Digital Commons Network^™

Design And Tissue Engineering Applications Of Microporous Annealed Particle (Map) Scaffolds, Nic D. Leipzig, Oluwaseyi Shofolawe-Bakare

University Research

Microporous annealed particle (MAP) scaffolds are emerging as a facile, yet sophisticated biomaterial platform with tremendous potential for tissue regenerative applications. These scaffolds are fabricated in situ through interparticle crosslinking of microgels using a variety of covalent or non-covalent techniques and possess excellent tunability and biocompatibility. The microporous structure of MAP scaffolds allows cellular infiltration and vascularization independent of degradation rate, making them more advantageous than traditional nanoporous bulk hydrogels. Moreover, the incorporation of in situ crosslinking allows MAP scaffolds to retain the key advantages of traditional microgel-based scaffolds—such as injectability and modularity—while providing the added benefit of a fixed …

Identification Of Microplastics And Additives From The Lake Erie Watershed And The Cuyahoga River Via Maldi-Ms And Dart-Ms, Chrys Wesdemiotis, Calum Bochenek, Luciana Rivera Molina, Robert Brand

University Research

Micro(nano)plastics have received increased attention as environmental contaminants due to their harmful effects on ecosystems and human health. Conventional extraction methods for microplastic analysis are often lengthy and complicated, resulting in the loss of important chemical components such as additives. In this study, we provide a complementary approach, utilizing matrix-assisted laser desorption/ionization (MALDI) and direct analysis in real time (DART) mass spectrometry (MS) techniques, with minimal extraction and sample preparation to preserve both polymer and additive information. MALDI-MS was applied to aqueous samples collected along the shores of Lake Erie and the Cuyahoga River, successfully identifying the base polymer(s) in …

Unilateral Online Ultrasound Stimulation Of Early Visual Cortex Suppresses Responses To Contralateral Visual Stimuli, Suraya Dunsford, Keith Murphy, Ema Darrieutort, Elsa Fouragnan, Giorgio Ganis

School of Psychology

INTRODUCTION: Transcranial ultrasound stimulation (TUS) shows great promise for inducing neuroplastic changes that persist long after stimulation. Evidence of stimulation-locked (online) neural changes would enable the development of closed-loop application of TUS. However, such responses have been difficult to distinguish from coincident neural activity caused by auditory and somatosensory effects of TUS.

METHODS: To dissociate genuine online neuromodulatory effects from peripheral confounds, we leveraged the contralateral retinotopic organization of the early visual cortex in nineteen subjects. Using a hemifield visual stimulation paradigm combined with high-precision, functional MRI-guided TUS, we applied TUS to the left early visual cortex while participants viewed …

Shaping The Future Of Vertical Bone Augmentation: A Detailed Review Of Additive Manufacturing And 3d Biodegradable Scaffolds, Sleem Abdelstar Farag, Refaie Ahmed Omar, Salah A. Salman, Ahmed Barhoum, Gomaa A. Abdalla, Abdalla Abdal Hay Ali

Research Outputs: 2025-Present

Achieving effective alveolar bone augmentation in the vertical dimension presents a significant challenge in periodontal tissue regeneration, particularly for optimizing dental implant procedures. Sufficient alveolar bone height is crucial for successful implant placement. To achieve this, several surgical approaches—such as autologous bone block grafting, distraction osteogenesis, and guided bone regeneration (GBR)—are commonly used, often in combination with natural or synthetic grafting materials. However, these conventional methods face limitations, including morbidity, dimensional instability, structural weaknesses, handling difficulties, and high failure rates. Recent advancements in additive manufacturing, present innovative solutions by enabling the creation of 3D porous scaffolds with essential properties for …

The Application, Construction, And Validation Of Hidden Markov Model Profiles For Carbonic Anhydrase Enzymes, Samuel F. Kaplan

