Digital Commons Network^™

The Chromatin Landscape Of Healthy And Injured Cell Types In The Human Kidney, Debora L Gisch, Jeannine Basta, Reetika Ghag, Charles Lu, Lisa Stout, Bo Zhang, Amanda Knoten, Shamim Mollah, Sanjay Jain, Michael Rauchman, Et Al.

2020-Current year OA Pubs

There is a need to define regions of gene activation or repression that control human kidney cells in states of health, injury, and repair to understand the molecular pathogenesis of kidney disease and design therapeutic strategies. Comprehensive integration of gene expression with epigenetic features that define regulatory elements remains a significant challenge. We measure dual single nucleus RNA expression and chromatin accessibility, DNA methylation, and H3K27ac, H3K4me1, H3K4me3, and H3K27me3 histone modifications to decipher the chromatin landscape and gene regulation of the kidney in reference and adaptive injury states. We establish a spatially-anchored epigenomic atlas to define the kidney's active, …

Genome-Wide Study Investigating Effector Genes And Polygenic Prediction For Kidney Function In Persons With Ancestry From Africa And The Americas, Odessica Hughes, Amy R Bentley, Charles E Breeze, Francois Aguet, Xiaoguang Xu, Girish Nadkarni, Quan Sun, Bridget M Lin, Thomas Gilliland, Mariah C Meyer, Jiawen Du, Laura M Raffield, Holly Kramer, Robert W Morton, Mateus H Gouveia, Elizabeth G Atkinson, Adan Valladares-Salgado, Niels Wacher-Rodarte, Nicole D Dueker, Xiuqing Guo, Yang Hai, Adebowale Adeyemo, Lyle G Best, Jianwen Cai, Guanjie Chen, Michael Chong, Ayo Doumatey, James Eales, Mark O Goodarzi, Eli Ipp, Marguerite Ryan Irvin, Minzhi Jiang, Alana C Jones, Charles Kooperberg, Jose E Krieger, Ethan M Lange, Matthew B Lanktree, James P Lash, Paulo A Lotufo, Ruth J F Loos, Vy Thi Ha My, Jesús Peralta-Romero, Lihong Qi, Leslie J Raffel, Stephen S Rich, Erik J Rodriquez, Eduardo Tarazona-Santos, Kent D Taylor, Jason G Umans, Jia Wen, Bessie A Young, Zhi Yu, Ying Zhang, Yii-Der Ida Chen, Tanja Rundek, Jerome I Rotter, Miguel Cruz, Myriam Fornage, Maria Fernanda Lima-Costa, Alexandre C Pereira, Guillaume Paré, Pradeep Natarajan, Shelley A Cole, April P Carson, Leslie A Lange, Yun Li, Eliseo J Perez-Stable, Ron Do, Fadi J Charchar, Maciej Tomaszewski, Josyf C Mychaleckyj, Charles Rotimi, Andrew P Morris, Nora Franceschini

Faculty, Staff and Students Publications

Chronic kidney disease is a leading cause of death and disability globally and impacts individuals of African ancestry (AFR) or with ancestry in the Americas (AMS) who are under-represented in genome-wide association studies (GWASs) of kidney function. To address this bias, we conducted a large meta-analysis of GWASs of estimated glomerular filtration rate (eGFR) in 145,732 AFR and AMS individuals. We identified 41 loci at genome-wide significance (p < 5 × 10−8), of which two have not been previously reported in any ancestry group. We integrated fine-mapped loci with epigenomic and transcriptomic resources to highlight potential effector genes relevant to kidney physiology and disease, and reveal key regulatory elements and pathways involved in renal function and development. We demonstrate the varying but increased predictive power offered by a multi-ancestry polygenic score for eGFR and highlight the importance of population diversity in GWASs and multi-omics resources to enhance opportunities for clinical translation for all.

