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Toward Clinical-Grade Evaluation Of Large Language Models, Amy C Moreno, Danielle S Bitterman Mar 2024

Toward Clinical-Grade Evaluation Of Large Language Models, Amy C Moreno, Danielle S Bitterman

Faculty, Staff and Student Publications

No abstract provided.


Clonal Dominance Defines Metastatic Dissemination In Pancreatic Cancer, I-Lin Ho, Chieh-Yuan Li, Fuchenchu Wang, Li Zhao, Jingjing Liu, Er-Yen Yen, Charles A Dyke, Rutvi Shah, Zhaoliang Liu, Ali Osman Çetin, Yanshuo Chu, Francesca Citron, Sergio Attanasio, Denise Corti, Faezeh Darbaniyan, Edoardo Del Poggetto, Sara Loponte, Jintan Liu, Melinda Soeung, Ziheng Chen, Shan Jiang, Hong Jiang, Akira Inoue, Sisi Gao, Angela Deem, Ningping Feng, Haoqiang Ying, Michael Kim, Virginia Giuliani, Giannicola Genovese, Jianhua Zhang, Andrew Futreal, Anirban Maitra, Timothy Heffernan, Linghua Wang, Kim-Anh Do, Gaetano Gargiulo, Giulio Draetta, Alessandro Carugo, Ruitao Lin, Andrea Viale Mar 2024

Clonal Dominance Defines Metastatic Dissemination In Pancreatic Cancer, I-Lin Ho, Chieh-Yuan Li, Fuchenchu Wang, Li Zhao, Jingjing Liu, Er-Yen Yen, Charles A Dyke, Rutvi Shah, Zhaoliang Liu, Ali Osman Çetin, Yanshuo Chu, Francesca Citron, Sergio Attanasio, Denise Corti, Faezeh Darbaniyan, Edoardo Del Poggetto, Sara Loponte, Jintan Liu, Melinda Soeung, Ziheng Chen, Shan Jiang, Hong Jiang, Akira Inoue, Sisi Gao, Angela Deem, Ningping Feng, Haoqiang Ying, Michael Kim, Virginia Giuliani, Giannicola Genovese, Jianhua Zhang, Andrew Futreal, Anirban Maitra, Timothy Heffernan, Linghua Wang, Kim-Anh Do, Gaetano Gargiulo, Giulio Draetta, Alessandro Carugo, Ruitao Lin, Andrea Viale

Faculty, Staff and Student Publications

Tumors represent ecosystems where subclones compete during tumor growth. While extensively investigated, a comprehensive picture of the interplay of clonal lineages during dissemination is still lacking. Using patient-derived pancreatic cancer cells, we created orthotopically implanted clonal replica tumors to trace clonal dynamics of unperturbed tumor expansion and dissemination. This model revealed the multifaceted nature of tumor growth, with rapid changes in clonal fitness leading to continuous reshuffling of tumor architecture and alternating clonal dominance as a distinct feature of cancer growth. Regarding dissemination, a large fraction of tumor lineages could be found at secondary sites each having distinctive organ growth …


Safety And Efficacy Of Ibrutinib In Combination With Rituximab And Lenalidomide In Previously Untreated Follicular And Marginal Zone Lymphoma: An Open Label, Phase 2 Study, Max J Gordon, Lei Feng, Paolo Strati, Hun Ju Lee, Fredrick B Hagemeister, Jason R Westin, Felipe Samaniego, Mario L Marques-Piubelli, Francisco Vega Vazquez, Edwin R Parra Cuentas, Luisa M Solis-Soto, Wencai Ma, Jing Wang, Linda Claret, Barbara Averill, Karina Ibanez, Luis E Fayad, Christopher R Flowers, Michael R Green, R Eric Davis, Sattva S Neelapu, Nathan H Fowler, Loretta J Nastoupil Mar 2024

Safety And Efficacy Of Ibrutinib In Combination With Rituximab And Lenalidomide In Previously Untreated Follicular And Marginal Zone Lymphoma: An Open Label, Phase 2 Study, Max J Gordon, Lei Feng, Paolo Strati, Hun Ju Lee, Fredrick B Hagemeister, Jason R Westin, Felipe Samaniego, Mario L Marques-Piubelli, Francisco Vega Vazquez, Edwin R Parra Cuentas, Luisa M Solis-Soto, Wencai Ma, Jing Wang, Linda Claret, Barbara Averill, Karina Ibanez, Luis E Fayad, Christopher R Flowers, Michael R Green, R Eric Davis, Sattva S Neelapu, Nathan H Fowler, Loretta J Nastoupil

Faculty, Staff and Student Publications

Background: Follicular lymphoma (FL) and marginal zone lymphoma (MZL) are indolent non-Hodgkin lymphomas (iNHL). Median survival for iNHL is approximately 20 years. Because standard treatments are not curative, patients often receive multiple lines of therapy with associated toxicity-rationally designed, combination therapies with curative potential are needed. The immunomodulatory drug lenalidomide was evaluated in combination with rituximab for the frontline treatment of FL in the phase 3 RELEVANCE study. Ibrutinib, an oral Bruton tyrosine kinase inhibitor, is active in NHL and was evaluated in combination with lenalidomide, rituximab, and ibrutinib (IRR) in a phase 1 study.

