Digital Commons Network^™

Ozone Pollution Reduction Partially Offsets The Negative Impact Of Climate Change Mitigation Efforts On Global Hunger, Shujuan Xia, Tomoko Hasegawa, Thanapat Jansakoo, Daniel Mason-D’Croz, Kazuaki Tsuchiya, Shinichiro Fujimori, Maksym Chepeliev, Marta Kozicka, Abhijeet Mishra, Willem-Jan Van Zeist, Xin Zhao, Thijs De Lange, Thais Diniz Oliveira, Jonathan C. Doelman, Matthew Gibson, Petr Havlík, Mario Herrero, Ipsita Kumar, Yuki Ochi, Timothy B. Sulser, Marina Sundiang, Kiyoshi Takahashi, Jun’Ya Takakura, Keith Wiebe

Department of Agricultural Economics Faculty Publications

Studies warning of the potential negative effects of climate mitigation on food security through the competing use of land for bioenergy and afforestation have overlooked the impact of reduced ozone and its potential enhancement of crop yields. Here we use six global agro-economic models to compare the impacts of climate change with climate mitigation policy and ozone reduction on agriculture. We find that ozone reduction could reduce the negative impact of a 1.5 °C-consistent climate change mitigation policy on global hunger by 15% in 2050. Sub-Saharan Africa and India, where hunger is most severe, account for 56% of this global …

Targeting Il-1 Signaling In Recessive Dystrophic Epidermolysis Bullosa: Improved Survival And Pathogenesis In Rdeb Mouse Model, Rahim Hirani

NYMC Student Theses and Dissertations

Recessive dystrophic epidermolysis bullosa (RDEB) is a devastating inherited blistering disorder caused by biallelic mutations in COL7A1, resulting in deficiency of type VII collagen (C7) and loss of dermal–epidermal adhesion. Beyond mechanical fragility, RDEB is characterized by chronic inflammation, progressive fibrosis, impaired wound healing, severe pain, and an exceptionally high risk of aggressive cutaneous squamous cell carcinoma. Emerging transcriptomic and cytokine profiling studies have identified interleukin-1 alpha (IL-1α) as a dominant and temporally upstream inflammatory mediator in RDEB skin. The central hypothesis of this dissertation is that IL-1α signaling functions as a key initiator and amplifier of inflammation-driven pathology …

Ifnγ-Induced Antigen Loss In Chimeric Antigen Receptor-T Cell Therapy, Miao Cao, Jasmine Alvarez, Ramkrishna Mitra, Michael Xu, Trevor R. Baybutt, Zhengyang Sun, Oluwatobiloba Taylor, Allison Doermann, Ross E Staudt, Scott A. Waldman, Adam E. Snook

Department of Pharmacology, Physiology, and Cancer Biology Faculty Papers

INTRODUCTION: FDA-approved chimeric antigen receptor (CAR)-expressing T cell therapies (CARTs) have revolutionized the treatment of blood cancers. Yet none have been successful for "solid" tumors, such as colorectal cancer (CRC), the 2nd leading cause of cancer deaths. Guanylyl cyclase C (GUCY2C) has emerged as a clinical-stage target for CART and bispecific T-cell engager (BiTE) therapies in CRC. IFNγ has been canonically recognized as beneficial for the effector functions of T cells by enhancing antigen processing and HLA presentation and is essential for CART targeting of solid malignancies by inducing adhesion molecule expression for synapse stabilization.

METHODS: Using

RESULTS: We identified …

Black Medic (Medicago Lupulina) Identification And Control In Residential Landscapes, Michael Caron, Taun Beddes, Corey Ransom

All Current Publications

Black medic (Medicago lupulina) is an herbaceous winter or summer annual broadleaf landscape weed. This fact sheet provides a weed description and describes suppression and control options.

Seeds Of Change - Building Community And Resilience With Plant Guilds, Roslynn Mccann, Liliane Dionne, Kevin White

All Current Publications

The goals of this Grade 6 living systems/biodiversity curriculum are to highlight Indigenous (First Nations, Métis, and Inuit) contributions to science, technology, and sustainable agriculture, with a focus on relational worldviews, permaculture practices, and respect for Mother Earth. Students will conduct plant experiments, learn Indigenous stories, make corn husk dolls, create a recipe, and enjoy eating their soup creation.

