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Modeling A Decision Support System For Covid-19 Using Systems Dynamics And Fuzzy Inference, Vinayaka Gude

Faculty Publications

Covid-19 has impacted the lives of people across the world with deaths and unprecedented economic damage. Countries have employed various restrictions and lockdowns to slow down the rate of its spread with varying degrees of success. This research aims to propose an optimal strategy for dealing with a pandemic taking the deaths and economy into account. A complete lockdown until vaccination is not suitable as it can destroy the economy, whereas having no restrictions would result in more Covid-19 cases. Therefore, there is a need for a dynamic model which can propose a suitable strategy depending on the economic and …

Attitudes Of Major Religious Organizations In Ukraine To Abortion And Reproductive Medicine, Kateryna Karpenko, Alla Guzhva

Occasional Papers on Religion in Eastern Europe

The attitude of the largest religions of Ukraine to reproductive medicine is determined by a variety of practical approaches, which are still in process of change between the rather strict negative official position of major religious organizations of Ukraine, on the one hand, and a rather liberal approach to reproductive medicine in secular legislation of Ukraine. The harsh negative official position of the main religious organizations of Ukraine to surrogacy and abortions is presented in a joint document adopted by the Ukrainian Council of Churches and Religious Organizations. While the diversity of practical approaches of these organizations is represented by …

Shared Nearest Neighbors Approach And Interactive Browser For Network Analysis Of A Comprehensive Non-Small-Cell Lung Cancer Data Set, Stephanie T Schmidt, Neal Akhave, Ryan E Knightly, Alexandre Reuben, Natalie Vokes, Jianhua Zhang, Jun Li, Junya Fujimoto, Lauren A Byers, Beatriz Sanchez-Espiridion, Lixia Diao, Jing Wang, Lorenzo Federico, Marie-Andree Forget, Daniel J Mcgrail, Annikka Weissferdt, Shiaw-Yih Lin, Younghee Lee, Erika Suzuki, Jeffrey J Kovacs, Carmen Behrens, Ignacio I Wistuba, Andrew Futreal, Ara Vaporciyan, Boris Sepesi, John V Heymach, Chantale Bernatchez, Cara Haymaker, Tina Cascone, Jianjun Zhang, Christopher A Bristow, Timothy P Heffernan, Marcelo V Negrao, Don L Gibbons, Icon Team

Faculty, Staff and Student Publications

Purpose: Advances in biological measurement technologies are enabling large-scale studies of patient cohorts across multiple omics platforms. Holistic analysis of these data can generate actionable insights for translational research and necessitate new approaches for data integration and mining.

Methods: We present a novel approach for integrating data across platforms on the basis of the shared nearest neighbors algorithm and use it to create a network of multiplatform data from the immunogenomic profiling of non-small-cell lung cancer project.

Results: Benchmarking demonstrates that the shared nearest neighbors-based network approach outperforms a traditional gene-gene network in capturing established interactions while providing new ones …

Alyref, A Novel Factor Involved In Breast Carcinogenesis, Acts Through Transcriptional And Post-Transcriptional Mechanisms Selectively Regulating The Short Neat1 Isoform, Christiane Klec, Erik Knutsen, Daniela Schwarzenbacher, Katharina Jonas, Barbara Pasculli, Ellen Heitzer, Beate Rinner, Katarina Krajina, Felix Prinz, Benjamin Gottschalk, Peter Ulz, Alexander Deutsch, Andreas Prokesch, Stephan W Jahn, S Mohammad Lellahi, Maria Perander, Raffaela Barbano, Wolfgang F Graier, Paola Parrella, George Adrian Calin, Martin Pichler