Methods: The authors conducted an …


Linking Shared Decision Making To Outcomes In Simulated Prenatal Genetic Counseling Sessions, Raquel C. Chavarria Mar 2024

Linking Shared Decision Making To Outcomes In Simulated Prenatal Genetic Counseling Sessions, Raquel C. Chavarria

USF Tampa Graduate Theses and Dissertations

Shared decision-making (SDM), defined as the collaborative process between patient and healthcare provider to arrive at a values-based clinical decision, may be valuable in genetic counseling (GC) given that patients are often faced with various options. Four published studies have measured or made conclusions about the use of SDM skills in GC settings, but only one study evaluated relationships between third-party observations of SDM in recorded GC sessions and patient-reported outcomes (i.e., anxiety and decisional conflict) and found no correlations between these measures. The purpose of this study was to evaluate relationships between SDM and measures of patient-reported experience (i.e., …


The Effect Of Severe Intraventricular Hemorrhage On The Biorhythms Of Feeding In Premature Infants, Hyun Ho Choi, Soo-Yoon Sung, Bo-In Lee, Hyun Cho, Yunho Jung, Jae Myung Park, Young-Seok Cho, Kang-Moon Lee, Sang Woo Kim, Hwang Choi, Hiun-Suk Chae, Myung-Gyu Choi Mar 2024

The Effect Of Severe Intraventricular Hemorrhage On The Biorhythms Of Feeding In Premature Infants, Hyun Ho Choi, Soo-Yoon Sung, Bo-In Lee, Hyun Cho, Yunho Jung, Jae Myung Park, Young-Seok Cho, Kang-Moon Lee, Sang Woo Kim, Hwang Choi, Hiun-Suk Chae, Myung-Gyu Choi

Faculty, Staff and Student Publications

BACKGROUND/AIMS: This study investigated whether the personality traits of endoscopists are associated with the effect of interventions for the improvement of colonoscopy quality.

METHODS: This prospective, multicenter, single-blind study was performed with 13 endoscopists in three health screening centers over a 12-month period. Quality indicators (QIs), including adenoma detection rate (ADR), polyp detection rate (PDR), and withdrawal time, were measured every 3 months. Consecutive interventions for the improvement of colonoscopy quality were conducted every 3 months, which included the personal notification of QIs, the in-group notification of QIs, and finally a targeted "quality education" session. The personality traits of each …


Impact Of The 2022 National Formula Shortage On Clinical Decision-Making Of Healthcare Providers In Switching Amino Acid Formulas For Infants With Cow’S Milk Protein Allergy: A Survey-Based Study, Jessica V. Baran, Jerry M. Brown, Andrew Farrar, Lea V. Oliveros, Jesse Beacker, Luke Lamos, Jared Florio, Abigail Fabbrini, Michael Wilsey Mar 2024

Impact Of The 2022 National Formula Shortage On Clinical Decision-Making Of Healthcare Providers In Switching Amino Acid Formulas For Infants With Cow’S Milk Protein Allergy: A Survey-Based Study, Jessica V. Baran, Jerry M. Brown, Andrew Farrar, Lea V. Oliveros, Jesse Beacker, Luke Lamos, Jared Florio, Abigail Fabbrini, Michael Wilsey

Student Publications

Background: In 2022, the United States experienced a national shortage of infant formula due to a global supply chain crisis and a large-scale domestic formula recall. The existing literature on healthcare providers' (HCPs) clinical decision-making during formula shortages is limited. This study aims to analyze the factors influencing pediatric HCP clinical decision-making when switching between amino acid formulas (AAF) for managing cow's milk protein allergy (CMPA) in infants under 24 months of age during an unprecedented national formula shortage.