Master's Theses

Carbonic anhydrases (CAs) catalyze the reversible hydration of CO2 and have evolved independently at least eight times, resulting in structurally distinct enzyme families (α, β, γ, δ, ζ, η, θ, ι). Traditional sequence alignment methods struggle to classify these convergently evolved proteins because their sequential similarity does not reliably indicate functional or evolutionary relationships. Many CA sequences in public databases are annotated generically without family assignments, and prior computational approaches have focused predominantly on the three well characterized families (α, β, γ), leaving the five recently discovered classes without robust classification tools. Family level assignment is often a prerequisite for …

Exploring Non-Conventional Substrates: The Role Of Hibiscus And Whey In Kombucha Fermentation, Benjamin J. Lee

Master's Theses

This study evaluated the impact of hibiscus and whey as alternative fermentation substrates on the physicochemical, phytochemical, and microbial properties of kombucha. A 2 × 2 full factorial design was used to compare four treatments: black tea + water (BW), black tea + whey (BH), hibiscus + water (HW), and hibiscus + whey (HH). The fermentation solvents (water or whey) were heated to 88 °C, infused with 0.6% (w/v) black tea or hibiscus for 10 minutes, sweetened with 10% (w/v) sucrose, cooled to 22 °C, and inoculated with 20% (v/v) kombucha starter culture. Fermentations were carried out at 22 °C …

Measurement And Control Of The Oxidation-Reduction Potential And Its Chemical And Sensory Consequences In Wines, William Jordan Wright

Master's Theses

The oxidation-reduction potential (ORP) is a measurement thought to reflect the overall ability of a solution to oxidize or reduce substances within that solution. In wine, there is no absolute agreement as to which substances control or dominate the ORP; however, oxygen, ethanol, iron-tartrate and copper-tartrate complexes, and glutathione are suspected to play key roles, while sulfur dioxide and phenolics may act as buffers. Anecdotally, some varieties of Vitis vinifera are prone to oxidation while others are prone to reduction, though the chemical basis of this remains unclear. The following works aim to further elucidate the influence of specific chemical …

Associations Between Nutrition-Related Chronic Disease And Food Insecurity: Data From The California State University, Elizabeth Ochoa

Master's Theses

Food insecurity is a growing public health concern consistently associated with elevated rates of nutrition-related chronic disease (NRCD) across the general population. Despite young adulthood being a critical window for dietary pattern formation, this relationship remains minimally explored among college students. This thesis examined associations between food insecurity and NRCD diagnosis, including hypertension, diabetes, hyperlipidemia, and cardiovascular disease, among undergraduate students across the California State University (CSU) system. Cross-sectional data were drawn from the Spring 2021 CSU National College Health Assessment, administered across all 23 campuses. After exclusions, the analytical sample comprised 13,762 students. Bivariate analyses assessed relationships between key …

Environmental Impact Of Preventative Fire-Retardant Applications On Soil Water Chemistry, Patrick C. Michelsen

Master's Theses

Between 1992 and 2012, 84% of all documented wildfires were started by humans. These fires often start around high-risk locations such as power lines and roadsides where fuel loads are near these potential human-caused ignition sources. Point source ignition sites that are surrounded by shrubs or grasslands are especially important because fires that occur within these biomes are responsible for far more destruction of property than forest fires. One strategy that is effective at mitigating the spread of fires from ignition sites that are within grassland or shrub biomes are preventative fire-retardant products (PFRPs). These PFRPs differ from traditional fire-retardant …

Empirical Comparisons Of Partial Dimension Reduction Algorithms In High-Dimensional Regression, Nathan Greenfield

Master's Theses

In high-dimensional regression problems, dimension reduction methods are often used to address the challenges of multicollinearity and estimation instability. Partial dimension reduction extends these ideas by applying dimension reduction to a subset of the predictors, while the remaining predictors are modeled without compression. This approach is particularly useful when it is important to retain variability and interpretability in certain predictors.