Faculty, Staff and Student Publications

The RNA-binding protein ALYREF (THOC4) is involved in transcriptional regulation and nuclear mRNA export, though its role and molecular mode of action in breast carcinogenesis are completely unknown. Here, we identified high ALYREF expression as a factor for poor survival in breast cancer patients. ALYREF significantly influenced cellular growth, apoptosis and mitochondrial energy metabolism in breast cancer cells as well as breast tumorigenesis in orthotopic mouse models. Transcriptional profiling, phenocopy and rescue experiments identified the short isoform of the lncRNA NEAT1 as a molecular trigger for ALYREF effects in breast cancer. Mechanistically, we found that ALYREF binds to the NEAT1 …

Feto-Maternal Outcomes Of Pre-Eclampsia: A Retrospective Study, Linda Varghese, Neenumol Babu, Niya V.C

Manipal Journal of Nursing and Health Sciences

Introduction: Pre-eclampsia is a multisystem multifactorial disease unique to pregnancy with unknown aetiology which is characterized by blood pressure ≥140/90 mmHg after 20 weeks of gestation associated with proteinuria ≥300 mg/24- hour urine specimen. It complicates about 2-10% of pregnancies worldwide. Objectives: To determine the prevalence and evaluate feto-maternal outcomes of pre-eclampsia. Methods: This was a retrospective study conducted at Amrita Institute of Medical Sciences, (AIMS) Kochi from 1 August 2017 to 31 July 2018. This study was done by retrospective analysis of the delivery register (Labour room) and hospital medical records. Results: The prevalence of pre-eclampsia is 2.5% and …

A Missing Piece Of The Puzzle: Patient And Provider Perspectives On Pain Management Needs And Opioid Prescribing In Inflammatory Bowel Disease Care, Salva N Balbale, Cassandra B Iroz, Willemijn L A Schäfer, Julie K Johnson, Jonah J Stulberg

Faculty, Staff and Student Publications

BACKGROUND: Recent data have shown high rates of opioid misuse among inflammatory bowel disease (IBD) patients. We conducted a qualitative study to explore IBD patient and provider perceptions and experiences with pain management and opioid prescribing.

METHODS: We conducted a focus group with IBD patients and semistructured interviews with IBD-focused physicians and nurses. We used an inductive approach for analysis and the constant comparison method to develop and refine codes and identify prominent themes. We analyzed interview and focus group data concurrently to triangulate themes.

RESULTS: Nine patients and 10 providers participated. We grouped themes into 3 categories: (1) current …

Prolonged Cardiac Nr4a2 Activation Causes Dilated Cardiomyopathy In Mice, Sadia Ashraf, Heinrich Taegtmeyer, Romain Harmancey

Faculty, Staff and Student Publications

Transcription factors play a fundamental role in cardiovascular adaptation to stress. Nuclear receptor subfamily 4 group A member 2 (NR4A2; NURR1) is an immediate-early gene and transcription factor with a versatile role throughout many organs. In the adult mammalian heart, and particularly in cardiac myocytes, NR4A2 is strongly up-regulated in response to beta-adrenergic stimulation. The physiologic implications of this increase remain unknown. In this study, we aimed to interrogate the consequences of cardiac NR4A2 up-regulation under normal conditions and in response to pressure overload. In mice, tamoxifen-dependent, cardiomyocyte-restricted overexpression of NR4A2 led to cardiomyocyte hypertrophy, left ventricular dilation, heart failure, …

Listen To The Voice Of A Nobel Prize Winner, Matt Richardson

TMC Library Newsletter (2015-)

Audio recordings featuring Nobel Prize winners Philip S. Hench and Edward C. Kendall are now available at The McGovern Historical Center collection.

Vital Signs, Summer 2022, Boonshoft School Of Medicine

Vital Signs

A seventeen page newsletter created by the Boonshoft School of Medicine to document the current affairs of the school. This issue includes a variety of feature articles, alumni profiles, class notes, and more.