Methods: The study included pediatric HCPs with experience managing CMPA in infants and toddlers under 24 months during the formula shortage …


On The Use Of Machine Learning And Data-Transformation Methods To Predict Hydration Kinetics And Strength Of Alkali-Activated Mine Tailings-Based Binders, Sahil Surehali, Taihao Han, Jie Huang, Aditya Kumar, Narayanan Neithalath Mar 2024

On The Use Of Machine Learning And Data-Transformation Methods To Predict Hydration Kinetics And Strength Of Alkali-Activated Mine Tailings-Based Binders, Sahil Surehali, Taihao Han, Jie Huang, Aditya Kumar, Narayanan Neithalath

Electrical and Computer Engineering Faculty Research & Creative Works

The escalating production of mine tailings (MT), a byproduct of the mining industry, constitutes significant environmental and health hazards, thereby requiring a cost-effective and sustainable solution for its disposal or reuse. This study proposes the use of MT as the primary ingredient (≥70%mass) in binders for construction applications, thereby ensuring their efficient upcycling as well as drastic reduction of environmental impacts associated with the use of ordinary Portland cement (OPC). The early-age hydration kinetics and compressive strength of MT-based binders are evaluated with an emphasis on elucidating the influence of alkali activation parameters and the amount of slag or cement …


The Hero’S Search For Identity In Momaday’S House Made Of Dawn, Akam Rashid Mohammed, Azad Hamad Mar 2024

The Hero’S Search For Identity In Momaday’S House Made Of Dawn, Akam Rashid Mohammed, Azad Hamad

Alustath Journal for Human and Social Sciences

Navarre Scott Momaday's novel, House Made of Dawn (1968), delves into the profound theme of identity loss and reclamation, encapsulated within Abel’s journey who is the protagonist of the novel. This study explores the intricate layers of Abel's quest to rediscover his Native American heritage in the face of cultural assimilation and invasion. Through a detailed analysis, it investigates the pivotal role of place for identity reclamation and the significance of cultural diversity. Momaday's narrative not only portrays Abel as a culturally torn outsider but also offers a captivating lens to examine themes of cultural preservation, identity, and the enduring …


Central Treaty Organization (Cento) And Description Of The Management Systems Of Ankara Agreement: National Representative And International Staff On November 9, 1960, Alaa Hamza Dwelee Mar 2024

Central Treaty Organization (Cento) And Description Of The Management Systems Of Ankara Agreement: National Representative And International Staff On November 9, 1960, Alaa Hamza Dwelee

Alustath Journal for Human and Social Sciences

The Central Treaty Organization (CENTO), is considered one of the important international alliances that was formed in the 1950s in the Middle East with the supported and endorsed of the U.S. and British governments, in order to maintain their interests in the region and to prevent its penetration by the Soviet Union. Whereas studies dealt with the political dimension of the roles of that alliance, while the administrative and structural building system did not take its share of study and research, including “Agreement on the Status of the Central Treaty Organization [CENTO], National Representative and International Staff.” Or the "Ankara …


Human Rights In Jamaica Kincaid's A Small Place, Hala Salman Hassan Mar 2024

Human Rights In Jamaica Kincaid's A Small Place, Hala Salman Hassan

Alustath Journal for Human and Social Sciences

The present study looks at how A Small Place (1988) a novel-autobiography by Jamaica Kincaid and the Universal Declaration of Human Rights (UDHR) interact. It analyzes how the legacy of the colonial and tourist sector has caused human rights violations against local communities in Antigua. The article argues that if Antigua and other comparable communities are to develop, the triangle of colonialism, tourism, and compromised government must adhere to the Universal Declaration of Human Rights (UDHR) and implement tangible measures to sustain human rights and advance workable developments. In the novel, Kincaid' furiously pinpoints the exploitations against the people of …


The Effectiveness Of A Training Program To Provide The Children Of Diyala Governorate With Traffic Culture Vocabulary, “A Community Study”, Asmaa Abbas Aziz Aldulaimy, Abbas Hussein Mar 2024

The Effectiveness Of A Training Program To Provide The Children Of Diyala Governorate With Traffic Culture Vocabulary, “A Community Study”, Asmaa Abbas Aziz Aldulaimy, Abbas Hussein

Alustath Journal for Human and Social Sciences

Traffic accidents that began with the invention of the first vehicle are still increasing, and they cause people to lose their lives or become disabled, in addition to material losses. Also, the increase in bicycles of all kinds and people of young ages driving them has led to an increase in accidents on secondary internal roads, not just the main streets. Because the researcher conducted a study to identify the level of traffic culture among children in Diyala Governorate, the results showed that they do not have traffic awareness and do not possess traffic culture vocabulary, and because providing children …


Re: Comments For The Butte Priority Soils Operable Unit (Bpsou) Butte Reclamation Evaluation System (Bres) Draft 2023 Bres Field Evaluation Summary Report And Technical Recommendations Proposal (Dated November 15, 2023) And 2023 Corrective Action Plans For Reclaimed Sites (Dated January 31, 2024), Molly Roby Mar 2024

Re: Comments For The Butte Priority Soils Operable Unit (Bpsou) Butte Reclamation Evaluation System (Bres) Draft 2023 Bres Field Evaluation Summary Report And Technical Recommendations Proposal (Dated November 15, 2023) And 2023 Corrective Action Plans For Reclaimed Sites (Dated January 31, 2024), Molly Roby

Silver Bow Creek/Butte Area Superfund Site

No abstract provided.