This thesis investigates the empirical performance of partial dimension reduction algorithms and introduces a novel algorithm, Iterative Partial Residual (IPR). Two algorithms are considered: a baseline algorithm, Marginal Residual (MR), and the proposed IPR method. Their predictive performance is evaluated …

Impact Of Femalized Kinesthetic Learning Model On African American Middle School Girls’ Career Interest, Mercy F. Fash, Andrea Ofori-Boadu

Journal of Global Education and Research

Engaging African American middle school girls in out-of-school-time (OST) Architecture, Engineering, and Construction (AEC) programs can boost interest in male-dominated AEC careers. This study adopts Lent’s Social Cognitive Career Theory to evaluate the impact of an OST feminized AEC kinesthetic learning model (fAEC-KLM) on the career interests of this demographic. Through a qualitative research approach, fourteen (14) African American middle school girls from Guilford County, NC, completed pre- and post-interviews on how fAEC-KLM interactions influenced their AEC career interests. Inductive thematic analysis was carried out on transcribed interviews. Results show that effective components, such as lectures on AEC, bridge construction …

Development Of An Automated Platform For Cell Biology Experiments, Dipendra Nepal

Shelby Hall Graduate Research Forum Posters

Cell biology experiments involve repetitive tasks such as pipetting, sample preparation, and imaging, which are typically performed manually. These manual processes can introduce variability, reduce efficiency, and increase the cost of biomedical research. To address these challenges, our lab is developing a modular robotic platform, iEye™, to automate key steps in cell biology workflows [1]. The system is designed as self-contained modules, allowing flexible development and integration of different functionalities. In this work, we focus on a sample preparation module that integrates a 6-degree-of-freedom robotic arm, a motorized stage, and a pneumatic pipetter. This module is being developed to automate …

Trophic Structure And Mercury Bioaccumulation In Walleye And Yellow Perch In The Upper And Lower Red Lake Basins, Marissa Pribyl

Biology Graduate Theses

Mercury is a persistent global contaminant that biomagnifies through aquatic food webs, with dietary and environmental factors serving as the primary drivers of accumulation in fishes. Trophic structure and methylmercury dynamics in Walleye (ogaa; Sander vitreus) and Yellow Perch (asaawens; Perca flavescens) were investigated in the Upper and Lower Red Lake basins in Red Lake, Minnesota, during 2024-2025. Diets of Walleye and Yellow Perch were assessed through stomach dissections, and tissue samples from both species were analyzed for total mercury concentrations. Additional analyses included shiners (gigoozens; Notropis spp., Hudsonius spp.) along with a variety of freshwater fish and …

Age-Specific Concentrations And Seroprevalence Of Antibodies Against Salmonella Enteritidis (O:9) And Salmonella Typhimurium (O:4,5) Across Three Sites In Kenya., Esther Muthumbi, Sean Elias, Alfred Mwanzu, Agnes Mutiso, Perpetual Wanjiku, Cecilia Mbae, Godfrey Bigogo, Jennifer Verani, Stefan Flasche, Samuel Kariuki

Population Health, East Africa

Background Seroprevalence studies can indicate the age distribution of first infection with nontyphoidal Salmonella and estimate the rate of infection by age.

Method We collected 1254 paired samples of serum and stool from healthy children and adults in Kilifi, Nairobi, and Siaya counties in Kenya, areas of low, medium, and high incidence of invasive nontyphoidal Salmonella disease, respectively. We quantified the age- and site-specific geometric mean concentrations (GMCs) of IgG and IgA antibodies against S Enteritidis O-antigen (O:9, serogroup D) and S Typhimurium O-antigen (O:4,5, serogroup B) using an in-house standardized enzyme-linked immunosorbent assay. Serum concentrations were estimated against a …

Awarded Research Grants As A Pathway To Sustainable Development Goals, Maha Inam, Salim S. Virani, Melaine D'Cruze, Veronica Robi, Peter Gatiti, Anil Khamis

Population Health, East Africa

The United Nations Sustainable Development Goals (SDGs) are a set of global goals that provide an agenda for sustainable growth and development across all sectors and disciplines. However, the contribution of academic institutions from the developing world towards the SDGs has not received adequate attention from the scientific community. A review of all the awarded grants in 2022 and 2023 at an international academic institution was conducted. The objectives outlined in the grant proposals were used to map the SDGs accordingly. A quantitative frequency analysis was conducted to tabulate the results. A total of 293 grants obtained in 2022 and …

Pharmacokinetic Modeling Strategies For Dynamic Hyperpolarized Urea Imaging, Keith A Michel, Collin J Harlan, Christopher M Walker, Matthew E Merritt, Yunyun Chen, Stephen Y Lai, James A Bankson

Faculty, Staff and Student Publications

Purpose: To evaluate pharmacokinetic modeling methods for quantification of tissue perfusion/permeability with hyperpolarized 13C urea.