Assessing The Coherence In Biological And Environmental Drivers Of Young Sea Bass Abundance Across Important Estuarine Nursery Areas Of The Northern European Sea Bass Stock, Joseph W. Watson, Zachary Radford, Hayley Bannister, Robin Bradley, Mary Brown, Benjamin J. Ciotti, Derek Goodwin, Jennifer A. Graham, Richard D.M. Nash, William K. Roche, Ciara Wogerbauer, Kieran Hyder

School of Biological and Marine Sciences

Year class strength is an important determinant of fish population size, but the drivers are often unknown. The northern stock of European sea bass (Dicentrarchus labrax) is an important target species for both commercial and recreational fisheries. Scientific assessments showed a rapid decline in spawning stock biomass from 2010-18 attributed to a combination of fishing mortality and poor year class strength. Recruitment to the adult stock is linked to the abundance and temporal dynamics of young bass in estuarine nursery areas, but little is known about the relative importance of environmental and biological drivers on the survival of these young …

A Structurally Precise Mechanism Links An Epilepsy-Associated Kcnc2 Potassium Channel Mutation To Interneuron Dysfunction, Jerome Clatot, Christopher B. Currin, Qiansheng Liang, Tanadet Pipatpolkai, Shavonne L. Massey, Ingo Helbig, Lucie Delemotte, Tim P. Vogels, Manuel Covarrubias, Ethan M. Goldberg

Farber Institute for Neuroscience Staff Papers and Presentations

De novo heterozygous variants in KCNC2 encoding the voltage-gated potassium (K+) channel subunit Kv3.2 are a recently described cause of developmental and epileptic encephalopathy (DEE). A de novo variant in KCNC2 c.374G > A (p.Cys125Tyr) was identified via exome sequencing in a patient with DEE. Relative to wild-type Kv3.2, Kv3.2-p.Cys125Tyr induces K+ currents exhibiting a large hyperpolarizing shift in the voltage dependence of activation, accelerated activation, and delayed deactivation consistent with a relative stabilization of the open conformation, along with increased current density. Leveraging the cryogenic electron microscopy (cryo-EM) structure of Kv3.1, molecular dynamic simulations suggest that a strong π-π stacking …

Editorial: Care During Pregnancy And Early Childhood For Growth And Development In Low- And Middle- Income Countries, Ranadip Chowdhury, Ravi Prakash Upadhyay, Bireshwar Sinha, Nita Bhandari, Sunita Taneja, Jai K. Das

Centre of Excellence in Women and Child Health

No abstract provided.

Tfeb Drives Mtorc1 Hyperactivation And Kidney Disease In Tuberous Sclerosis Complex, Nicola Alesi, Damir Khabibullin, Dean M Rosenthal, Elie W Akl, Pieter M Cory, Michel Alchoueiry, Samer Salem, Melissa Daou, William F Gibbons, Jennifer A Chen, Long Zhang, Harilaos Filippakis, Laura Graciotti, Caterina Miceli, Jlenia Monfregola, Claudia Vilardo, Manrico Morroni, Chiara Di Malta, Gennaro Napolitano, Andrea Ballabio, Elizabeth P Henske

Duncan NRI Faculty and Staff Publications

Tuberous Sclerosis Complex (TSC) is caused by TSC1 or TSC2 mutations, leading to hyperactivation of mechanistic target of rapamycin complex 1 (mTORC1) and lesions in multiple organs including lung (lymphangioleiomyomatosis) and kidney (angiomyolipoma and renal cell carcinoma). Previously, we found that TFEB is constitutively active in TSC. Here, we generated two mouse models of TSC in which kidney pathology is the primary phenotype. Knockout of TFEB rescues kidney pathology and overall survival, indicating that TFEB is the primary driver of renal disease in TSC. Importantly, increased mTORC1 activity in the TSC2 knockout kidneys is normalized by TFEB knockout. In TSC2-deficient …

Apkc Inhibitors And Methods Of Treating A Neurodegenerative Disease Or Disorder, Robert Vito Farese, Mini Paliyath Sajan, Margaret Genevieve Higgs

USF Patents

Provided herein are formulations effective for and methods of treating or preventing a neurodegenerative disorder in a subject in need thereof that can include administering an amount of an aPKC inhibitor to a subject in need thereof.