Seasonal Dynamics And Trends Of Environmental Conditions In Lake Louise, Georgia, Daniel Kwawuvi, James A. Nienow

Georgia Journal of Science

Lakes are important aquatic ecosystems that are extensively influenced by seasonal variations. In this study we investigate the seasonal dynamics and trends of three environmental variables, water temperature, conductivity and dissolved oxygen (DO), in Lake Louise, a sinkhole lake located in southern Georgia. These variables were measured in-situ along a depth profile from January 27, 2024 to January 17, 2025. We also accessed archived data from field campaigns in 2003, 2004, and 2017 in order to test whether a recent increase in the number of hurricanes impacting the region, five since August, 2017, may have significantly altered the seasonal dynamics …

Radiation Doses To Cardiac Substructures Predict Elevation In High-Sensitivity Cardiac Troponin T Levels In Radiation Therapy For Lung Cancer, Xinru Chen, Xiaodong Zhang, Ting Xu, Radhe Mohan, Ruitao Lin, Mei Chen, Rachel C Maguire, Yao Zhao, Efstratios Koutroumpakis, Nicolas L Palaskas, Anita Deswal, Ali Ajdari, Joshua S Niedzielski, Sanjay S Shete, Laurence E Court, Jinzhong Yang, Zhongxing Liao

Faculty, Staff and Student Publications

Purpose: Cardiotoxicity is a major concern for patients undergoing thoracic radiation therapy. This study compared the predictive power of radiation dose-volume histogram (DVH) parameters and radiomic/dosiomic features of the whole heart (WH) and cardiac substructures for elevated circulating high-sensitivity cardiac troponin T (hs-cTnT), a biomarker for early detection of cardiac adverse events.

Methods and materials: A retrospective cohort of 160 patients with non-small cell lung cancer (NSCLC) from a completed prospective trial and a prospective cohort of 57 patients with NSCLC enrolled in an ongoing trial were analyzed. The endpoint was hs-cTnT elevation, indicated by an increase of ≥5 ng/L …

High Dietary Fiber Is Associated With Improved Outcomes In Patients With Melanoma And Sarcoma Treated With Immunotherapy Regardless Of Gut Microbiome Dysbiosis And Social Vulnerability, Brittany C Fields, Raymond S Traweek, Kai Jiang, Russell G Witt, Ashish Damania, Yi-Ju Chiang, Nadim Ajami, Elise Nassif-Haddad, Emily Z Keung, Manoj Chelvanambi, Xiaotao Zhang, Christine B Peterson, Jennifer A Wargo, Carrie R Daniel, Christina L Roland, Ashley M Holder

Faculty, Staff and Student Publications

Background: Social vulnerability, dietary fiber, and the gut microbiome have been individually implicated in clinical outcomes for melanoma and sarcoma patients. This study hypothesized that increasing social vulnerability is associated with insufficient dietary fiber intake and negatively associated with microbiome composition and clinical outcomes.

Methods: Clinicopathologic data, baseline fiber intake, and gut microbiome profiles were assessed in 153 patients with melanoma or sarcoma treated with immune checkpoint blockade (ICB) and prospectively followed. Patients' social vulnerability index (SVI) and fiber intake were evaluated for associations with microbiome composition, treatment response, and overall survival (OS).

Results: SVI percentile was 0.4 (interquartile ratio …

Misregulated Alternative Splicing In Endometriosis: A Role For Aberrant Mrna Variants In Endometriotic Cell Growth, Venkata Naga Goutham Davuluri, Michelle Dias, Roxanna Llinas, Kamath Neha, Pooja Popli, Shannon M Hawkins, Chandrakant Tayade, Elise T Courtois, Hari Krishna Yalamanchili, Ramakrishna Kommagani