Methods: Three models for quantitative analysis of dynamic HP urea imaging data were proposed and evaluated in numerical simulations and a thyroid cancer mouse model. A multicompartment model resembling the extended Tofts model for DCE-MRI (Model I) and two simplified models were used. The simplified models each eliminate a volume parameter representing vascular (Model II) or impermeable cellular space (Model III). Signal curves were generated from Model I, and models were fit to these synthetic data to quantify the effects of acquisition settings, bias in …

Information Extraction From Clinical Notes: Are We Ready To Switch To Large Language Models?, Yan Hu, Xu Zuo, Yujia Zhou, Xueqing Peng, Jimin Huang, Vipina K Keloth, Vincent J Zhang, Ruey-Ling Weng, Cathy Shyr, Qingyu Chen, Xiaoqian Jiang, Kirk E Roberts, Hua Xu

Faculty, Staff and Student Publications

Objectives: To assess the performance, generalizability, and computational efficiency of instruction-tuned Large Language Model Meta AI (LLaMA)-2 and LLaMA-3 models compared to bidirectional encoder representations from transformers (BERT) for clinical information extraction (IE) tasks, specifically named entity recognition (NER) and relation extraction (RE).

Materials and methods: We developed a comprehensive annotated corpus of 1588 clinical notes from 4 data sources-UT Physicians (UTP) (1342 notes), Transcribed Medical Transcription Sample Reports and Examples (MTSamples) (146), Medical Information Mart for Intensive Care (MIMIC)-III (50), and Informatics for Integrating Biology and the Bedside (i2b2) (50), capturing 4 clinical entities (problems, tests, medications, other treatments) …

A Patient-Derived Organ-On-Chip Platform For Modeling The Tumor Microenvironment And Drug Responses In Pancreatic Cancer, Darbaz Adnan, Natan Roberto De Barros, Luca S Santovito, Xuhong Cheng, Kristi M Lawrence, Mariah K Barnett, Martine D Boetto, Neal Mehta, Ajaypal Singh, Lin Cheng, Xiangsheng Huang, Faraz Bishehsari

Faculty, Staff and Student Publications

Pancreatic ductal adenocarcinoma (PDAC) is a fatal malignancy. Current conventional chemotherapeutics are inadequate in controlling the disease; hence, there is an urgent need for precision medicine. Ex vivo models that replicate the tumor and its microenvironment can advance precision medicine in PDAC. Patient‐derived organoids (PDOs) offer a promising solution by retaining the functional features of the tumor, allowing for individualized study of cancer biology and drug response. However, PDOs fall short in replicating the tumor microenvironment (TME), which includes various stromal and immune cells influencing tumor growth and chemoresistance. We hypothesize that combining PDO technology with organ‐on‐a‐chip (OoC) systems can …

[Factors Associated With Adhd Medication Adherence And Treatment Outcomes, Hali Temkin, Kerri L Daniel, Diana Martinez, Julia C Bennett, Paris A Nix, Linh Nguyen, Yen-Chi Le, Bruno Kluwe-Schiavon, Cesar A Soutullo

Faculty, Staff and Student Publications

Introduction: Attention-Deficit/Hyperactivity Disorder (ADHD) is a neurodevelopmental disorder that affects 5 to 8% of youth and 2.5 to 4% of adults. Pharmacological treatments are among the most effective when treating ADHD, yet adherence to medication is still sub-optimal. We reviewed the literature on clinical and socio demographic factors that may influence adherence and compared it to our clinical data.

