Life Sciences Commons^™

Taxonomy Of Endophytic Fungi Associated With Vallisneria Neotropicalis, Md. Arafat Rashid

Graduate Theses and Dissertations (2019 - present)

This study presents the first comprehensive taxonomic and ecological investigation of endophytic fungi (EF) associated with the submerged aquatic macrophyte Vallisneria neotropicalis in the southern United States. Over a 12 month period, from April 2023 to March 2024, leaf samples were collected from two distinct sites in Mobile Bay, Alabama a disturbed, brackish Causeway location and a cleaner, less impacted site at Meaher State Park. Using culture dependent methods, a total of 257 fungal endophytes were isolated from 1,200 leaf segments. All isolates belonged to the phylum Ascomycota, distributed across 3 classes, 6 orders, 10 families, and 19 taxa. The …

Improved Model For Neurodegeneration In C. Elegans, Jean-Pierre Arditi

Graduate Theses and Dissertations (2019 - present)

During Alzheimer's disease (AD), insoluble amyloid beta (AP) peptides accumulate to form extracellular aggregates (plaques). The direct cause of neuronal dysfunction observed in AD has been broadly investigated. The amyloid hypothesis states that AP plaques are neurotoxic, but recent studies support the AP oligomer hypothesis, which states that intracellular AP (iAP) is neurotoxic. To test this hypothesis, I used CRISPR-Cas9 gene editing to generate two transgenic Caenorhabditis elegans (C. elegans) strains. I generated a strain (RSLl 11) using the rab-3 promoter to co-express GFP in neurons, which showed no gross behavioral changes but had a 50% reduced egglaying rate. RSLl …

Twim #222: Biosensors In Bacteria, Madison Hayes, Alexis Austin, Dillon Nguyen, Angela Wilson, Rebecca Seipelt-Thiemann

School of Medical Diagnostics & Translational Sciences Publications

Podcast annotation TWiM #222: Biosensors in Bacteria from the weekly podcast series "This Week in Microbiology" (TWiM), a podcast where experts in microbiology discuss academic papers in their field in an informal way.

Twim #243: Beef And Bacillus, Sakiem Winston, Madison Wolford, Rebecca Seipelt-Thiemann, Angela Wilson

School of Medical Diagnostics & Translational Sciences Publications

Podcast annotation TWiM #243: Beef and Bacillus from the weekly podcast series "This Week in Microbiology" (TWiM), a podcast where experts in microbiology discuss academic papers in their field in an informal way.

Twim #286: Integrons And Invasion, Andrea Ayala-Lopez, Brittney Heist,, Thomas Salazar, Rebecca Seipelt-Thiemann, Mel Melendrez-Vallard, Angela Wilson

School of Medical Diagnostics & Translational Sciences Publications

Podcast annotation TWiM #286: Integrons and Invasion from the weekly podcast series "This Week in Microbiology" (TWiM), a podcast where experts in microbiology discuss academic papers in their field in an informal way.

Population Observations And Microhabitat Use Of Isthmohyla Tica (Anura: Hylidae) In San Ramón, Costa Rica, Pablo Marin Pacheco, Jerson Santamaria Martinez, Jose Manuel Mora, Jennifer L. Stynoski, Randall Arguedas

Biology Faculty Publications and Presentations

Isthmohyla tica, the Tica Frog, is a critically endangered species endemic to Costa Rica and supposedly Panama that has only been seen in a few sites in recent decades. To aid in its conservation, we assessed the population status and microhabitat preferences of this frog in a section of the Danta stream at Rancho Alegre farm, San Ramón, Costa Rica. We conducted 18 nocturnal surveys and collected data on perch types, vegetation associations, stream characteristics, and environmental variables for each sighting of the Tica Frog. To identify potential microhabitat preferences, we compared these features between sites with or without frogs …

Impact Of Polystyrene Nanoplastics On Oncogenic Signaling Pathways In Prostate Cells, Luis Alfonso Adel-Alvarez