Modulating Angiogenesis By Proteomimetics Of Vascular Endothelial Growth Factor, Jianfeng Cai, Sami Abdulkadir

USF Patents

Provided herein are novel VEGF mimics, pharmaceutical compositions thereof, and methods of their use in increasing or reducing angiogenesis.

Reducing Global Food Loss And Waste Could Improve Air Quality And Lower The Risk Of Premature Mortality, Alessandro Gatto, Maksym Chepeliev

Department of Agricultural Economics Faculty Publications

While the global food system substantially contributes to environmental degradation and climate change, significant amounts of lost or wasted foods along the food supply chain actively contribute to global air pollution and related health risks. In this study, we use an environmentally-extended input–output model to quantify air pollution embedded in global food loss and waste (FLW) and investigate how FLW reduction policies can mitigate air pollution linked to food consumption, decreasing associated premature mortality risks across global regions. While estimating a positive impact of FLW reduction policies on decreasing air pollution levels (from −1.5% of SO2 emissions to −10.2% of …

Autogenic Splenic Implantation Versus Splenectomy In Patients Undergoing Distal Pancreatectomy For Benign Or Low-Grade Malignant Lesions Of The Distal Pancreas: Study Protocol For A Multicentre, Open-Label, Randomized Controlled Trial (Restore), Horacio Asbun

All Publications

Background: The spleen plays a significant role in the clearance of circulating microorganisms. Sequelae of splenectomy, especially immunodeficiency, can have a deleterious effect on a patient's health and even lead to death. Hence, splenectomy should be avoided and spleen preservation during elective surgery has become a treatment goal. However, this cannot be achieved in every patient due to intraoperative technical difficulties or oncological reasons. Autogenic splenic implantation (ASI) is currently the only possible way to preserve splenic function when a splenectomy is necessary. Experience largely stems from trauma patients with a splenic rupture. Splenic immune function can be measured by …

Coded Social Control: China’S Normalization Of Biometric Surveillance In The Post Covid-19 Era, Michelle Miao

Washington Journal of Law, Technology & Arts

This article investigates the longevity of health QR codes, a digital instrument of pandemic surveillance, in post-COVID China. From 2020 to 2022, China widely used this tri-color tool to combat the COVID-19 pandemic. A commonly held assumption is that health QR codes have become obsolete in post-pandemic China. This study challenges such an assumption. It reveals their persistence and integration - through mobile apps and online platforms - beyond the COVID-19 public health emergency. A prolonged, expanded and normalized use of tools which were originally intended for contact tracing and pandemic surveillance raises critical legal and ethical concerns. Moreover, their …

Common Heart Failure With Preserved Ejection Fraction Animal Models Yield Disparate Myofibril Mechanics, Axel J. Fenwick, Vivek P. Jani, D. Brian Foster, Thomas E. Sharp, Traci T. Goodchild, Kyle Lapenna, Jake E. Doiron, David J. Lefer, Joseph A. Hill, David A. Kass, Anthony Cammarato

School of Medicine Faculty Publications

No abstract provided.

Indigenous Peoples And Local Communities Report Ongoing And Widespread Climate Change Impacts On Local Social-Ecological Systems, Victoria Sharakhmatova, Victoria Reyes-García, David García-Del-Amo, Santiago Álvarez-Fernández, Petra Benyei, Laura Calvet-Mir, André B. Junqueira, Vanesse Labeyrie, Xiaoyue Li, Sara Miñarro, Vincent Porcher, Anna Porcuna-Ferrer, Anna Schlingmann, Christoph Schunko, Ramin Soleymani, Adrien Tofighi-Niaki, Mariam Abazeri, Emmanuel M.N.A.N. Attoh, Ayansina Ayanlade, Julia Vieira Da Cunha Ávila, Daniel Babai, Rodrigo C. Bulamah, Joao Campos-Silva, Rosario Carmona, Julián Caviedes, Rumbidzayi Chakauya, Mouna Chambon, Zhuo Chen, Fasco Chengula, Esther Conde, Aida Cuní-Sanchez

