohort Study, Ali H. Ziyab, Abdullah Al-Taiar, Reem Al-Sabah, Majeda S. Hammoud, Saeed Akhtar

Epidemiology, Biostatistics, & Environmental Health Faculty Publications

Objective:

To determine whether gestational vitamin D status modulates the effect of pre-pregnancy obesity on gestational diabetes mellitus (GDM) risk while stratifying by maternal age.

Design:

Birth cohort.

Setting:

A major maternity hospital in Kuwait.

Participants:

Pregnant women in their second/third trimester of gestation were enrolled. Pre-pregnancy body mass index (BMI, kg/m²) was categorized as under/normal weight (< 25.0), overweight (25.0 to < 30.0), and obesity (≥30.0). Gestational 25-hydroxyvitamin D concentrations were categorized as deficiency (< 50 nmol/L) or insufficiency/sufficiency (≥50 nmol/L). GDM status was ascertained according to international guidelines. Adjusted odds ratios (aOR) and 95% confidence intervals (CI) were estimated using logistic regression.

Results:

Data from 957 pregnant women were analyzed, with GDM affecting 166 (17.4%) pregnancies. Pre-pregnancy obesity and gestational vitamin D deficiency was ascertained in 275 (28.7%) and 533 (55.7%) pregnant women, respectively. The association between pre-pregnancy obesity and GDM risk differed according …

Urban Trees In The Urban Hydrology Cycle, Jorge R. Vera

Theses, Dissertations and Capstones

In urban forestry, trees provide numerous economic, ecological, and aesthetic benefits to the surrounding community. One of their key roles is intercepting stormwater runoff, reducing flooding risk, and improving water quality. Chapter 1 of this thesis characterized the ecological and economic contributions of urban trees on the Marshall University campus and provides guidance on their management and conservation in the future. Chapter 2 examined how urban tree species modify the urban hydrology cycle by altering the volume and timing of precipitation delivery. In Chapter 1, we inventoried 114 acres of Marshall University's main campus in Huntington, WV, from June 28 …

The Diagnostic Value Of Serum Ferritin In Telogen Effluvium, Sara Khaled Mohamed Elbasiouny, Marwa H. Elnagdy, Sherif R. Ismaeil, Fawzia A. Saafan

Mansoura Medical Journal

Background Telogen effluvium (TE) is a common cause of hair loss (HL) in females, characterized by diffuse HL. Iron deficiency has a significant relationship with emotional stress, and anxiety is another prevalent cause for HL. So, our aim was to evaluate the serum ferritin levels among TE patients, compared to healthy controls. Methods This case-control study was conducted on 100 subjects, and they were divided into 2 groups, group (A) included 50 patients with Telogen Effluvium and group (B) included 50 healthy normal volunteers matching for age and sex with the patients. Clinical examination of diffuse shedding and positive pull …

Use Of Thyroid Imaging Reporting And Data Systems (Tirads) Ultrasound In Differential Diagnosis Of Thyroid Nodules, Aya Mohamed Hamed Abdelaal, Ghada M Ahmed Gaballah, Donia Mohamed Sobh

Mansoura Medical Journal

Background: Thyroid nodules refer to masses of abnormally proliferating cells with abnormal tissue stiffness in thyroid. This study aimed to assess diagnostic accuracy of Thyroid Imaging Reporting and Data System in differentiating benign from malignant thyroid nodules.

Methods: This cross-sectional study included forty adult patients with sixty-two thyroid nodules. A 7.5-10 MHz linear array transducer was used to perform imaging protocol. Three-dimensional measurements were done on nodules. All thyroid nodules were  examined using doppler ultrasound. All thyroid nodules were described in terms of composition, echogenicity, margins, shape and echogenic foci.  According to ACR TI-RADS,  the points were given …

Clinical And Dermoscopic Nail Changes In Patients With Chronic Kidney Disease: A Cross-Sectional Study, Ghada Nagy Mansour Borham, Hassan Abdel-Raheim Fayed, Eman Nagy Ahmed Abdelrazik, Amany Awad Mohamed

Mansoura Medical Journal

Background: Nail abnormalities are commonly observed among patients with chronic kidney disease (CKD) and may reflect underlying systemic and metabolic alterations. Dermoscopy (Onychoscopy) has emerged as a valuable noninvasive tool for detecting subtle nail changes.