Open Access Theses & Dissertations

Prostate cancer (PC) remains the most prevalent malignant disease among the male population worldwide, with a dramatic increase observed in the European Union from the 1980s to the 2000s. The etiology of PC is attributed to both hereditary factors and environmental pollutants. Among these, endocrine disruptors and polystyrene nanoparticles (PSNPs) interact with the prostate gland via the circulatory system, inducing intense oxidative stress. This study aims to characterize, for the first time, the pathobiological effects of PSNPs in both non-malignant (RWPE1) and malignant (22RV1) prostate cell lines. The objective was to elucidate the mechanisms by which environmental pollutants, such as …

Spatial Patterns In Plant Structural Diversity Across A Shrub Encroachment–Native Grassland Landscape Mosaic In The Northern Chihuahuan Desert, Bindu Poudel

Open Access Theses & Dissertations

Drylands are heterogeneous landscapes that provide important ecosystem services, but they are threatened by global change factors that may influence aspects of their diversity and function. Environmental factors may influence the three-dimensional physical characteristics of vegetation structure (structural diversity) across spatial scales in arid ecosystems. This study investigated how environmental factors, including shrub cover, landform, and elevation, are related to vegetation structural diversity metrics across different spatial scales and scopes across the Jornada Experimental Range, a long-term ecological research site located in the northern Chihuahuan Desert. A canopy height model generated by Airborne Observation Platform (AOP) LiDAR data and collected …

Gpu-Based Electromagnetic Microwave Tomography For Brain Imaging And Stroke Detection, Pablo Sotelo Torres

Open Access Theses & Dissertations

Each year, an estimated 795,000 people in the U.S. suffer a stroke, with approximately 610,000 being first-time cases. Of these, 87% are ischemic strokes, while the remaining 13% are hemorrhagic. Current imaging methods, such as Computed Tomography (CT), Positron Emission Tomography (PET), and Magnetic Resonance Imaging (MRI), provide useful information into brain tissue properties; while each technique has its advantages, they remain expensive, non-portable, and often too slow for emergency bedside or in-ambulance use. Electromagnetic Microwave Tomography (EMT) offers a promising alternative: an affordable, portable, rapid, and safe method for stroke detection. By contrasting dielectric properties between healthy and affected …

The Unilateral Neuromuscular Effects Of Cross Education Eccentric-Focused Isokinetic Strength Training With Blood Flow Restriction In Sedentary And Recreationally Active Males, Bryan Mixumi

Theses and Dissertations

PURPOSE: The purpose of this study was to determine if BFR unilateral training protocols can elicit the same or greater cross-education effect as observed with HIGH protocols.

RESULTS: Significant time main effects and trained vs. untrained interactions revealed both training groups improved in isometric and isokinetic strength, work and power across limbs (P < 0.05). EMG analyses showed significant increases in vastus lateralis activation, with limb-specific neural adaptations but no group differences (P < 0.05) suggesting potential cross-education influence in the lower musculature.

CONCLUSION: With lower workloads, the BFR training protocols produced improvements in isometrics and isokinetic strength, work, power, and EMG that were comparable to those of the HIGH group across the trained and untrained limbs. The magnitude and limb-specific patterns varied across isometric, isokinetic, and EMG variables, but …

The Transition Zone Hypothesis On Biodiversity Of The Indian River Lagoon System, Florida, Richard L. Turner

Ocean Engineering and Marine Sciences Faculty Publications

The Indian River Lagoon System (IRL) is regarded as having a high level of biodiversity. The level of biodiversity is often attributed in part to the 2-degree latitudinal span (251 km) of the IRL and to its position in a transitional zone between tropical and temperate biotic provinces. This hypothesis was tested for submerged aquatic vegetation (SAV) based on a recent treatise (Littler, Littler, and Hanisak, 2008). Five of seven species of seagrass are tropical, and two have either a broad or very narrow latitudinal distribution; the transition-zone hypothesis does not hold for seagrasses. Most macroalgae (131 spp.) are tropical/subtropical; …

Evaluation Of Ramp Instead Of Forage During Grain Adaptation And Different Sorghum Varieties On Enteric Methane Production From Cattle, Jack T. Fort