Utilizing Molecular Pathways To Provide Generalizable, Explainable, And Translatable Models From Cancer Drug Response Prediction, Yi-Ching Tang

Dissertations and Theses (Open Access)

There is a crucial need to develop computational methods to identify the best fitting drug for each cancer patient. Cancer cell lines are still the most popular models for drug screening, supported by massive amounts of genomic profiling and drug sensitivity profiles measured against single agents and combination therapies. However, the challenge stays in finding genomic-matched drugs and evaluating their efficacies in the clinic. Three factors form this challenge. First, the high dimensionality of genomic data requires large data to distinguish predictive features and generalize to new samples. Second, the differences in cancer cell lines and tumors in patients poses …

Institute For Global Health And Development : Issue 4 - July - Sept 2022, Institute For Global Health And Development

IGHD Newsletters

• Research Highlights
• Key Publications
• News
• Reflections from IGHD’s Associate Faculty
• Reflections from IGHD’s Summer Interns
• Webinars and Dialogues
• Mark your Calendars: Upcoming Event
• Obituary
• Collaborate With Us

Living With Ulcerative Colitis: Exploring Dietary Inflammatory Intake, Physical Activity, And Methods To Manage The Burden Of Illness, Kelli E. Dubois

Theses and Dissertations

Ulcerative Colitis (UC) is a chronic illness under the umbrella of Inflammatory Bowel Disease (IBD). IBD is becoming a global health issue as incidence rates are rising throughout the world. UC is characterized by chronic inflammation and ulcerations in the colon’s mucosal lining due to abnormal inflammatory and immune system responses. Patients with UC experience a range of gastrointestinal and extraintestinal symptoms as well as psychosocial challenges throughout the course of illness that generate a significant burden on daily life. Periods of active disease, or flares, present exacerbations of disease symptoms and the greatest burden on daily functioning, yet disease …

Crystal Growth Of Inorganic Halides And Oxide-Halides For Scintillation Applications And Radiation Detection, Gyanendra B. Ayer

Theses and Dissertations

Scintillators, materials which emit light when struck by high energy X-rays and y- rays, are extensively used in various fields including medical imaging, computed tomography, high-energy physics, and more recently in homeland security for the prevention of nuclear and radiological terrorism. While comparing with the traditional scintillators, which have long-term instability, high synthetic cost, toxicity, and hygroscopicity issues, metal halides have been reported to exhibit effective excitonic radioluminescence and greatly contribute in the field of scintillating applications and radiation detection. Currently, the mixed-anion oxide-fluorides have emerged as a prospective new class of scintillators, in which the mixed oxide-fluoride environment …

Elucidating The Sources Supplying Aerosol Iron, Zinc, And Cadmium To The Surface Of The North Pacific Ocean With Stable Isotopes, Zach B. Bunnell

USF Tampa Graduate Theses and Dissertations

Transition metals, such as iron (Fe), zinc (Zn) and cadmium (Cd), are found at just trace amounts within the global oceans yet are vital for many biological functions of phytoplankton. As a result, these metals influence the ocean’s efficacy for carbon sequestration. Atmospheric dust is the primary input of Fe to various surface waters and may also supply Zn and Cd to oligotrophic surface waters. Here, I present Fe, Zn, and Cd isotope data from the US North Pacific GEOTRACES Section GP15 (Alaska-Tahiti) from the low-dust season (Sept. – Nov. 2018). Using this data and aerosol enrichment factors, I show …

Color Defined: An Autoethnographic Exploration Of How Race, Trauma, Gun Violence, And Grief Connect For A Black Mother, Kokita Dirton Wilson

USF Tampa Graduate Theses and Dissertations

Black mothers are disproportionately affected by fatal shootings and the need for making meaning and finding purpose remains overlooked as a vital component of building resilience in their grief journey. The purpose of this study was to (a) reflect on being a Black mother of a fatal shooting victim; (b) understand the grief and healing process that follows; (c) connect my experiences to those within the larger Black grief community, and (d) by example, help other grieving mothers navigate through their grief struggles. I used two research questions: 1) How can I learn about my grief process by using personal …