Children’s Nutrition Research Center Staff Publications

Endometriosis is a chronic gynecological disorder marked by the growth of endometrial-like tissue outside the uterus, often leading to pelvic pain, inflammation, and infertility. Despite its global prevalence, diagnosis remains delayed, and effective non-surgical treatments are lacking. While recent transcriptomic studies have identified mRNA transcript changes in ectopic lesions, the contribution of alternative pre-mRNA splicing, a key posttranscriptional regulatory layer, remains largely unknown. In this study, we performed a comprehensive analysis of alternative splicing (AS) events in endometriotic lesions using transcriptomic data. We uncovered distinct alterations in alternative splicing events are associated with endometriosis, highlighting a previously underappreciated layer of …

Simulated Hearing Loss In Healthy Young And Older Adults Results In Poor Reaction Time In Older Adults., Victoria Kowalewski, Nicoleta Bugnariu, Rita M. Patterson, Jessica Hartos

Pacific Journal of Health

Emerging evidence links hearing loss to increased fall risk in older adults, yet mechanisms remain unclear. This study examined the impact of simulated hearing loss on reactive balance control in healthy young and older adults. Participants performed dual-task scenario involving auditory sentence repetition and unexpected surface translations. Hearing loss was simulated using Adobe Audition, applying frequency-specific attenuation based on moderate sensorineural hearing loss levels from the literature.

Speech-in-noise performance significantly declined under simulated hearing loss for both age groups (p < .001), confirming effective simulation, but not significant differences were found between age groups. Maximum COP-COM displacement (the scalar distance between Center of Pressure and Center of Mass) increased with perturbation intensity (Level 1 vs. Level 2: p < .001), but no significant differences were found between hearing conditions or age groups (p > .05), suggesting compensatory step execution was preserved.

Reaction time analysis revealed a significant interaction between hearing condition and perturbation level …

Advancements In Extracellular Vesicle Research, Lucia R. Languino

Department of Pharmacology, Physiology, and Cancer Biology Faculty Papers

The AAEV (American Association of Extracellular Vesicles) Annual Meeting at the John P. McGovern Commons in Houston, TX convened over 300 leading re- searchers, clinicians, and industry experts from around the world to advance the rapidly evolving field of extracellular vesicle (EV) science. EVs, nanoscale lipid- bound particles released by all prokaryotic and eukaryotic cells, have emerged as crucial mediators of intercellular communication, trans- porting proteins, nucleic acids, and lipids that influence a wide spectrum of physiological and pathological processes. Their involvement in immune modulation, tissue regeneration, cancer progression, metabolic regulation, and other complex biological functions positions EVs as promising …

Ccr7 Immune Cell Receptor Expression In Inflammatory Breast Cancer, Jennifer H Chen, Wintana Balema, Savitri Krishnamurthy, Alison N Lawrence, Natalie W Fowlkes, Richard A Larson, Surbhi Shivhare, Caren Sanchez, Megan M Rodriguez, Jangsoon Lee, Emilly S Villodre, Bisrat G Debeb, Naoto T Ueno, Steve Van Laere, Francois Bertucci, Hyunwoo Cho, Erik P Sulman, Bora Lim, Wendy A Woodward

Faculty, Staff and Student Publications

No abstract provided.

Patterns Of Failure Following Stereotactic Radiosurgery Salvage For Recurrent High-Grade Glioma, Shivani Bindal, Brandon Gonzalez, Antonio Dono, Roy Riascos, Jay-Jiguang Zhu, Sigmund Hsu, Nitin Tandon, Angel Blanco, Yoshua Esquenazi, Mark Amsbaugh

Faculty, Staff and Student Publications

Background and objectives: Re-irradiation with stereotactic radiosurgery (SRS) is an increasingly used treatment for recurrent high-grade glioma (HGG). We analyzed the patterns of failure after salvage SRS to better identify which patients would most benefit.

Methods: We reviewed all patients who received SRS for recurrent HGG over 12 years at our institution. Pattern of failure was defined by the distance of recurrence from the SRS isodose line. Overall-survival (OS), progression-free survival (PFS), and local-failure-free survival (LFS) were estimated using Kaplan-Meier methods, and regression model analysis was performed to analyze clinical predictors of failure.