Development And Preliminary Validation Of The Sexual Minority Identity Emotion Scale, Jacob Goffnet, Samantha Robinson, Anna Hamaker, Mohammod Mahmudar Rahman, Sheree M. Schrager, Jeremy T. Goldbach Mar 2024

Development And Preliminary Validation Of The Sexual Minority Identity Emotion Scale, Jacob Goffnet, Samantha Robinson, Anna Hamaker, Mohammod Mahmudar Rahman, Sheree M. Schrager, Jeremy T. Goldbach

Biological Sciences Faculty Publications and Presentations

Emotions influence health behaviors and outcomes, yet little research has examined the emotion–health relationship among sexual minorities. The few studies in this area have used general measures of feelings without regard for identity, despite the literature positing emotions as culturally and contextually specific. This critical limitation obscures inferences made in studies that have found emotions to predict mental health outcomes for sexual minorities. This study begins to address this gap by developing and examining the preliminary validation of the Sexual Minority Identity Emotion Scale, a measure of shame and pride specific to the identity experiences of sexual minority adolescents. The …


Contralateral Second Dose Improves Antibody Responses To A 2-Dose Mrna Vaccination Regimen, Sedigheh Fazli, Archana Thomas, Abram E. Estrada, Hiro A. P. Ross, David Xthona Lee, Steven Kazmierczak, Mark K. Slifka, David Montefiori, William B. Messer, Marcel E. Curlin Mar 2024

Contralateral Second Dose Improves Antibody Responses To A 2-Dose Mrna Vaccination Regimen, Sedigheh Fazli, Archana Thomas, Abram E. Estrada, Hiro A. P. Ross, David Xthona Lee, Steven Kazmierczak, Mark K. Slifka, David Montefiori, William B. Messer, Marcel E. Curlin

OHSU-PSU School of Public Health Faculty Publications and Presentations

BACKGROUND. Vaccination is typically administered without regard to site of prior vaccination, but this factor may substantially affect downstream immune responses. METHODS. We assessed serological responses to initial COVID-19 vaccination in baseline seronegative adults who received second-dose boosters in the ipsilateral or contralateral arm relative to initial vaccination. We measured serum SARSCoV-2 spike–specific Ig, receptor-binding domain–specific (RBD-specific) IgG, SARS-CoV-2 nucleocapsid–specific IgG, and neutralizing antibody titers against SARS-CoV-2.D614G (early strain) and SARS-CoV-2.B.1.1.529 (Omicron) at approximately 0.6, 8, and 14 months after boosting. RESULTS. In 947 individuals, contralateral boosting was associated with higher spike-specific serum Ig, and this effect increased over time, …


The Prevalence And Perceptions Of Self-Relevant Research (“Me-Search”) In Psychological Science, Andrew R. Devendorf Mar 2024

The Prevalence And Perceptions Of Self-Relevant Research (“Me-Search”) In Psychological Science, Andrew R. Devendorf

USF Tampa Graduate Theses and Dissertations

Self-relevant research (i.e., me-search; SRR) is research that is informed by lived experience or having close connections to a topic. The disclosure of SRR may impact how a researcher is viewed in professional contexts, like an application to graduate school, and thus can impact who is recruited and retained in psychology. Although SRR appears to be common in psychology, little systematic research exists on its prevalence by subfield of psychology or how SRR is perceived. This study examined SRR across psychology disciplines. An online survey was administered to faculty and graduate students (N = 1313) affiliated with accredited doctoral programs …


Evaluation Of Pediatric Genetics Clinics’ Workflows, Efficiencies, & Genetic Counselor Job Satisfaction, Ashlyn M. Keziah Mar 2024

Evaluation Of Pediatric Genetics Clinics’ Workflows, Efficiencies, & Genetic Counselor Job Satisfaction, Ashlyn M. Keziah

USF Tampa Graduate Theses and Dissertations

The organizational structures and workflows of pediatric/general genetics clinics exhibit significant variability across institutions. However, there is a notable lack of studies exploring which structural components within pediatric clinics contribute to increased patient volumes, while concurrently upholding genetic counselor work satisfaction and mitigating burnout risks. To address this gap, this multiple case study delves into the operational dynamics of several pediatric genetics clinics located throughout the state of Florida. We employed surveys and interviews to identify shared patterns and distinctions in clinic workflows and structures, subsequently evaluating efficiency and genetic counselor job satisfaction/burnout at each site. This study includes survey …