Zooplankton Biodiversity In The Northeast Gulf Of Mexico And On The West Florida Shelf From 2005 - 2014, Megan Ferguson

USF Tampa Graduate Theses and Dissertations

Zooplankton abundance and biodiversity was measured in the northeast Gulf of Mexico (NEGoM) and on the West Florida Shelf. Bongo net samples were collected between May 2005 to September 2009 through the SEAMAP program, and between July 2010 to August 2014 through the C-IMAGE program. Calanoid copepods were the most abundant zooplankton group in most of the samples collected, but ostracods, larvaceans, and chaetognaths were also abundant. Shannon and Inverse Simpson indices were calculated for all zooplankton samples and generally showed similar trends, but only Shannon indices were used for statistical analyses. In the winter and spring there were significant …

A Protein-Based Therapeutic Combination For The Treatment Of Hard-To-Heal Wounds, Graham L. Strauss

USF Tampa Graduate Theses and Dissertations

Chronic wounds present many clinical challenges in relation to the successful treatment and closure of the damaged tissue. Most current treatment methods focused on one or two aspects to drive wound closure, while most chronic wounds are multifactorial environments with many of those dependencies relying on the termination of one another to effectively gain tissue construction, closure, and full skin thickness and composition. Natural wound healing processes allude to potential biologics that can impede the chronic breakdown of tissue, while restoring deposition of new tissue, and effectively leading to a healed wound. Proteases secreted by the body’s immune system lay …

Lymphatic Function And Anatomy In Early Stages Of Lipedema, John C Rasmussen, Melissa B Aldrich, Caroline E Fife, Karen L Herbst, Eva M Sevick-Muraca

Faculty, Staff and Student Publications

Objective: Lipedema is an inflammatory subcutaneous adipose tissue disease that develops in women and may progress to lipolymphedema, a condition similar to lymphedema, in which lymphatic dysfunction results in irresolvable edema. Because it has been shown that dilated lymphatic vessels, impaired pumping, and dermal backflow are associated with presymptomatic, cancer-acquired lymphedema, this study sought to understand whether these abnormal lymphatic characteristics also characterize early stages of lipedema prior to lipolymphedema development.

Methods: In a pilot study of 20 individuals with Stage I or II lipedema who had not progressed to lipolymphedema, lymphatic vessel anatomy and function in upper and lower …

Platelet Function In Trauma: Is Current Technology In Function Testing Missing The Mark In Injured Patients?, Jacob B Schriner, Mitchell J George, Jessica C Cardenas, Scott D Olson, Kimberly A Mankiewicz, Charles S Cox, Brijesh S Gill, Charles E Wade

Faculty, Staff and Student Publications

Platelets are subcellular anucleate components of blood primarily responsible for initiating and maintaining hemostasis. Following injury to a blood vessel, platelets can be activated via several pathways, resulting in changed shape, adherence to the injury site, aggregation to form a plug, degranulation to initiate activation in other nearby platelets, and acceleration of thrombin formation to convert fibrinogen to fibrin before contracting to strengthen the clot. Platelet function assays use agonists to induce and measure 1 or more of these processes to identify alterations in platelet function that increase the likelihood of bleeding or thrombotic events. In severe trauma, these assays …

Algorithmic Approach To The Diagnosis Of Organizing Pneumonia: A Correlation Of Clinical, Radiologic, And Pathologic Features, Sujith V Cherian, Dhara Patel, Stephen Machnicki, David Naidich, Diane Stover, William D Travis, Kevin K Brown, Jason J Naidich, Akhilesh Mahajan, Michael Esposito, Bushra Mina, Viera Lakticova, Stuart L Cohen, Nestor L Muller, Jenna Schulner, Rakesh Shah, Suhail Raoof