Department of Animal Science: Dissertations, Theses, and Student Research

Two experiments were conducted to evaluate the use of RAMP (Cargill Corn Milling, Blair, Nebraska) compared with traditional forage-based adaptations on methane (CH₄) and carbon dioxide (CO₂) emissions, performance, and carcass characteristics. Experiment 1, 64 yearling British × Continental steers (initial BW = 423 ± 6 kg) were adapted using 100% RAMP (RAMP) or a traditional forage diet (CON; 43% forage) before transitioning 22 d to a common finishing diet containing 65.6% steam-flaked corn. Emissions were measured in paired replications using a two-chamber indirect calorimetry barn. During adaptation RAMP did not affect CH₄ production (g/d; …

Impact Of Constant Versus Variable Inclusions Of Modified Distillers Grains Plus Solubles On Feedlot Cattle Performance And Carcass Characteristics And Impact Of The Frequency Of Varying Modified Distillers Grains Plus Solubles Inclusions In Feedlot Diets On Performance, Carcass Characteristics, Feeding Behavior, And Ruminal Ph Of Finishing Steers, Paige M. Madison

Department of Animal Science: Dissertations, Theses, and Student Research

Inconsistent availability or supply of distillers grains (DGS) can cause more variation in DGS inclusions throughout the feeding period. Two feedlot experiments evaluated the effects of varying inclusions of modified distillers grains plus solubles (MDGS) in feedlot diets. Beef steers (n = 400; initial BW = 287) were used in a 2 × 2 + 1 factorial experiment with treatments including: control with no MDGS compared to 2 inclusions (10% and 25%) of MDGS diet inclusions fed consistently or variably. No interactions were observed between MDGS consistency and inclusion for any performance or carcass characteristics (P > 0.10), so …

Integrating Innovative Sensing And Ground Measurements For Forage Mass Estimation In Rye Pasture, Pedro Henrique Jota Fernandes

Department of Animal Science: Dissertations, Theses, and Student Research

The United States beef industry relies on forages to provide up to 80% of total lifetime dry matter intake, making accurate forage mass estimation essential for determining stocking rates, improving grazing efficiency, and supporting economic sustainability. Traditional methods to quantify forage mass, however, are time-consuming and labor-intensive. This thesis presents research efforts to achieve accurate forage mass estimation in cereal rye pasture by integrating novel sensing technologies.

Chapter 1 reviews the importance and evolution of forage mass estimation methods, from destructive clipping to indirect approaches based on canopy measurements. It then introduces remote sensing, from proximal tools to drone- and …

Investigation Of Changes In Exotic Bird Serum Vitamin D Levels Between Indoor And Outdoor Housing, Alexander J. Marley

Department of Animal Science: Dissertations, Theses, and Student Research

Vitamin D is a fat-soluble vitamin that is directly related to sunlight and is involved in multiple physiological processes including calcium metabolism, feather quality, and chick development. Most vertebrate species are capable of both absorption of exogenous vitamin D and internal synthesis of vitamin D, with vitamin D3 (cholecalciferol), being more accessible and bioactive in bird species. In exotic bird species, dietary requirements for vitamin D3 are largely unknown, and the ability to maintain adequate serum concentrations of vitamin D3 metabolites without direct sunlight exposure also requires evaluation. Concerns arise in situations where individuals may be housed indoors for extended …

Spotted Seal Coastal Haul Out Behavior In Arctic Alaska, Maeghan Connor

Biological Sciences

Hauling out - the act of exiting the water to rest, molt, breed, and pup on solid surfaces - is a key behavior of pinnipeds worldwide. Unlike other ice seals (i.e., ice-associated phocid species), spotted seals (Phoca largha) in Alaska frequently use terrestrial substrates to haul out during the summer and fall open-water period in the Chukchi and Beaufort Seas. Despite being a core aspect of spotted seal ecology, their terrestrial haul out behavior remains understudied. To address this, we analyzed data collected from 2020 - 2022 near two known haul out sites in Dease Inlet, Alaska, including time-lapse camera …

Exploring Phenological Mismatch And The Role Of Aquatic Insects For Olive-Sided Flycatchers (Contopus Cooperi) Breeding In Boreal Alaska, Ian Kwit