Retirement And Cognitive Aging: Modifying Factors, Britney M. Veal Mar 2024

Retirement And Cognitive Aging: Modifying Factors, Britney M. Veal

USF Tampa Graduate Theses and Dissertations

Due to the increase in the aging population and individuals spending more years in retirement, researchers and public health policymakers have expressed a growing interest in understanding retirement and the overall effects on health and aging. One area that is gaining attention is retirement and its effect on cognition. However, the association between retirement and cognition remains unclear, and pre-retirement modifying factors such as reasons for retirement and longest-held occupation have not been thoroughly assessed. Therefore, using data from the Health and Retirement Study (HRS; n = 3,838) and mixed effects models, this dissertation aimed to examine the association between …


Running To Or Running From: Exploring The Phenomenology Of Off-Cycle Turnover In Entry Level Housing Professionals, Kate Gannon-Cullinan Mar 2024

Running To Or Running From: Exploring The Phenomenology Of Off-Cycle Turnover In Entry Level Housing Professionals, Kate Gannon-Cullinan

LSU Doctoral Dissertations

Housing and residence life as a functional area serves as a major entry point for careers in higher education and student affairs. With the majority of annual job postings within entry-level, live-in housing roles, the future of the field may well be predicted in these high-impact, high-turnover positions on college campuses. As these functional areas continue to struggle to find themselves fully-staffed throughout their academic year cycle, the impact on both the student experience and organizational health is impacted. This study utilized an interpretive phenomenological approach to explore the experiences and feelings of those entry-level, live-in housing professionals who chose …


Dolutegravir-Induced Neural Tube Defects In Mice Are Folate Responsive, Gabriel L Tukeman, Hui Wei, Ying L Lin, Bogdan J Wlodarczyk, Richard H Finnell, Robert M Cabrera Mar 2024

Dolutegravir-Induced Neural Tube Defects In Mice Are Folate Responsive, Gabriel L Tukeman, Hui Wei, Ying L Lin, Bogdan J Wlodarczyk, Richard H Finnell, Robert M Cabrera

Faculty, Staff and Students Publications

Objectives: In 2018, the Botswana Tsepamo Study reported a nine-fold increased risk of neural tube defects in infants whose mothers were treated with dolutegravir (DTG) from the time of conception. As maternal folate supplementation and status is a well known modifier of neural tube defect (NTD) risk, we sought to evaluate birth outcomes in mice fed normal and low folic acid diets treated with DTG during pregnancy.

Design: DTG was evaluated for developmental toxicity using pregnant mice fed normal or low folic acid diet.

Methods: CD-1 mice were provided diet with normal (3 mg/kg) or low (0.3 mg/kg) folic acid. …


A Comparative Analysis Of Tonebp Conditional Knockout Mouse Models Reveals Inter-Dependency Between Compartments Of The Intervertebral Disc, Greig Couasnay, Haley Garcia, Florent Elefteriou Mar 2024

A Comparative Analysis Of Tonebp Conditional Knockout Mouse Models Reveals Inter-Dependency Between Compartments Of The Intervertebral Disc, Greig Couasnay, Haley Garcia, Florent Elefteriou

Faculty, Staff and Students Publications

Interactions between notochord and sclerotome are required for normal embryonic spine patterning, but whether the postnatal derivatives of these tissues also require interactions for postnatal intervertebral disc (IVD) growth and maintenance is less established. We report here the comparative analysis of four conditional knockout mice deficient for TonEBP, a transcription factor known to allow cells to adapt to changes in extracellular osmotic pressure, in specific compartments of the IVD. We show that TonEBP deletion in nucleus pulposus (NP) cells does not affect their survival or aggrecan expression, but promoted cell proliferation in the NP and in adjacent vertebral growth plates …


Hematologic Dnmt3a Reduction And High-Fat Diet Synergize To Promote Weight Gain And Tissue Inflammation, Jaime M Reyes, Ayala Tovy, Linda Zhang, Angelina S Bortoletto, Carina Rosas, Chun-Wei Chen, Sarah M Waldvogel, Anna G Guzman, Rogelio Aguilar, Sinjini Gupta, Ling Liu, Matthew T Buckley, Kalyani R Patel, Andrea N Marcogliese, Yumei Li, Choladda V Curry, Thomas A Rando, Anne Brunet, Ronald J Parchem, Rachel E Rau, Margaret A Goodell Mar 2024

Hematologic Dnmt3a Reduction And High-Fat Diet Synergize To Promote Weight Gain And Tissue Inflammation, Jaime M Reyes, Ayala Tovy, Linda Zhang, Angelina S Bortoletto, Carina Rosas, Chun-Wei Chen, Sarah M Waldvogel, Anna G Guzman, Rogelio Aguilar, Sinjini Gupta, Ling Liu, Matthew T Buckley, Kalyani R Patel, Andrea N Marcogliese, Yumei Li, Choladda V Curry, Thomas A Rando, Anne Brunet, Ronald J Parchem, Rachel E Rau, Margaret A Goodell