Faculty, Staff and Student Publications

Organizing pneumonia (OP), characterized histopathologically by patchy filling of alveoli and bronchioles by loose plugs of connective tissue, may be seen in a variety of conditions. These include but are not limited to after an infection, drug reactions, radiation therapy, and collagen vascular diseases. When a specific cause is responsible for this entity, it is referred to as "secondary OP." When an extensive search fails to reveal a cause, it is referred to as "cryptogenic OP" (previously called "bronchiolitis obliterans with OP"), which is a clinical, radiologic, and pathologic entity classified as an interstitial lung disease. The clinical presentation of …

A Spef1-Interacting Microtubule Quartet Protein In Trypanosoma Brucei Promotes Flagellar Inheritance By Regulating Basal Body Segregation, Kieu T M Pham, Qing Zhou, Kyu Joon Lee, Ziyin Li

Faculty, Staff and Student Publications

The human parasite Trypanosoma brucei contains a motile flagellum that determines the plane of cell division, controls cell morphology, and mediates cell-cell communication. During the cell cycle, inheritance of the newly formed flagellum requires its correct positioning toward the posterior of the cell, which depends on the faithful segregation of multiple flagellum-associated cytoskeletal structures including the basal body, the flagellar pocket collar, the flagellum attachment zone, and the hook complex. A specialized group of four microtubules termed the microtubule quartet (MtQ) originates from the basal body and runs through the flagellar pocket collar and the hook complex to extend, along …

Efficacy Of Niraparib By Time Of Surgery And Postoperative Residual Disease Status: A Post Hoc Analysis Of Patients In The Prima/Engot-Ov26/Gog-3012 Study, Roisin E O'Cearbhaill, Jose-Alejandro Pérez-Fidalgo, Bradley J Monk, Ignacio Tusquets, Colleen Mccormick, Jose Fuentes, Richard G Moore, Christof Vulsteke, Mark S Shahin, Frédéric Forget, William H Bradley, Sakari Hietanen, David M O'Malley, Anne Dørum, Brian M Slomovitz, Klaus Baumann, Frédéric Selle, Paula M Calvert, Grazia Artioli, Tally Levy, Aalok Kumar, Izabela A Malinowska, Yong Li, Divya Gupta, Antonio González-Martín

Faculty, Staff and Student Publications

OBJECTIVE: To evaluate the association between surgical timing and postoperative residual disease status on the efficacy of niraparib first-line maintenance therapy in patients with newly diagnosed advanced ovarian cancer at high risk of recurrence.

METHODS: Post hoc analysis of the phase 3 PRIMA/ENGOT-OV26/GOG-3012 (NCT02655016) study of niraparib in patients with newly diagnosed primary advanced ovarian, primary peritoneal, or fallopian tube cancer with a complete/partial response to first-line platinum-based chemotherapy. Progression-free survival (PFS) was assessed by surgical status (primary debulking surgery [PDS] vs neoadjuvant chemotherapy/interval debulking surgery [NACT/IDS]) and postoperative residual disease status (no visible residual disease [NVRD] vs visible residual …

Obscurin Regulates Ankyrin Macromolecular Complex Formation, Janani Subramaniam, Gokay Yamankurt, Shane R Cunha

Faculty, Staff and Student Publications

Obscurin is a large scaffolding protein in striated muscle that maintains sarcolemmal integrity and aligns the sarcoplasmic reticulum with the underlying contractile machinery. Ankyrins are a family of adaptor proteins with some isoforms that interact with obscurin. Previous studies have examined obscurin interacting with individual ankyrins. In this study, we demonstrate that two different ankyrins interact with obscurin's carboxyl terminus via independent ankyrin-binding domains (ABDs). Using in-vitro binding assays, co-precipitation assays, and FLIM-FRET analysis, we show that obscurin interacts with small ankyrin 1.5 (sAnk1.5) and the muscle-specific ankyrin-G isoform (AnkG107). While there is no direct interaction between sAnk1.5 and AnkG107, …