Results: 146 patients with HGG underwent SRS …

Pimicotinib Versus Placebo For Tenosynovial Giant Cell Tumour (Maneuver): An International, Randomised, Placebo-Controlled, Phase 3 Trial, Hairong Xu, Xiaohui Niu, Vinod Ravi, Javier Martin-Broto, Albiruni Abdul Razak, Ramy Saleh, Yong Zhou, Jingnan Shen, Tang Liu, Kamlesh Kumar Sankhala, César Serrano, Silvia Stacchiotti, Jing Wang, Giacomo G Baldi, Yi Feng, Yingqi Hua, Tao Li, Piotr Rutkowski, Xiaojing Zhang, Gabriel Tinoco, Qingping Zou, Boyao Shan, Xiangyu Zhu, Hans Gelderblom

Faculty, Staff and Student Publications

Background: Tenosynovial giant cell tumour (TGCT) is a rare, locally aggressive neoplasm that affects otherwise healthy adults. There are few systemic treatment options, highlighting an unmet need. We report the results of part 1 of the MANEUVER trial, which aimed to evaluate the efficacy and safety of pimicotinib, a highly selective, potent, colony-stimulating factor-1 receptor inhibitor, in patients with TGCT.

Methods: MANEUVER is a randomised, placebo-controlled, phase 3 study done in 40 specialised hospitals in Asia, Europe, and North America. Patients aged 18 years and older with unresectable, symptomatic TGCT (patient-reported worse stiffness or worst pain of at least 4 …

Exploring The Roles Of The Coach Developer: A Uscce White Paper, Christine Nash, Melissa Thompson, Sean Dahlin, Andrea Woodburn, Jeremy Elliott

Journal of Coach Development

Organizational white papers serve as a mechanism for strategic communication and to establish thought leadership, build credibility, and drive informed decision-making across stakeholder groups. It is the belief of the USCCE that the official launch of the Journal of Coach Development offers the appropriate outlet and timing to publish this official stance of the organization to explore the multiple roles of the coach developer. As the field continues to evolve, our shared understanding of the roles and responsibilities of those serving to support the growth and development of sport coaches will be essential. Further, as a critical focus of the …

What Is Coach Development? A Uscce White Paper, Melissa Thompson, Christine Nash, Sean Dahlin, Andrea Woodburn, Jeremy Elliott

Journal of Coach Development

Organizational white papers serve as a mechanism for strategic communication and to establish thought leadership, build credibility, and drive informed decision-making across stakeholder groups. It is the belief of the USCCE that the official launch of the Journal of Coach Development offers the appropriate outlet and timing to publish this official stance of the organization defining the term ‘coach development.’ As an emerging term in the field, there is need for clarity around what coach development is and what it looks like in practice. Further, as a critical focus of the Journal of Coach Development, this paper will serve to …

Water Sources And Livelihood Choices Among Pastoralist Households In Monduli District, Tanzania, Fredrick Alleni Mfinanga, Jacqueline Temba, Monica F. Timbuka

Journal of Humanities and Social Sciences

This paper investigates the association between types of water sources for livestock and livelihood choices of pastoralist households in semi-arid areas of Monduli District, Tanzania. Specifically, it aims to examine the influence of the types of water sources for livestock on livelihood diversification of pastoralist households. Using a mixed research methods approach, the data were collected from 367 households through three methods: surveys, interviews, and focus group discussions. The quantitative data were analysed using descriptive statistics such as frequencies and counts, and inferential statistics, Chi-square tests and correlation, while the qualitative data were analysed using content analysis. The findings revealed …

The Nexus Between Perceived And Scientific Weather Patterns And Its Effects On Cereal Crop Production In Manyoni District, Tanzania, Fadhili Lufunyo Ngajilo, Helena Elias Myeya, Evarist Fundisha Swai

Journal of Humanities and Social Sciences

This study examines the nexus between perceived and scientific weather patterns, and its effects on cereal crop production in Manyoni District; and involved 157 participants. Both quantitative and qualitative data were collected through a mixed methods research approach. The data were collected through a household survey, FGDs, in-depth interviews and documentary review methods for triangulation and complementarity purposes. The quantitative data were analysed through descriptive and inferential statistics with IBM SPSS (version 27) and Microsoft Excel Office (version 2007). The results indicate that smallholder farmers perceived that rainfall had been fluctuating with increasing trends, while temperature and wind had been …