Faculty, Staff and Students Publications

During aging, blood cell production becomes dominated by a limited number of variant hematopoietic stem cell (HSC) clones. Differentiated progeny of variant HSCs are thought to mediate the detrimental effects of such clonal hematopoiesis on organismal health, but the mechanisms are poorly understood. While somatic mutations in DNA methyltransferase 3A (DNMT3A) frequently drive clonal dominance, the aging milieu also likely contributes. Here, we examined in mice the interaction between high-fat diet (HFD) and reduced DNMT3A in hematopoietic cells; strikingly, this combination led to weight gain. HFD amplified pro-inflammatory pathways and upregulated inflammation-associated genes in mutant cells along a pro-myeloid trajectory. …


The Evidence Of Electronic Cigarettes For Harm Reduction Is Not There, Manuel C Pacheco Gallego, Harold J Farber Mar 2024

The Evidence Of Electronic Cigarettes For Harm Reduction Is Not There, Manuel C Pacheco Gallego, Harold J Farber

Faculty, Staff and Students Publications

No abstract provided.


Tissue-Resident Memory T Cell Signatures From Single-Cell Analysis Associated With Better Melanoma Prognosis, Chongming Jiang, Cheng-Chi Chao, Jianrong Li, Xin Ge, Aidan Shen, Vadim Jucaud, Chao Cheng, Xiling Shen Mar 2024

Tissue-Resident Memory T Cell Signatures From Single-Cell Analysis Associated With Better Melanoma Prognosis, Chongming Jiang, Cheng-Chi Chao, Jianrong Li, Xin Ge, Aidan Shen, Vadim Jucaud, Chao Cheng, Xiling Shen

Faculty, Staff and Students Publications

Tissue-resident memory T cells (TRM) are a specialized T cell population residing in peripheral tissues. The presence and potential impact of TRM in the tumor immune microenvironment (TIME) remain to be elucidated. Here, we systematically investigated the relationship between TRM and melanoma TIME based on multiple clinical single-cell RNA-seq datasets and developed signatures indicative of TRM infiltration. TRM infiltration is associated with longer overall survival and abundance of T cells, NK cells, M1 macrophages, and memory B cells in the TIME. A 22-gene TRM–derived risk score was further developed to effectively classify patients into low- and high-risk categories, distinguishing overall …


Autoantibodies To Ace2 And Immune Molecules Are Associated With Covid-19 Disease Severity., Eric S. Geanes, Rebecca Mclennan, Cas Lemaster, Todd Bradley Mar 2024

Autoantibodies To Ace2 And Immune Molecules Are Associated With Covid-19 Disease Severity., Eric S. Geanes, Rebecca Mclennan, Cas Lemaster, Todd Bradley

Manuscripts, Articles, Book Chapters and Other Papers

BACKGROUND: Increased inflammation caused by SARS-CoV-2 infection can lead to severe coronavirus disease 2019 (COVID-19) and long-term disease manifestations. The mechanisms of this variable long-term immune activation are poorly defined. One feature of this increased inflammation is elevated levels of proinflammatory cytokines and chemokines. Autoantibodies targeting immune factors such as cytokines, as well as the viral host cell receptor, angiotensin-converting enzyme 2 (ACE2), have been observed after SARS-CoV-2 infection. Autoantibodies to immune factors and ACE2 could interfere with normal immune regulation and lead to increased inflammation, severe COVID-19, and long-term complications.

METHODS: Here, we deeply profiled the features of ACE2, …


Identification Of Genetically Predicted Dna Methylation Markers Associated With Non-Small Cell Lung Cancer Risk Among 34,964 Cases And 448,579 Controls, Xiaoyu Zhao, Meiqi Yang, Jingyi Fan, Mei Wang, Yifan Wang, Na Qin, Meng Zhu, Yue Jiang, Olga Y Gorlova, Ivan P Gorlov, Demetrius Albanes, Stephen Lam, Adonina Tardón, Chu Chen, Gary E Goodman, Stig E Bojesen, Maria Teresa Landi, Mattias Johansson, Angela Risch, H-Erich Wichmann, Heike Bickeböller, David C Christiani, Gad Rennert, Susanne M Arnold, Paul Brennan, John K Field, Sanjay Shete, Loïc Le Marchand, Geoffrey Liu, Rayjean J Hung, Angeline S Andrew, Lambertus A Kiemeney, Shanbeh Zienolddiny, Kjell Grankvist, Mikael Johansson, Neil E Caporaso, Penella J Woll, Philip Lazarus, Matthew B Schabath, Melinda C Aldrich, Alpa V Patel, Michael P A Davies, Hongxia Ma, Guangfu Jin, Zhibin Hu, Christopher I Amos, Hongbing Shen, Juncheng Dai Mar 2024