Biological Sciences

Migratory insectivorous birds are an increasingly threatened group worldwide. These birds rely on an ephemeral resource of insects during a short window in which they arrive at breeding territories to rear young. Climate change has the potential to create a phenological mismatch between the timing of bird breeding and the availability of key insect prey. This study investigates the potential for such a phenological mismatch in a population of olive-sided flycatchers (Contopus cooperi). We used data on breeding phenologies and the composition of insect communities around nests in three regions of Alaska, Anchorage, Fairbanks, and Tetlin National Wildlife Refuge, to …

Evaluating Dietary Protein Sources And Protein Balance In Herbivorous Mammals Using Stable Isotope Analysis Of Amino Acids, Garrett A. Savory

Biological Sciences

Knowing how large herbivorous mammals acquire nutrients is critical to understanding how they can survive and reproduce in seasonally nutrient-limited landscapes. Gut bacteria and other microorganisms in herbivores digest plant fiber, providing energy, and potentially protein. In my first data chapter, I evaluated the importance of dietary and gut microbial protein to herbivores with different digestive physiologies using carbon isotopes of essential amino acids as markers of protein source. Foregut fermenters, moose (Alces dices) and muskox (Ovibos moschatus), and a hindgut fermenter with coprophagy, snowshoe hares (Lepus americanus), derived half of their protein from gut bacteria, whereas horses (Equusferus caballus), …

Molecular And Immunological Features Associated With Long-Term Benefits In Metastatic Nsclc Patients Undergoing Immune Checkpoint Blockade, Pedro Rocha, Rafael Bach, Laura Masfarré, Sharia Hernandez, Nil Navarro-Gorro, Adrià Rossell, Xavier Villanueva, Mario Giner, Ignacio Sanchéz, Miguel Galindo, Raúl Del Rey-Vergara, Albert Iñañez, Beatriz Sanchéz-Espiridion, Wei Lu, Ariadna Acedo-Terrades, Pau Berenguer-Molins, Albert Sánchez-Font, Roberto Chalela, Victor Curull, Álvaro Taus, Max Hardy-Werbin, Mark Sausen, Andrew Georgiadis, James White, Jennifer B Jackson, Laura Moliner, Sergi Clavé, Beatriz Bellosillo, Ana Rovira, Ignacio Wistuba, Luisa M Solis Soto, Júlia Perera-Bel, Edurne Arriola

Faculty, Staff and Student Publications

Introduction: Immunotherapy is firmly established as a treatment regimen in various solid tumors, driven by its exceptional benefits in a selected group of patients. Despite widespread adoption of immune checkpoint blockade (ICB) across diverse solid tumors, the quest for a clinically informative biomarker for long-term benefit remains unmet.

Methods: A total of 49 patients with metastatic NSCLC treated with ICB were included. Long-term (LTR) and short-term responders (STR) were defined as those with a response to ICB lasting more than 24 months or less than 6 months, respectively. Longitudinal blood specimens were collected before ICB treatment initiation and early-on treatment. …

Symptom Burden, Healthcare Utilization, And Risky Behaviors In Survivors Of The Childhood Cancer Survivor Study (Ccss): An Observation Cohort Study, Rachel Webster, Deo Kumar Srivastava, Lu Xie, Himani Darji, Wei Liu, Meghan E Mcgrady, Tara M Brinkman, Nicole M Alberts, Kirsten K Ness, Bernard Fuemmeler, Alicia S Kunin-Batson, I-Chan Huang, Gregory T Armstrong, Rebecca M Howell, Daniel M Green, Yutaka Yasui, Kevin R Krull

Faculty, Staff and Student Publications

Background: Childhood cancer survivors face physical, psychological, and neurological symptoms that contribute to risky health behaviors and increased healthcare utilization. Traditional survivorship care models overlook risk associated with this symptom burden. The current study examined symptoms phenotypes to identify high-risk groups.