Methods: We conducted a targeted literature review on factors associated with ADHD medication adherence. These factors were compared within our sample of patients aged 3-18 with ADHD at the Child and Adolescent Mood Disorders Program (ChAMP) at (UT Health) - Houston. …

Childhood Pulmonary Outcomes After Late Preterm Antenatal Corticosteroids, Cynthia Gyamfi-Bannerman, Rebecca G Clifton, Robert A Wise, Alan T N Tita, Jessica A De Voest, Sharon A Mcgrath-Morrow, Elizabeth C Matsui, Sean C Blackwell, Monica Longo, Sabine Z Bousleiman, Felecia Ortiz, Sankaran Krishnan, Dwight J Rouse, Torri D Metz, George R Saade, Maged M Costantine, Kent D Heyborne, John M Thorp, Kelly S Gibson, Geeta K Swamy, William A Grobman, Yasser Y El-Sayed, George A Macones, Eunice Kennedy Shriver National Institute Of Child Health And Human Development Maternal-Fetal Medicine Units Network And The National Heart, Lung, And Blood Institute

Faculty, Staff and Student Publications

Objective: To evaluate whether antenatal betamethasone affects childhood respiratory impairment.

Methods: This was a prospective follow-up study of children aged 6 years and older from parents in the ALPS (Antenatal Late Preterm Steroids) trial randomized to betamethasone or placebo from 34 0/7 to 36 6/7 weeks of gestation. Primary outcome composite included the following: 1) abnormal spirometry, forced expiratory volume in 1 second (FEV 1 ) below the lower limit of normal, FEV 1 /forced vital capacity (FVC) below the lower limit of normal, or FVC below the lower limit of normal, defined as below the 5th percentile by the …

Impact Of Mutational Landscape And Burden On Rbc Transfusion Response In Patients With Lower-Risk Myelodysplastic Syndromes (Lr-Mds) In The Commands Study, Rami S Komrokji, Sheida Hayati, Manuel Ugidos, Guillermo Garcia-Manero, Matteo Giovanni Della Porta, Amer M Zeidan, Valeria Santini, Uwe Platzbecker, Anita K Gandhi, Rajasekhar N V S Suragani

Faculty, Staff and Student Publications

The COMMANDS trial established luspatercept as a first‐line treatment for anemia in transfusion‐dependent lower‐risk (LR) myelodysplastic syndromes (MDS). Here we report red blood cell (RBC) transfusion response analysis based on somatic mutations profile and disease risk for patients treated with luspatercept or epoetin alfa in the COMMANDS trial. Of 350 evaluable patients, 238 (68.0%) had MDS with multiple lineage dysplasia and ring sideroblasts (RS) according to World Health Organization 2016 criteria, and 320 (91.4%) had somatic mutations in ≥ 1 gene (median, 2) with median variant allele frequencies (VAF) of 2%–59%. Mutation profiles were similar in the treatment groups. Luspatercept …

Reconstruction Of A Composite Heel Defect Using Achilles Tendon Allograft And Latissimus Dorsi Free Flap: Case Report And Literature Review, Georgios Karamitros, Carolyn Drogt, Stephen J Warner, Michael P Grant, Gregory A Lamaris

Faculty, Staff and Student Publications

Background: Composite heel defects involving the Achilles tendon and overlying soft tissue are rare and technically demanding. Successful management requires restoration of tendon continuity and durable coverage. We reviewed the literature and presented a representative case to illustrate current strategies.

Methods: A literature review of 28 studies that reported outcomes of Achilles tendon reconstruction with concomitant soft tissue coverage was performed. Tendon restoration techniques(allografts, autografts, vascularized grafts) and flap types (muscle and fasciocutaneous) were analyzed for functional recovery, complication rates, and donor-site morbidity. Additionally, we report the case of a 14-year-old woman with a 7-cm Achilles tendon defect and full-thickness …

Beyond Short Microhomologies: Mismatch-Compatible Pol Θ-Mediated Dna Damage Repair, Yuzhen Li, Richard D Wood