Faculty Publications

The effects of climate change depend on specific local circumstances, posing a challenge for worldwide research to comprehensively encompass the diverse impacts on various local social-ecological systems. Here we use a place-specific but cross-culturally comparable protocol to document climate change indicators and impacts as locally experienced and analyze their distribution. We collected first-hand data in 48 sites inhabited by Indigenous Peoples and local communities and covering all climate zones and nature-dependent livelihoods. We documented 1,661 site-agreed reports of change corresponding to 369 indicators. Reports of change vary according to climate zone and livelihood activity. We provide compelling evidence that climate …

My Journey With Faith, Jocelyn Rodriguez

Masters Theses

A memoir of my life and my faith. I was able to recollect moments when my faith was tested, doubted, and its growth. It's a story of truth, understanding, and wonder of my life was molded not just by my surroundings but by my growing relationship with my faith.

Naturalism, Christian Molinism, And The Problem Of Evil, Caleb Blackman

Masters Theses

The purpose of this thesis is to create a Christian theodicy by forming an abductive argument showing that Christian Molinism can provide reasons for the existence of evil, and compared to naturalism, it provides the best explanation. This is accomplished by considering the naturalistic explanation of evil and building upon defenses and concepts such as the Free Will Defense and Molinism.

Improves Intrusion Detection Performance Inwireless Sensor Networks Through Machine Learning, Enhanced By An Accelerated Deep Learning Model With Advanced Feature Selection, Hadeel M. Saleh, Hend Marouane, Ahmed Fakhfakh

Iraqi Journal for Computer Science and Mathematics

Wireless Sensor Networks (WSNs) have been securing a big position in the new aspect of security network attacks, where these suffer from various serious cyber threats that can play with their data integrity and reliability. Due to the key importance of WSN in a wide spectrum range of applications such as environmental monitoring and military field, building reliable, robust and efficient intrusion detection systems (IDS) is necessary. Although traditional machine learning approaches have been intended to detect these threats, they often lack high accuracy due to the complexity and dimensionality of WSN data.To address these limitations, the study introduces an …

Effectiveness Of Emotionally Focused Therapy (Eft) With Chinese Couple Clients: From The Chinese Eft Therapists' Cultural Lens, Yifan Wang

Doctoral Dissertations and Projects

The purpose of this phenomenological study is to understand the Chinese EFT (Emotionally Focused Therapy) therapists’ experiences of working with Chinese couples in EFT sessions, as well as to discover how the cultural factors play a role in the effectiveness of EFT use with Chinese couples. This study was conducted by finding out 10 EFT-oriented therapists and analyzing via online interviews their experiences of working with Chinese couples. The theories guiding this study are based on Emotionally Focused Therapy (EFT). One of the founding therapists of this approach is Dr. Sue Johnson. EFT is heavily influenced by attachment theory, which …

The Effects Of High School Instrumental Music Performance Anxiety On The Accelerated Recovery Of Social Anxiety, Staci Leigh Hatmaker

Doctoral Dissertations and Projects

This quantitative correlational study aims to examine the challenges secondary students encounter in sustaining positive mental health and how the benefits of music performance anxiety in secondary school students can aid in the accelerated recovery of social anxiety. There is a present gap in the research exploring the benefits of situational anxiety on clinically diagnosed anxiety disorders and noting that this situational anxiety is a standard expectation and volunteered for when participating in performing arts environments. The objective is to understand the therapeutic benefits of micro-dosing the brain with music performance anxiety in a controlled environment and its potential uses …

The Unprecedented Stressors Of Early Childhood Educators During The Covid-19 Pandemic And Post-Pandemic Restoration: A Case Study, Ida Mae Lewis