Larvicidal Activity Of Β-Asarone And Acorus Calamus Linn. (Sweet Flag) Extract Against Aedes Aegypti (Dipotera: Culicidae): Enzyme Inhibition, Midgut Histopathology, And In Silico Analysis, Rizal Subahar, Surya Dwira

Indonesian Journal of Medical Chemistry and Bioinformatics

Aedes aegypti (Diptera: Culicidae), the primary vector of dengue, poses a significant public health threat in tropical and subtropical regions. Botanical insecticides and phytochemicals such as β- asarone, derived from essential oils,offer a promising alternative to synthetic larvicides. The rhizome of Acorus calamus L. (sweet flag), traditionally known for its neuroprotective and antioxidant properties, contains β-asarone as its principal bioactive constituent.This study evaluated the larvicidal efficacy of β-asarone and A. calamus rhizome extract against Ae. aegypti larvae, focusing on detoxification enzyme inhibition, midgut histopathology, and in silico molecular interactions.Third- and fourth-instar larvae were exposed to β-asarone and crude extract at …

Ionic Liquid Pilocarpine Serves As Therapeutic Cosolvent And Permeation Enhancer For Glaucoma Medication, Ashish Trital, Lei Xu, Burhan Ates, Tzu Chen Wang, Vimalin Mani, Hu Yang

Chemical and Biochemical Engineering Faculty Research & Creative Works

The efficacy of hydrophobic ocular drugs is significantly hindered by their low bioavailability, for which poor water solubility is a major contributing factor. In this work, we synthesized pilocarpine-derived ionic liquid [Pilo-OEG] Cl (PO) and evaluated its cosolvent properties for the codelivery of the hydrophobic antiglaucoma drug brimonidine (BM) for glaucoma therapy. Pilocarpine was quaternized with 2-[2-(2-chloroethoxy) ethoxy] ethanol in a one-pot reaction to yield PO, and its structure was confirmed using ¹H NMR and FT-IR spectroscopy methods and further characterized for its rheological property and thermal stability. The HET-CAM assay and cell viability study showed that PO was …

Persistent Microglial Activation Following Neonatal Cmv Infection Mediates Neurodegeneration, Jessica L. Mccord, Debotri Chatterjee, John Y.S. Han, Drew Scoles, Richard J. Smeyne, Nancy J. Philp, Christopher M. Snyder

Department of Microbiology and Immunology Faculty Papers

Human cytomegalovirus (HCMV) causes the most common congenital viral infection in the United States, with well-known acute and late-onset neurological pathologies. Moreover, HCMV, like multiple herpesviruses, has been associated with neuroinflammation and neurodegeneration. Using a well-established neonatal murine (M)CMV infection model, we found that early-life infection drove adult-onset neuron loss and neuropathology in the retina and brain, without evident viral reactivation. Pathology was associated with the persistence of highly activated and inflammatory damage-associated microglia. Transient depletion of these microglia before the development of pathology resulted in repopulation of the tissue by microglia with a more reparative profile, which was then …

Unraveling Metabolic Determinants Of Isoniazid Susceptibility In Mycobacterium Tuberculosis, Erin Rilu Wang

Arts & Sciences Graduate Student Theses and Dissertations

Mycobacterium tuberculosis (Mtb) causes the disease tuberculosis (TB) and is one of the leading causes of death worldwide by an infectious agent. Furthermore, the emergence and evolution of drug resistance has significantly hindered global health efforts to combat this deadly epidemic. Thus, there is a critical need for development of new antibiotics with unique mechanisms of action and design of novel strategies for optimizing the efficacy of existing therapeutic regimens. It is estimated that 10.7% of new infected and 27.2% of previously treated TB cases are resistant to the frontline antibiotic isoniazid (INH), a central component of TB chemotherapeutic regimens. …

Identification And Full Genome Sequencing Of Previously Unknown Sandfly-Borne Phleboviruses Using A Newly Established Capture-Based Next-Generation Sequencing Approach, Edwin O. Ogola, Inga Slothouwer, Gilbert Rotich, Anne Kopp, Armanda D. Bastos, Caroline Getugi, Julia Melchert, Terence C. Jones, Dorcus C. Omoga, Rosemary Sang, Baldwyn Torto, David P. Tchouassi, Sandra Junglen