Aim:  To describe the patterns and dermoscopic features of nail changes in patients with chronic kidney disease (CKD) and to explore their association with disease severity and renal function parameters.

Methods: This cross-sectional descriptive study included 127 patients with different stages of CKD. All participants underwent a comprehensive clinical and dermoscopic evaluation of the nail apparatus. Dermoscopic findings included longitudinal ridging, white …

A Comparative Study Of Topical 5% 5-Fluorouracil With Needling Versus 100% Trichloroacetic Acid With Needling Versus Needling Alone In Treatment Of Multiple Warts, Nesma Abd-Elmonem Saad, Hassan A. Fayed, Manar Ali

Mansoura Medical Journal

Aim: This study aimed to compare the efficacy and safety of topical 5% 5-Fluorouracil (5-FU) with Needling versus 100% Trichloroacetic acid (TCA) with Needling versus Needling Alone in treatment of multiple warts.

Methods: This study included a total of 60 patients clinically diagnosed with multiple warts, who were randomly allocated (computer-generated simple randomisation, 1:1:1, concealed in sequentially numbered opaque sealed envelopes) into three equal groups (n=20 per group). The first group received 100% TCA with Needling; the second group received topical 5% 5-FU combined with Needling; the third group underwent Needling alone. The study was single-blinded at the level …

Diffusion Mri Characterization Of Paranasal Sinus Masses, Fatma Elsayed Ali, Doaa Khedr Mohamed, Mohamed Magdy El-Rakhawy

Mansoura Medical Journal

Background: In ordinary clinical practice, a number of nasal cavity lesions, both neoplastic and non-neoplastic, are often seen. Because diffusion-weighted MRI imaging (DWI) captures the random migration of water protons, it provides superior characterization of tissues and their physiological processes. Therefore, the current study's goal was to use echoplanar DWI to classify malignant and non-malignant sinonasal lesions.

Methods: Fifty patients with paranasal sinus masses who were sent to Mansoura University Hospitals' Diagnostic Radiology Department for radiological examination, including a traditional MRI procedure, were included in this prospective research, Diffusion Weighted Images (DWI) and apparent diffusion coefficient (ADC). The final diagnosis …

Clinical Outcomes Of Anticoagulant Therapy In Cirrhotic Patients With Benign Portal Vein Thrombosis, Dalia Elsayed Tawfik, Muhammad Abdulaty Diasty, Aya Ahmed Elboghdady, Hatem Abdel Wahab Elalfy

Mansoura Medical Journal

Background

Portal vein thrombosis (PVT) is among the recognized vascular complications encountered in cirrhotic patients and may significantly influence disease progression and survival. The clinical course of PVT differs according to its etiology, particularly when hepatocellular carcinoma (HCC) is absent. This study was designed to assess the outcomes of benign portal vein thrombosis in cirrhotic patients.

Methods

This prospective observational study enrolled 18 cirrhotic patients diagnosed with non-malignant portal vein thrombosis. All participants underwent comprehensive clinical evaluation, laboratory investigations, and radiological assessment. Severity of liver disease was determined using the Child–Pugh classification and MELD score. Radiological imaging was utilized to …

Intelligence Quotient In Egyptian Children With Attention-Deficit/Hyperactivity Disorder, Yomna Sh. Abdrabouh, Zeinab A. Gomaa, Mohammed A. Elwasify, Ibrahem H. Elkalla

Mansoura Medical Journal

Background: Attention-Deficit/Hyperactivity Disorder (ADHD) affects cognitive functioning in children, yet evidence remains limited in Middle Eastern populations regarding comprehensive IQ evaluation and associated clinical characteristics. This study aimed to assess verbal, non-verbal, and total IQ in Egyptian children with ADHD and examine their associations with sociodemographic, developmental, educational, and clinical factors while identifying factors associated with IQ classification.