Methods: Five-year survivors (N = 17,231; Mean [standard deviation] age = 27.4 [5.98]; 80% non-Hispanic White; 48% female) from the Childhood Cancer Survivor Study (NCT01120353) self-reported symptoms and risky behavior at baseline and first follow-up (original cohort data collection: baseline 1994-1998 and follow-up 2002-2004; expansion cohort: baseline 2008-2010 and follow-up 2014-2016). Medical records were extracted through chart …

Meniscal Repair In The Setting Of Revision Anterior Cruciate Ligament Reconstruction: 6-Year Follow-Up Results From The Mars Cohort, Jake A Fox, Laura J Huston, Amanda K Haas, Jacquelyn S Pennings, Christina R Allen, Daniel E Cooper, Thomas M Deberardino, Warren R Dunn, Brett Brick A Lantz, Kurt P Spindler, Michael J Stuart, Annunziato Ned Amendola, Christopher C Annunziata, Robert A Arciero, Bernard R Bach, Champ L Baker, Arthur R Bartolozzi, Keith M Baumgarten, Jeffrey H Berg, Geoffrey A Bernas, Stephen F Brockmeier, Robert H Brophy, Charles A Bush-Joseph, J Brad Butler V, James L Carey, James E Carpenter, Brian J Cole, Jonathan M Cooper, Charles L Cox, R Alexander Creighton, Tal S David, David C Flanigan, Robert W Frederick, Theodore J Ganley, Charles J Gatt, Steven R Gecha, James Robert Giffin, Sharon L Hame, Jo A Hannafin, Christopher D Harner, Norman Lindsay Harris, Keith S Hechtman, Elliott B Hershman, Rudolf G Hoellrich, David C Johnson, Timothy S Johnson, Morgan H Jones, Christopher C Kaeding, Ganesh V Kamath, Thomas E Klootwyk, Bruce A Levy, C Benjamin Ma, G Peter Maiers, Robert G Marx, Matthew J Matava, Gregory M Mathien, David R Mcallister, Eric C Mccarty, Robert G Mccormack, Bruce S Miller, Carl W Nissen, Daniel F O'Neill, Brett D Owens, Richard D Parker, Mark L Purnell, Arun J Ramappa, Michael A Rauh, Arthur C Rettig, Jon K Sekiya, Kevin G Shea, Orrin H Sherman, James R Slauterbeck, Matthew V Smith, Jeffrey T Spang, Col Ret Steven J Svoboda, Timothy N Taft, Joachim J Tenuta, Edwin M Tingstad, Armando F Vidal, Darius G Viskontas, Richard A White, James S Williams, Michelle L Wolcott, Brian R Wolf, James J York, Rick W Wright

Faculty, Staff and Student Publications

Background: Meniscal preservation has been demonstrated to contribute to long-term knee health and has been a successful intervention in isolation and in patients with anterior cruciate ligament reconstruction (ACLR). The long-term results of meniscal repair in the setting of revision ACLR have yet to be documented.

Purpose: To report the incidence of meniscal repair failures at the 6-year follow-up in a cohort of patients who underwent concurrent revision ACLR and primary meniscal repair.

Study design: Prospective cohort study; Level of evidence, 2.

Methods: All revision ACLRs with concomitant primary meniscal repair cases from a multicenter group between 2006 and 2011 …

Tubulin Regulates Stability And Localization Of Stmn2 By Binding Preferentially To Its Soluble Form, Xiang Deng, Gary A Bradshaw, Marian Kalocsay, Timothy Mitchison

Faculty, Staff and Student Publications

The small, tubulin-binding protein STMN2 is highly expressed in neurons and is implicated in amyotrophic lateral sclerosis. STMN2 degrades rapidly and accumulates at axotomy sites, suggesting fast turnover is crucial for its neuroprotective function. We show that STMN2 was primarily degraded by the ubiquitin-proteasome system. Its membrane-targeting N-terminal domain promoted fast turnover, whereas its tubulin-binding domain promoted stabilization. Proximity labeling and imaging showed that tubulin binding reduced STMN2 targeting to trans-Golgi network membranes. Pull-down assays showed that tubulin binds preferentially to soluble over membrane-bound STMN2. Our observations suggest that STMN2 interconverts between a soluble, tubulin-bound form and a membrane-bound, tubulin-free …