All Peer-Reviewed Publications

Sandfly-borne phleboviruses cause febrile illness and neuroinvasive disease in humans. While infections are reported in the Mediterranean region, the discovery of previously unknown phleboviruses in sandflies from Kenya suggests a wider geographic distribution. Detection and characterization of novel phleboviruses are often hindered by low-quality and low-viral-load samples. We developed a capture-based target enrichment next-generation sequencing approach that showed a 99%-100% fold enrichment of viral genomes from primary material and provides a robust tool for generating complete genomes of both known and previously unknown viruses. From a collection of 15,652 sandflies in Kenya, we recovered seven complete coding sequences of Embossos, …

Gastrointestinal Symptoms After Sport-Related Concussion In Irish Athletes, Emma Finnegan, Ed Daly, Katherine Hunzinger, Lisa Ryan

Department of Exercise Science Faculty Papers

Background/Objectives: Sport-related concussion (SRC) elicits multi-systemic symptoms, including nausea, fatigue, and cognitive changes. Gastrointestinal (GI) symptoms are not well captured in current concussion assessments and may be under-recognised in clinical follow-up. GI disturbances may influence intake tolerance and day-to-day fuelling during post-SRC recovery. This study investigated the prevalence and severity of self-reported GI symptoms in Irish athletes after their most recent SRC, examined sex-based patterns, and evaluated the rationale for integrating GI symptom checks into standard concussion tools (e.g., SCAT6) and post-injury monitoring. Methods: An online survey was completed by recreational, competitive, and elite athletes who retrospectively self-reported concussion history, …

Breaking Into Hiv-1'S Epigenetic Vault: Cure Strategies To Eliminate The Viral Reservoir, Joanna Jones, Chelsea Gunderson, Brian Wigdahl, Michael Nonnemacher

Kimmel Cancer Center Faculty Papers

Human immunodeficiency virus type 1 (HIV-1) is a retrovirus that integrates into the host cell's DNA as a provirus. Transcription from the provirus is regulated in large part by cellular proteins and epigenetic factors. These may be repressive or permissive to productive infection. The host factors that regulate this balance are therefore attractive targets for HIV-1 therapeutics. Indeed, proviral chromatin is the focus of two of the current HIV-1 cure strategies. "Shock and Kill" uses latency reversal agents to open the provirus's chromatin, promoting high levels of gene expression that induce the killing of infected cells. "Block and Lock" uses …

A Survey-Based Exploratory Study Of Factors Influencing Women's Intentions To Utilise Pre-Exposure Prophylaxis In The Eastern Cape Province, South Africa: Sociodemographic Characteristics, Hiv Risk Behaviours And Transactional Sex, Rosemary Kalenga, Gary Sharp, Anne M. Teitelman, Monde Makiwane, Larry D. Icard, John B. Jemmott

College of Nursing Faculty Papers & Presentations

BACKGROUND: South Africa has the third-highest adult prevalence rate globally, with women comprising 64% of cases. Despite the accessibility of pre-exposure prophylaxis (PrEP), its adoption among women, particularly young women, remains alarmingly low.

OBJECTIVES: The objective of this initial investigation is to explore factors influencing the intentions of South African women to use PrEP, focusing on sociodemographic factors, HIV sexual risk behaviours and involvement in transactional sex.

DESIGN: The research utilised an exploratory design employing surveys.

METHODS: Surveys were conducted in 2015 with 64 women aged 19-49 residing in the Eastern Cape Province of South Africa. The data were analysed …

The Efficacy And Safety Of Serratus Anterior Plane Block In Patients Undergoing Cardiac Surgery: A Systematic Review And Meta-Analysis, Xu-Bo Cui, Ming-Zhu Cui, Qiu-Ju Yang, Yang Liu, Meng-Qi Yi, Xiao-Yang Zhang, Yun-Tai Yao

Faculty, Staff and Student Publications

Background: Serratus anterior plane block (SAPB) is a widely used fascial block that reduces postoperative pain and perioperative opioid consumption. This meta-analysis assessed the efficacy and safety of SAPB in cardiac surgery patients.