Doctoral Dissertations and Projects

The purpose of this case study was to describe the unprecedented stressors of early childhood educators (ECE) during the COVID-19 pandemic and the post-pandemic restoration at two early childhood education centers (ECEC) in a midwestern state. The central research question was: How did the COVID-19 pandemic’s unprecedented stressors impact ECE in the post-pandemic era? Data collection included structured interviews with open-ended questions, focus groups, and documents. The three data sources were triangulated for themes, perspectives, and interpretations, and coding was used to help gain a deep understanding of the stressors experienced by early childhood educators. The conceptual framework guiding this …

An Existential-Phenomenological Exploration Of The Experience Of Being A White Undergraduate Psychology Student In A Multicultural Counseling Course, Mona Lynnette Swallow

Doctoral Dissertations and Projects

This existential-phenomenological study sought to explore the experiences of White undergraduate psychology students enrolled in a multicultural counseling course to gain an understanding of how White students described their lived experiences while enrolled in the course. This was accomplished by conducting virtual interviews with nine participants recruited through an online university announcement. Three key experiential constituents emerged from the data supporting previous research of the conflicts White students experience as they process understanding their racialized identities as members of the dominant ethnic-racial group in U.S. society in context to the topics discussed in the course. This lack of understanding was …

Differences In Out-Of-School Suspensions Between Black And White High School Students When Controlling For Student Factors, School Factors, And Delinquency, Steven Craig Davidson

Doctoral Dissertations and Projects

This quantitative, correlational study aims to determine how accurately out-of-school suspensions can be predicted from a linear combination of student delinquency, in-school delinquency, and prior suspensions for Black and White high school students. Further, a causal-comparative design is used to determine if there is a statically significant difference in out-of-school suspensions between Black and White high school students when controlling for student factors, school factors, and student delinquency factors. The study consists of five guiding theories that inform two general hypotheses. The first hypothesis, referred to as the differential selection hypothesis, is guided by critical race theory (CRT) and implicit …

Shaping The Future Of Global Access To Safe, Effective, Appropriate And Quality Health Products, Raffaella Ravinetto, Rodrigo Henriquez, Prashant N Srinivas, Hazel Bradley, Renier Coetzee, Theresa J Ochoa, Jean Claude Semuto Ngabonziza, Jean-Baptiste Mazarati, Wim Van Damme, Remco Van De Pas, Nico Vandaele, Els Torreele

Faculty, Staff and Student Publications

No abstract provided.

Development Of A Suspended Aerobic Membrane Bioreactor (Sambr) For Sustainable Wastewater Treatment On Early Planetary Bases, Talon James Bullard

USF Tampa Graduate Theses and Dissertations

Environmental Control and Life Support Systems (ECLSS) ideally should treat all “waste” streams for recovery in a sustainable and near closed-loop manner. This will be critical for Partial Gravity Habitats (PGH) and Early Planetary Bases (EPB) that will be established on the Moon and Mars due to the lack of readily available resources. Currently, the Water Recovery System (WRS), onboard the International Space Station (ISS), recovers and purifies water from urine and graywater. While efficient, this system is not optimized for future missions and utilizes physical-chemical technologies that operate with single-use and hazardous consumables. In response to the lack of …

Effects Of Kras Genetic Interactions On Outcomes In Cancers Of The Lung, Pancreas, And Colorectum, Isabella N Grabski, John V Heymach, Kenneth L Kehl, Scott Kopetz, Ken S Lau, Gregory J Riely, Deborah Schrag, Rona Yaeger, Rafael A Irizarry, Kevin M Haigis

Faculty, Staff and Student Publications

Background: KRAS is among the most commonly mutated oncogenes in cancer, and previous studies have shown associations with survival in many cancer contexts. Evidence from both clinical observations and mouse experiments further suggests that these associations are allele- and tissue-specific. These findings motivate using clinical data to understand gene interactions and clinical covariates within different alleles and tissues.