Decoding Fibrosis In Nonresolvable Covid-19: A Role For Myeloid-Specific Hif1a Deletion, Kemly Philip, Hannah P Thompson, Scott D Collum, Isabella Lefebvre, Bindu Akkanti, Bihong Zhao, Rahat Hussain, Manish Patel, Michael R Blackburn, Tingting W Mills, Harry Karmouty-Quintana

Faculty, Staff and Student Publications

A complication of viral lung infections is the development of pulmonary fibrosis. This phenomenon is most evident in patients with COVID-19, where in its most aggressive form patients developed nonresolvable (NR) COVID-19 requiring lung transplantation. NR-COVID-19 was characterized by the presentation of a fulminant fibrotic lung injury that progressed rapidly, even in patients with limited comorbidities. However, the mechanisms that led to this rapidly progressing form of fibrosis are not fully understood. A common clinical manifestation in the most severe cases of COVID-19 was the presence of "silent" hypoxemia. Thus, we hypothesized that a dysfunctional hypoxic response may result in …

Utility Of Serum Matrix Metalloproteinase-7 As A Biomarker In Cholestatic Infants With Congenital Heart Disease, Sindhu Pandurangi, Michael E Kim, Nicolas Noriega, Bradley Conant, Jangdong Seo, Reena Mourya, Pranavkumar Shivakumar, Anna L Peters, Andrew Misfeldt, Meghan Chlebowski

Faculty, Staff and Student Publications

Background: Matrix metalloproteinase 7 (MMP-7) is a novel biomarker for diagnosis of biliary atresia (BA), the most common cholestatic liver disease in infancy. There is a pressing need to determine the utility of MMP-7 levels in infants with congenital heart disease (CHD) to avoid unnecessary invasive diagnostic procedures in this high-risk population. We investigated the utility of MMP-7 in discriminating BA from non-BA cholestasis in infants with CHD and whether MMP-7 elevation was present in infants requiring treatment for clinically significant PH.

Methods: This is a single-center cross-sectional study including infants < 180 days of age with cholestasis and serum MMP-7 levels collected from 2019 to 2023. Demographic data and descriptive statistics were summarized with medians with interquartile ranges and frequencies with percentages. Median MMP-7 levels were assessed via Wilcoxon rank-sum test.

Results: A total of 149 patients were included. Patients …

Statistical Innovations In Clinical Trial Design With A Focus On Drug Combinations, Factorials, And Other Multiple Therapy Issues, Donald A Berry

Faculty, Staff and Student Publications

Statistical methods in clinical research tend to become entrenched. Innovations threaten the status quo. The "right way" becomes frozen in lore. This is so even when the "right way" is not best. "Statistical significance" and the associated requirement of "high power" is an example. This attitude is an impediment to efficient design. Willingness to address some design issues with moderate power enables building highly informative and highly efficient clinical trials. This article considers several types of clinical trials, including dose-finding, combinations, and factorial designs. Bayesian adaptive methods are used to show that trials can be made more efficient and more …

Research Hotspots And Trends In The Field Of Immune Checkpoint Inhibitors (Icis) For Cervical Cancer: A Bibliometric Study From 2014 To 2024, Chaoyan Shen, Juan Zhang, Guanyu Zhang, Hao Luo, Shuangke Zhang, Quan Yuan, Wei Xu, Wei Wang, Lele Miao

Faculty, Staff and Student Publications

In recent years, immune checkpoint inhibitors (ICIs) have emerged as a novel immunotherapeutic approach, offering renewed hope for enhancing cervical cancer patient prognosis. This study represents the inaugural bibliometric analysis of ICIs in the context of cervical cancer, covering the period from 2014 to 2024. A total of 422 articles were identified through the Web of Science Core Collection database, amassing 10,977 citations, with a consistent annual increase in the number of publications. The leading contributors in terms of countries, institutions, journals, and authors included China, the University of Texas System, Frontiers in Oncology, and Bradley J. Monk, respectively. …

Improvement And Maintenance Of Clinical Outcome Assessments In Atopic Dermatitis With Amlitelimab, Andrew Blauvelt, Raj Chovatiya, Joseph F Merola, Stephan Weidinger, Ken Igawa, Ella Brookes, Christine Weber, Jennifer Wang, Cori Gray

Faculty, Staff and Student Publications

Background: Amlitelimab, a fully human, nondepleting, anti-OX40 ligand monoclonal antibody, demonstrated reductions in lesional and pruritic endpoints in adults with moderate-to-severe atopic dermatitis (AD) in phase 2a and 2b trials.