Methods: A cross-sectional observational study enrolled 150 Egyptian children aged 6-12 years diagnosed with ADHD according to DSM-5 criteria with IQ above 80 at Mansoura University Hospital from February 2022 to October 2023. Intellectual functioning was evaluated using the Stanford-Binet Intelligence Scale, …

Validation Of Anorectal Manometry Based On The Continence Clinical Scoring Systems For Evaluation Of Fecal Continence In Patients With Anorectal Malformations, Momen Abdelglil, Mohamed El-Sherbiny, Mahmoud Abdelwahab, Adham Elsaeid

Mansoura Medical Journal

Background/purpose: Anorectal malformations (ARM) are complex anomalies associated with long-term problems such as fecal incontinence. Clinical scoring systems are commonly used to assess bowel function but lack proper validation. Anorectal manometry is an objective tool for evaluating anorectal function. This study aimed to correlate anorectal manometric parameters and clinical continence scoring systems to enhance the postoperative evaluation of children with ARMs.

Patients and methods:

We conducted a descriptive cross-sectional study including 47 children who had undergone definitive surgical repair for ARMs between January 2010 and June 2021. Fecal continence was assessed using the Kelly and Templeton & Ditesheim scoring systems. …

Roles Of Transcription Factors In Mediating Abiotic Stress Responses In Cereals, Shikha Bharti, Joshwa A. Gandy, Ishita Bajaj Hengge, Javier Ramos, Bradley O. Christoffersen, Michael W. Persans, Manohar Chakrabarti

School of Integrative Biological & Chemical Sciences Faculty Publications

Cereals are staple crops for the majority of the global population, making their sustained productivity essential for food security. However, abiotic stresses significantly threaten their growth and overall yield by disrupting essential physiological, cellular, and biochemical processes. Enhancing stress resilience in cereals is therefore a critical objective for agricultural improvement under changing climatic conditions. A fundamental step toward this goal involves understanding the roles of transcription factors (TFs), which are primary regulators of changes in gene expression in response to stresses. TFs regulate complex signaling networks that enable plants to adjust their biochemical and physiological functions under abiotic stress conditions. …

A Generalized Framework For The “Core” Thalamocortical Circuit Computation, Charles Liu

Dartmouth College Ph.D Dissertations

This thesis explores a biologically inspired computational framework based on a common excitatory-inhibitory circuit in the superficial layers of the cortex. By varying the strength of local feedback inhibition, this single circuit gives rise to distinct unsupervised learning behaviors: strong inhibition leads to clustering and hierarchical clustering, while weak inhibition produces principal component-like representations. From this principle, we develop three algorithms: Lateral Inhibition Clustering (LI-C), Lateral Inhibition Hierarchical Clustering (LI-HC), and Antipodal Iterative Mean Estimation (AIME).

LI-C performs clustering without requiring a predefined number of clusters, using a competitive learning rule to extract dominant patterns from data. LI-HC extends this …

Liver X Receptor Α (Lxrα) Regulates 5Β-Reductase (Akr1d1) Expression In Avian Embryos: Implications For Yolk Steroid Metabolism, Ryan T. Paitz, Sara E. Waters, Delaney K. Reynolds, Emily M. Drew, Emily P. Harders

Faculty Publications – Biological Sciences

Steroid-mediated maternal effects are well-studied as a source of phenotypic variation. In bird eggs, the yolk contains various steroids that can influence embryonic development. However, one complicating factor in understanding how yolk steroids affect development is that the embryo metabolizes yolk steroids to regulate exposure. The 5β-reduction of steroids by the enzyme 5β-reductase (AKR1D1) has been identified as a pathway through which yolk progesterone, testosterone, and corticosterone are all metabolized early in avian development. We set out to characterize the mechanism through which AKR1D1 expression is regulated in chickens (Gallus gallus) during embryonic development. We found …