Identification Of Genetically Predicted Dna Methylation Markers Associated With Non-Small Cell Lung Cancer Risk Among 34,964 Cases And 448,579 Controls, Xiaoyu Zhao, Meiqi Yang, Jingyi Fan, Mei Wang, Yifan Wang, Na Qin, Meng Zhu, Yue Jiang, Olga Y Gorlova, Ivan P Gorlov, Demetrius Albanes, Stephen Lam, Adonina Tardón, Chu Chen, Gary E Goodman, Stig E Bojesen, Maria Teresa Landi, Mattias Johansson, Angela Risch, H-Erich Wichmann, Heike Bickeböller, David C Christiani, Gad Rennert, Susanne M Arnold, Paul Brennan, John K Field, Sanjay Shete, Loïc Le Marchand, Geoffrey Liu, Rayjean J Hung, Angeline S Andrew, Lambertus A Kiemeney, Shanbeh Zienolddiny, Kjell Grankvist, Mikael Johansson, Neil E Caporaso, Penella J Woll, Philip Lazarus, Matthew B Schabath, Melinda C Aldrich, Alpa V Patel, Michael P A Davies, Hongxia Ma, Guangfu Jin, Zhibin Hu, Christopher I Amos, Hongbing Shen, Juncheng Dai

Faculty, Staff and Student Publications

BACKGROUND: Although the associations between genetic variations and lung cancer risk have been explored, the epigenetic consequences of DNA methylation in lung cancer development are largely unknown. Here, the genetically predicted DNA methylation markers associated with non-small cell lung cancer (NSCLC) risk by a two-stage case-control design were investigated.

METHODS: The genetic prediction models for methylation levels based on genetic and methylation data of 1595 subjects from the Framingham Heart Study were established. The prediction models were applied to a fixed-effect meta-analysis of screening data sets with 27,120 NSCLC cases and 27,355 controls to identify the methylation markers, which were …


Characterization Of Flavonoids With Potent And Subtype-Selective Actions On Estrogen Receptors Alpha And Beta, Michael J Bolt, Jessica Oceguera, Pankaj K Singh, Kazem Safari, Derek H Abbott, Kaley A Neugebauer, Maureen G Mancini, Daniel A Gorelick, Fabio Stossi, Michael A Mancini Mar 2024

Characterization Of Flavonoids With Potent And Subtype-Selective Actions On Estrogen Receptors Alpha And Beta, Michael J Bolt, Jessica Oceguera, Pankaj K Singh, Kazem Safari, Derek H Abbott, Kaley A Neugebauer, Maureen G Mancini, Daniel A Gorelick, Fabio Stossi, Michael A Mancini

Faculty, Staff and Students Publications

The initial step in estrogen-regulated transcription is the binding of a ligand to its cognate receptors, named estrogen receptors (ERα and ERβ). Phytochemicals present in foods and environment can compete with endogenous hormones to alter physiological responses. We screened 224 flavonoids in our engineered biosensor ERα and ERβ PRL-array cell lines to characterize their activity on several steps of the estrogen signaling pathway. We identified 83 and 96 flavonoids that can activate ERα or ERβ, respectively. While most act on both receptors, many appear to be subtype-selective, including potent flavonoids that activate ER at sub-micromolar concentrations. We employed an orthogonal …


Multiomics Profiling Of Urothelial Carcinoma In Situ Reveals Cis-Specific Gene Signature And Immune Characteristics, Meenakshi Anurag, Trine Strandgaard, Sung Han Kim, Yongchao Dou, Eva Comperat, Hikmat Al-Ahmadie, Brant A Inman, Ann Taber, Iver Nordentoft, Jørgen Bjerggaard Jensen, Lars Dyrskjøt, Seth P Lerner Mar 2024

Multiomics Profiling Of Urothelial Carcinoma In Situ Reveals Cis-Specific Gene Signature And Immune Characteristics, Meenakshi Anurag, Trine Strandgaard, Sung Han Kim, Yongchao Dou, Eva Comperat, Hikmat Al-Ahmadie, Brant A Inman, Ann Taber, Iver Nordentoft, Jørgen Bjerggaard Jensen, Lars Dyrskjøt, Seth P Lerner

Faculty, Staff and Students Publications

Urothelial carcinoma in situ (CIS) is an aggressive phenotype of non-muscle-invasive bladder cancer. Molecular features unique to CIS compared to high-grade papillary tumors are underexplored. RNA sequencing of CIS, papillary tumors, and normal urothelium showed lower immune marker expression in CIS compared to papillary tumors. We identified a 46-gene expression signature in CIS samples including selectively upregulated known druggable targets MTOR, TYK2, AXIN1, CPT1B, GAK, and PIEZO1 and selectively downregulated BRD2 and NDUFB2. High expression of selected genes was significantly associated with CIS in an independent dataset. Mutation analysis of matched CIS and papillary …