Methods: We systematically searched PubMed, Web of Science, Cochrane Library, Embase, China National Knowledge Infrastructure, and Wanfang databases on May 10, 2024. Pooled relative risks and mean differences (MD) with 95% confidence intervals (CI) were calculated for dichotomous and continuous outcomes, respectively. Heterogeneity was assessed using the I2 statistic, and publication bias was evaluated using Egger test. Subgroup analyses were stratified by study design (randomized controlled trials …

Uncovering Hidden Prognostic Patterns In Colorectal Cancer Histology Using Unsupervised Learning: A Computational Pathology Study, Wen-Tong Zhou, Yong Liu, Gang Yu, Kuan-Song Wang, Chao Xu, Jonathan Greenbaum, Chong Wu, Lin-Dong Jiang, Christopher J Papasian, Hong-Mei Xiao, Hong-Wen Deng

Faculty, Staff and Student Publications

Colorectal cancer (CRC) remains a leading cause of cancer mortality globally, yet current histopathological diagnostics capture only limited features. This study aimed to discover subtle, prognostically significant histomorphological patterns in CRC tissues using unsupervised deep learning. We developed a framework integrating convolutional neural networks with deep clustering, trained on 23,341 image patches from 493 patients. We identified 30 distinct histomorphological clusters from CRC tissue images. Through univariate and multivariate survival analyses, three clusters (Cluster13, Cluster19, and Cluster24) were consistently associated with patient prognosis. These clusters were integrated with clinical factors (T stage, N stage, and differentiation degree) to construct a …

Telemedicine As A Gateway To Early-Phase Oncology Trials: Lessons From 14,000 Patients And Future Directions For Global Access And Equity, Carlos Torrado, Clark R Andersen, Lei Kang, Amanda L Brink, Taiwo Adesoye, Hung Le, Clover J Patterson, Anna Poullard, Jessica A Osburn, Harold N Tan, Mohamed A Gouda, Sheena Charles, Gabriele E Urschel, Tin-Yun Tang, David S Hong, Stephane Champiat, Aung Naing, Apostolia M Tsimberidou, Ecaterina E Dumbrava, Sarina A Piha-Paul, Jordi Rodon, Timothy A Yap, Paula R Pohlmann, Funda Meric-Bernstam, Siqing Fu

Faculty, Staff and Student Publications

Background: Telemedicine expanded rapidly during the COVID-19 pandemic, but its role in early-phase oncology trials remains uncertain. We evaluated its impact on recruitment, enrollment, equity, and access in a large phase I program.

Patients and methods: We retrospectively analyzed patients seen for first consultation in the MD Anderson Phase I Program (2016-2023). Recruitment (consent) and enrollment (treatment initiation) were compared by visit type, race/ethnicity, and geography across pre-pandemic (2016-2019), pandemic (2020-March 11, 2023), and post-public health emergency (PHE; March-December 2023) periods. A chart review of 400 patients validated findings.

Results: Of 14,085 patients, 7,247 were evaluated post-pandemic, with 36% (n …

Pan-Cancer Evolution Signatures Link Clonal Expansion To Dynamic Changes In The Tumor Immune Microenvironment, Xinyu Yang, Wei Liu, Geoff Macintyre, Peter Van Loo, Florian Markowetz, Peter Bailey, Ke Yuan

Faculty, Staff and Student Publications

Cancer is an evolutionary process characterized by profound intratumor heterogeneity (ITH), which can be quantified using in silico estimates of cancer cell fractions (CCFs) of tumor-specific somatic mutations. We demonstrate a data-driven approach based on CCF distributions to identify 4 robust pan-cancer evolutionary signatures from 4,146 tumors across 17 cancer types in The Cancer Genome Atlas (TCGA). These signatures define a continuum of cancer cell fractions reflecting neutral evolution, clonal expansion, and clonal fixation. Correlating evolutionary signatures with mutational and biological programs reveals that tumors enriched for clonal expansion and fixation are associated with immune evasion and distinct changes in …