Faculty, Staff and Student Publications

DNA polymerase θ (Pol θ)-mediated end-joining (TMEJ), one of several pathways for repairing DNA double-strand breaks, is traditionally thought to initiate via anchoring at short, consecutive, and perfectly matched microhomologies (MHs). Emerging evidence indicates that Pol θ can utilize MHs containing mismatches both in vitro and in vivo. This revised definition of MH provides a mechanistic explanation for a broader spectrum of Pol θ-dependent repair outcomes. Here, we summarize recent findings on the revised definition of MHs utilized by Pol θ, assess the applicability of this concept across species, and compare TMEJ with other (micro)hom(e)ology-mediated repair pathways. We explore how …

Glomerular Transcriptome Analysis Reveals Endothelial Disturbances In Patients With Idiopathic Nephrotic Syndrome., Sarah K. Nelson-Taylor, Jonathan Troost, Courtney Giannini, Colin Bauer, Tarak Srivastava, Jarcy Zee, Markus Bitzer, Laura Barisoni, Llse Daehn, Julie A. Dougherty, William E. Smoyer, Bryce A. Kerlin, Audrey Fetsko, Imtiazul Islam, Xin Wang, Christine Sethna, Richard J. Johnson, Carmen De Lucas Collantes, Kazunari Kaneko, Gabriel Cara-Fuentes

Manuscripts, Articles, Book Chapters and Other Papers

RATIONALE & OBJECTIVE: Idiopathic nephrotic syndrome (INS) is viewed as a podocyte-specific disease. Recent reports indicate endothelial involvement, but its significance is unclear. Here, we investigated the relationship between the glomerular expression of selected genes relevant to endothelial health and clinical markers of disease severity.

STUDY DESIGN: A cross-sectional study.

SETTING & PARTICIPANTS: Patients with INS (n = 70 minimal change disease and n = 83 focal segmental glomerulosclerosis) from the Nephrotic Syndrome Study Network cohort study and 53 control participants. Validation studies, including animal and cell culture experiments, were performed.

EXPOSURE: Gene expression analysis from micro-dissected human glomeruli. The …

Epidemiology Of Aspergillosis Diagnoses In Us Adults Using A National Ehr Database, 2013-2023., Brittany L. Morgan Bustamante, Elijah G. Martinez, Aidan Lee, Natalie J. Kane, Simon K. Camponuri, Rose M. Reynolds, Theo T. Snow, Juliana G E Bartels, Mark A. Hoffman, Theodore C. White, Justin V. Remais

Manuscripts, Articles, Book Chapters and Other Papers

BACKGROUND: Aspergillosis is a fungal infection associated with rising hospitalizations and substantial morbidity and mortality. In the United States, data remain fragmented due to the absence of centralized surveillance. This study aimed to evaluate demographic, geographic, and temporal trends in aspergillosis diagnoses across the United States and evaluate changes in those patterns following the emergence of COVID-19.

METHODS: We conducted a retrospective cohort study using electronic health record data from 142 US healthcare systems (Oracle Health), including adults aged ≥18 years who received care between 2013 and 2023. The cohort included over 76 million patients and 127 million person-years. Aspergillosis …

Shiny-Magec: A Bayesian R Shiny Application For Meta-Analysis Of Censored Adverse Events, Zihan Zhou, Zizhong Tian, Christine Peterson, Le Bao, Shouhao Zhou

Faculty, Staff and Student Publications

Accurate assessment of adverse event (AE) incidence is critical in clinical research for drug safety. While meta-analysis serves as an essential tool to comprehensively synthesize the evidence across multiple studies, incomplete AE reporting in clinical trials remains a persistent challenge. In particular, AEs occurring below study-specific reporting thresholds are often omitted from publications, leading to left-censored data. Failure to account for these censored AE counts can result in biased AE incidence estimates. We present an R Shiny application that implements a Bayesian meta-analysis model specifically designed to incorporate censored AE data into the estimation process. This interactive tool provides a …

Frontotemporal Network Interactions Causally Support Rapid Concreteness Judgments During Reading, Elliot Murphy, Oscar Woolnough, Cale W Morse, Xavier Scherschligt, Nitin Tandon