Single Cell Atlas Of Human Gastric Muscle Immune Cells And Macrophage-Driven Changes In Idiopathic Gastroparesis, Lakshmikanth L Chikkamenahalli, Erik Jessen, Cheryl E Bernard, W K Eddie Ip, Margaret Breen-Lyles, Gianluca Cipriani, Suraj R Pullapantula, Ying Li, Shefaa Alasfoor, Laura Wilson, Kenneth L Koch, Braden Kuo, Robert J Shulman, Bruno P Chumpitazi, Travis J Mckenzie, Todd A Kellogg, James Tonascia, Frank A Hamilton, Irene Sarosiek, Richard Mccallum, Henry P Parkman, Pankaj J Pasricha, Thomas L Abell, Gianrico Farrugia, Surendra Dasari, Madhusudan Grover, Niddk Gastroparesis Clinical Research Consortium (Gpcrc) Mar 2024

Single Cell Atlas Of Human Gastric Muscle Immune Cells And Macrophage-Driven Changes In Idiopathic Gastroparesis, Lakshmikanth L Chikkamenahalli, Erik Jessen, Cheryl E Bernard, W K Eddie Ip, Margaret Breen-Lyles, Gianluca Cipriani, Suraj R Pullapantula, Ying Li, Shefaa Alasfoor, Laura Wilson, Kenneth L Koch, Braden Kuo, Robert J Shulman, Bruno P Chumpitazi, Travis J Mckenzie, Todd A Kellogg, James Tonascia, Frank A Hamilton, Irene Sarosiek, Richard Mccallum, Henry P Parkman, Pankaj J Pasricha, Thomas L Abell, Gianrico Farrugia, Surendra Dasari, Madhusudan Grover, Niddk Gastroparesis Clinical Research Consortium (Gpcrc)

Faculty, Staff and Students Publications

Gastrointestinal immune cells, particularly muscularis macrophages (MM) interact with the enteric nervous system and influence gastrointestinal motility. Here we determine the human gastric muscle immunome and its changes in patients with idiopathic gastroparesis (IG). Single cell sequencing was performed on 26,000 CD45+ cells obtained from the gastric tissue of 20 subjects. We demonstrate 11 immune cell clusters with T cells being most abundant followed by myeloid cells. The proportions of cells belonging to the 11 clusters were similar between IG and controls. However, 9/11 clusters showed 578-11,429 differentially expressed genes. In IG, MM had decreased expression of tissue-protective and microglial …


Deep Dive Into The Chronic Toxicity Of Tyre Particle Mixtures And Their Leachates, Paul Boisseaux, Cassandra Rauert, Pradeep Dewapriya, Marie Laure Delignette-Muller, Robyn Barrett, Lee Durndell, Florian Pohl, Richard Thompson, Kevin V. Thomas, Tamara Galloway Mar 2024

Deep Dive Into The Chronic Toxicity Of Tyre Particle Mixtures And Their Leachates, Paul Boisseaux, Cassandra Rauert, Pradeep Dewapriya, Marie Laure Delignette-Muller, Robyn Barrett, Lee Durndell, Florian Pohl, Richard Thompson, Kevin V. Thomas, Tamara Galloway

School of Geography, Earth and Environmental Sciences

Particles from the tread of vehicle tyres are a global pollutant, which are emitted into the environment at an approximate rate of 1.4 kg.year−1 for an average passenger-car. In this study, popular tyre brands were used to generate a tyre tread microparticle mixture. The chronic toxicity of both particles and chemical leachates were compared on a planktonic test species (Daphnia magna). Over 21 days of exposure, pristine tyre tread microparticles were more toxic (LC50 60 mg.L−1) than chemical lechates alone (LC50 542 mg.L−1). Microparticles and leachates showed distinct effects on reproduction and morphological development at …


State Of Health And Remaining Useful Life Prediction Of Lithium-Ion Batteries With Conditional Graph Convolutional Network, Yupeng Wei, Dazhong Wu Mar 2024

State Of Health And Remaining Useful Life Prediction Of Lithium-Ion Batteries With Conditional Graph Convolutional Network, Yupeng Wei, Dazhong Wu

Faculty Research, Scholarly, and Creative Activity

Graph convolutional networks (GCNs) have been increasingly used to predict the state of health (SOH) and remaining useful life (RUL) of batteries. However, conventional GCNs have limitations. Firstly, the correlation between features and the SOH or RUL is not considered. Secondly, temporal relationships among features are not considered when projecting aggregated temporal features into another dimensional space. To address these issues, two types of undirected graphs are introduced to simultaneously consider the correlation among features and the correlation between features and the SOH or RUL. A conditional GCN is built to analyze these graphs. A dual spectral graph convolutional operation …