Methods: We analyze genomic and clinical data from the AACR Project GENIE Biopharma Collaborative for samples from lung, colorectal, and pancreatic cancers. For each of these cancer types, we report epidemiological associations for different KRAS alleles, apply principal component analysis (PCA) to …

Synthetic Oct-A Blood Vessel Maps Using Fundus Images And Generative Adversarial Networks, Ashanul Haque, Mohd Wajid Ali Khan, Khalaf M Alenezi, Raoudha Soury, Muhammad S Khan, Shahzaib Ahamad, Md Mushtaque, Dinesh Gupta

Faculty, Staff and Student Publications

The design and development of new small-molecule glycation inhibitors are essential for preventing various chronic diseases, including diabetes mellitus, immunoinflammation, cardiovascular, and neurodegenerative diseases. 4-Thiazolidinone or thiazolidine-4-one is a well-known heterocyclic compound with the potential to inhibit the formation of advanced glycation end products. In the present work, we report the synthesis and characterization of four new 5-arylidene 3-cyclopropyl-2-(phenylimino)thiazolidin-4-one (1–4) compounds and their human serum albumin glycation inhibitory activity. One of the compounds 5-(2H-1,3-benzodioxol-5-ylmethylidene)-3-cyclopropyl-2-(phenylimino)-1,3-thiazolidin-4-one (3) showed potent inhibition in the synthesis of initial, intermediary, and final products of glycation reactions. Besides, conformational …

Curated Zones: Musical Possession And Colonial Identity Expression In Early 20th Century Cairo Through “The Sphinx: English Illustrated Weekly 1892-1947”, Gabriel Donnelly

Student Scholarship

No abstract provided.

“As If I Were Buried Beneath These Words”: An Exploration Of Power, Voice, And The Female Corpus, Grace Lukens

Student Scholarship

No abstract provided.

Electric Avenue Why The Marxist Revolution Hasn’T Happened Yet., Maya Ordóñez Landsberg

Student Scholarship

No abstract provided.

Steeper Size Spectra With Decreasing Phytoplankton Biomass Indicate Strong Trophic Amplification And Future Fish Declines, Angus Atkinson, Axel G. Rossberg, Ursula Gaedke, Gary Sprules, Ryan F. Heneghan, Stratos Batziakas, Maria Grigoratou, Elaine Fileman, Katrin Schmidt, Constantin Frangoulis

School of Geography, Earth and Environmental Sciences

Under climate change, model ensembles suggest that declines in phytoplankton biomass amplify into greater reductions at higher trophic levels, with serious implications for fisheries and carbon storage. However, the extent and mechanisms of this trophic amplification vary greatly among models, and validation is problematic. In situ size spectra offer a novel alternative, comparing biomass of small and larger organisms to quantify the net efficiency of energy transfer through natural food webs that are already challenged with multiple climate change stressors. Our global compilation of pelagic size spectrum slopes supports trophic amplification empirically, independently from model simulations. Thus, even a modest …

Scalable And Consolidated Microbial Platform For Rare Earth Element Leaching And Recovery From Waste Sources, Nathan M. Good, Christina S. Kang-Yun, Morgan Z. Su, Alexa M. Zytnick, Colin C. Barber, Huong N. Vu, Joseph M. Grace, Hoang H. Nguyen, Wenjun Zhang, Elizabeth Skovran, Maohong Fan, Dan M. Park, Norma Cecilia Martinez-Gomez

Faculty Research, Scholarly, and Creative Activity

Chemical methods for the extraction and refinement of technologically critical rare earth elements (REEs) are energy-intensive, hazardous, and environmentally destructive. Current biobased extraction systems rely on extremophilic organisms and generate many of the same detrimental effects as chemical methodologies. The mesophilic methylotrophic bacterium Methylobacterium extorquens AM1 was previously shown to grow using electronic waste by naturally acquiring REEs to power methanol metabolism. Here we show that growth using electronic waste as a sole REE source is scalable up to 10 L with consistent metal yields without the use of harsh acids or high temperatures. The addition of organic acids increases …