Faculty, Staff and Student Publications

Neurobiological models of conceptual processing have been limited in spatiotemporal resolution, and uncertainty remains about the causal role of specific regions in concept representation. We utilized intracranial recordings in human neurosurgical patients with epilepsy (n = 19) during a concreteness judgement paradigm of single word reading. Concrete concepts showed greater high-frequency activation across a frontal and ventrotemporal network, while greater activation for abstract words was found in lateral posterior middle temporal cortex. Intercortical communications, measured by high-frequency partial direct coherence, revealed bidirectional frontal and ventral plus lateral temporal interactions. Words occupying the middle range of the concreteness scale (e.g., "profit") …

Large Language Models For Bioinformatics, Wei Ruan, Yanjun Lyu, Jing Zhang, Jiazhang Cai, Peng Shu, Yang Ge, Yao Lu, Shang Gao, Yue Wang, Peilong Wang, Lin Zhao, Tao Wang, Yufang Liu, Luyang Fang, Ziyu Liu, Zhengliang Liu, Yiwei Li, Zihao Wu, Junhao Chen, Hanqi Jiang, Yi Pan, Zhenyuan Yang, Jingyuan Chen, Shizhe Liang, Wei Zhang, Terry Ma, Yuan Dou, Jianli Zhang, Xinyu Gong, Qi Gan, Yusong Zou, Zebang Chen, Yuanxin Qian, Shuo Yu, Jin Lu, Kenan Song, Xianqiao Wang, Andrea Sikora, Gang Li, Xiang Li, Quanzheng Li, Yingfeng Wang, Lu Zhang, Yohannes Abate, Lifang He, Wenxuan Zhong, Rongjie Liu, Chao Huang, Wei Liu, Ye Shen, Ping Ma, Hongtu Zhu, Yajun Yan, Dajiang Zhu, Tianming Liu

Faculty, Staff and Student Publications

With the rapid advancements in large language model technology and the emergence of bioinformatics-specific language models (BioLMs), there is a growing need for a comprehensive analysis of the current landscape, computational characteristics, and diverse applications. This survey aims to address this need by providing a thorough review of BioLMs, focusing on their evolution, classification, and distinguishing features, alongside a detailed examination of training methodologies, datasets, and evaluation frameworks. We explore the wide-ranging applications of BioLMs in critical areas such as disease diagnosis, drug discovery, and vaccine development, highlighting their impact and transformative potential in bioinformatics. We identify key challenges and …

Tuscan: Tumor Segmentation And Classification Analysis In Spatial Transcriptomics, Chenxuan Zang, Charles C Guo, Yaohong Wang, Peng Wei, Ziyi Li

Faculty, Staff and Student Publications

The identification of tumor cells is pivotal for understanding tumor heterogeneity and the tumor microenvironment. Recent advances in spatially resolved transcriptomics (SRT) have revolutionized the way that transcriptomic profiles are characterized and have enabled the simultaneous quantification of transcript locations in intact tissue samples. SRT is a promising alternative method to study gene expression patterns in spatial domains. Nevertheless, the precise detection of tumor regions within intact tissue remains a great challenge. A common strategy for identifying tumor cells is via tumor-specific marker gene expression signatures, which are highly dependent on marker accuracy. Another effective approach is through aneuploid copy …

Severe Renal Phenotype Across A Multigenerational Tuberous Sclerosis Complex (Tsc) Family, Elena Tuller, Joshua A Samuels, Hope Northrup, Kate Richardson

Faculty, Staff and Student Publications

Background: Tuberous sclerosis complex (TSC) is an autosomal dominant genetic disorder characterized by the formation of hamartomas in the brain, kidney, and heart, along with other complex clinical manifestations, including TSC-associated neuropsychiatric disorder (TAND). Development of genotype-phenotype correlations within TSC can aid clinicians in providing prognostic data and improve clinical management. We present here a multigenerational family who has a pathogenic variant in TSC2 displaying a severe renal phenotype.

Methods: A 23-year-old Caucasian male (Patient 1) was determined to have a molecularly confirmed diagnosis of TSC at approximately 2 months of age. The nonsense pathogenic variant (c.1372C>T (p.Arg458*)) in …