Following The Water: Tree Water Sources In Coastal Northern California Forests, Kaitlyn Briggs

Cal Poly Humboldt theses and projects

Increasing drought intensity and declining summer water availability in Mediterranean- climate forests raise concerns about forest resilience and streamflow persistence. This study evaluated how tree water sources vary with hillslope position, season, species, and watershed context across three coastal northern California forests. Stable isotopes of hydrogen (δD) and oxygen (δ18O), soil moisture time series, linear mixed-effects models, and site-specific Bayesian mixing models (MixSIAR) were used to estimate proportional contributions of shallow soil, deep soil, stream-associated, and fog water to tree xylem water. Across sites, xylem water isotopic signatures overlapped primarily with soil water, indicating dominant reliance on subsurface sources, while …

Geographic Variation In Proteomic Responses To Ocean Acidification In A Cold-Water Coral (Balanophyllia Elegans), Keana A. Richmond

Cal Poly Humboldt theses and projects

In the face of a rapidly changing climate, assessing organismal responses to future stressors in the context of current, natural exposure to stress could provide key insights to understanding marine ecosystem resilience. I used Balanophyllia elegans, a cold-water, solitary, azooxanthellate coral as a model to better understand how varying oceanographic conditions across its geographic range have shaped its ability to tolerate and potentially adapt to current and future ocean acidification conditions. I collected B. elegans individuals from four sites across 2,500km of their range and subjected them to two pH treatments to investigate site-specific protein expression in response to …

Species Boundaries Of The Rare Menzies’ Wallflower (Brassicaceae: Erysimum Menziesii), An Endemic Of The Northern California Coast, Cameron M. Jones

Cal Poly Humboldt theses and projects

Morphological similarity among geographically isolated populations can obscure deep evolutionary divergence, especially when convergent evolution under similar environmental conditions yields comparable phenotypes across independent lineages. Such cryptic diversity is likely underestimated in hotspots like the California Floristic Province (CFP), a global biodiversity hotspot, defined by its Mediterranean-like climate and encompassing most of California, southwestern Oregon, and northwest Baja California. The CFP is home to a disproportionate number of narrow endemics whose origins and evolutionary relationships remain poorly understood. Here, I investigate the evolutionary origins of Erysimum menziesii (Brassicaceae), a federally endangered California coastal dune endemic whose fragmented distribution has led …

Assessing A Half-Century Of Change In Understory Plant Range And Frequency In The Klamath Mountains Of California, Emily Jean Jackson

Cal Poly Humboldt theses and projects

The effects of climate change have and will continue to impact plant communities, including by potentially shifting species’ ranges towards topographically sheltered, cooler locations or higher elevations. In 2024, I resampled 140 vegetation plots established in 1969 in the Klamath Mountains of Northern California to assess range shifts of 46 understory species over a 55-year period. During this time, the elevational distribution of all species has increased significantly by an average of 26.9 m, but this increase was slower than necessary to track historic temperature niches given regional warming (215-311 m). Despite this overall increase, only four species exhibited significant …

Chromnet: A Multi-Task Learning Framework For Cross-Cell Type Prediction Of 3d Chromatin Interactions Using Epigenetic Signals, Bin Wang, Shaokai Wang, Liqing Ding, Hongdong Li, Yaohang Li, Jianxin Wang

Computer Science Faculty Publications

The 3D organization of chromatin plays a fundamental role in gene regulation, cellular function, and disease mechanisms. However, current experimental techniques, such as Hi-C, remain costly and labor-intensive, limiting their application in large-scale and disease-related studies. To address this challenge, ChromNet is presented, a multi-task learning framework that integrates epigenetic signals across diverse cell types to enable high-precision prediction of chromatin architecture. By incorporating noise perturbation and auxiliary classification tasks, ChromNet improves the identification of topologically associating domains (TADs) and cell-type-specific chromatin structures, demonstrating superior generalization performance. Notably, ChromNet accurately predicts chromatin interactions in acute myeloid leukemia (AML) samples by …