Objectives: Here, we examined the effect and durability of amlitelimab on clinical outcome assessments (COAs) in the randomized STREAM-AD phase 2b trial.

Methods: Adults with moderate-to-severe AD with prior inadequate response to or inadvisability of topical medications received subcutaneous amlitelimab (250 mg with 500-mg loading dose, 250 mg, 125 mg or 62.5 mg) or placebo every 4 weeks in Part 1 (Weeks 0-24; 1:1:1:1:1 randomization). In Part 2, Week 24 …

Smart Spatial Omics (S2-Omics) Optimizes Region Of Interest Selection To Capture Molecular Heterogeneity In Diverse Tissues, Musu Yuan, Kaitian Jin, Hanying Yan, Amelia Schroeder, Chunyu Luo, Sicong Yao, Bernhard Dumoulin, Jonathan Levinsohn, Tianhao Luo, Jean R Clemenceau, Inyeop Jang, Minji Kim, Yunhe Liu, Minghua Deng, Emma E Furth, Parker Wilson, Anupma Nayak, Idania Lubo, Luisa Maren Solis Soto, Linghua Wang, Jeong Hwan Park, Katalin Susztak, Tae Hyun Hwang, Mingyao Li

Faculty, Staff and Student Publications

Spatial omics technologies have transformed biomedical research by enabling high-resolution molecular profiling while preserving the native tissue architecture. These advances provide unprecedented insights into tissue structure and function. However, the high cost and time-intensive nature of spatial omics experiments necessitate careful experimental design, particularly in selecting regions of interest (ROIs) from large tissue sections. Currently, ROI selection is performed manually, which introduces subjectivity, inconsistency and a lack of reproducibility. Previous studies have shown strong correlations between spatial molecular patterns and histological features, suggesting that readily available and cost-effective histology images can be leveraged to guide spatial omics experiments. Here we …

The Deubiquitinating Enzyme Cezanne Stabilizes Brca1 By Counteracting Apc/C And Ube2s-Dependent Lys11-Linked Ubiquitination, Longqiang Wang, Xiao Wu, Atanu Paul, Jun Yao, Bin Wang

Faculty, Staff and Student Publications

The breast and ovarian tumor suppressor BRCA1 is a cell cycle-regulated protein and tumors with reduced BRCA1 protein level may share molecular features of BRCA1-mutant tumor and respond to PARPi therapy. Here, we identify that BRCA1 protein stability is controlled through ubiquitin lysine 11 (K11)-linkage modification under the regulation of Cezanne deubiquitinating enzyme, APC/C E3 ligase, and Ube2S E2 conjugating enzyme in a cell cycle-dependent manner. Cezanne-deficiency leads to increased BRCA1 K11-ubiquitination, decreased BRCA1 protein level, and increased cellular sensitivity to PARPi. The BRCA1 K11-linked ubiquitination is carried out through a degron on BRCA1 that is recognized by APC/C cofactor …

Bayesian Prediction Of Event Times Using Mixture Model For Blinded Randomized Controlled Trials, Jingyan Fu, Dan Zhao, Donia Skanji, Hua Liu, Rui Sammi Tang, Ying Yuan

Faculty, Staff and Student Publications

Accurate prediction of key milestone dates, such as the timing of interim and final analyses, is crucial in event-driven clinical trials with time-to-event endpoints. These predictions facilitate timely decision-making, enhance strategic planning and optimize resource allocation while minimizing patient exposure to potentially ineffective or harmful therapies. Existing methods for predicting event timing in blinded randomized clinical trials (RCTs) typically assume identical time-to-event distributions for the treatment and control arms, implying no treatment effect. This assumption fails when the treatment is more effective than the control, which is often the very outcome the trial seeks to detect, leading to biased predictions. …