Guidelines On Models Of Diabetic Heart Disease, Lisa C Heather, Anne D Hafstad, Ganesh V Halade, Romain Harmancey, Kimberley M Mellor, Paras K Mishra, Erin E Mulvihill, Miranda Nabben, Michinari Nakamura, Oliver J Rider, Matthieu Ruiz, Adam R Wende, John R Ussher

Faculty, Staff and Student Publications

Diabetes is a major risk factor for cardiovascular diseases, including diabetic cardiomyopathy, atherosclerosis, myocardial infarction, and heart failure. As cardiovascular disease represents the number one cause of death in people with diabetes, there has been a major emphasis on understanding the mechanisms by which diabetes promotes cardiovascular disease, and how antidiabetic therapies impact diabetic heart disease. With a wide array of models to study diabetes (both type 1 and type 2), the field has made major progress in answering these questions. However, each model has its own inherent limitations. Therefore, the purpose of this guidelines document is to provide the …

Opposing Roles Of Hdac6 In Liver Regeneration And Hepatocarcinogenesis, Sophors Phorl, Azra Memon, Yuri Seo, Thi Oanh Hoang, Trung Nghia Tran, Le Minh Tri Nguyen, Chang Hoon Lee, Woon Kyu Lee, Joo-Yong Lee

Faculty, Staff and Student Publications

Histone deacetylase 6 (HDAC6), a deacetylase of p53, has emerged as a privileged inhibitory target for cancer therapy because of its deacetylating activity for p53 at K120 and K373/382. However, intricate roles of HDAC6 in hepatocellular carcinogenesis have been suggested by recent evidence, namely that HDAC6 ablation suppresses innate immunity, which plays critical roles in tumor immunosurveillance and antitumor immune responses. Therefore, it is valuable to determine whether HDAC6 ablation inhibits hepatocellular carcinogenesis using in vivo animal models. Here, we firstly showed that HDAC6 ablation increased K320 acetylation of p53, known as pro-survival acetylation, in all tested animal models but …

Rising Temperatures, Rising Tensions: Climate Change And Power Transition Theory, Anthony Rodin

Journal of Strategic Security

Two of the biggest issues in international politics today are climate change and the ongoing power transition between the United States and China. However, very few works examine the way these issues interact with each other. This paper attempts to resolve this by integrating climate change into power transition theory (PTT), which attempts to capture the behavior of states in the midst of transition to or from global power. This paper first analyzes the literatures on the (tenuous) links between environmental degradation and interstate conflict as well as PTT. Opportunities for integration are then examined, especially focusing on climate change's …

Scientist's Warning On Climate Change And Insects, Jeffrey A. Harvey, Kévin Tougeron, Rieta Gols, Robin Heinen, Mariana Abarca, Et Al

Biological Sciences: Faculty Publications

Climate warming is considered to be among the most serious of anthropogenic stresses to the environment, because it not only has direct effects on biodiversity, but it also exacerbates the harmful effects of other human-mediate threats. The associated consequences are potentially severe, particularly in terms of threats to species preservation, as well as in the preservation of an array of ecosystem services provided by biodiversity. Among the most affected groups of animals are insects—central components of many ecosystems—for which climate change has pervasive effects from individuals to communities. In this contribution to the scientists’ warning series, we summarize the effect …

Ocean Eddies And Frontal Zones In The Gulf Of Mexico And Straits Of Florida, Yingjun Zhang

USF Tampa Graduate Theses and Dissertations

Ocean eddies and fronts in the Gulf of Mexico (GoM) and the Straits of Florida (SoF) play important roles in ocean physics, biology, and ecology. These two ubiquitous physical features have been studied worldwide for decades, yet many questions remain unanswered or poorly studied for the GoM and SoF. This study aims to improve the understanding of ocean eddies and frontal zones in the GoM and SoF using satellite remote sensing, in situ observations and model outputs, as well as state-of-the-art algorithms, with the following objectives: 1) analyze the three-dimensional (3-D) statistical characteristics and thermohaline structure of mesoscale eddies in …

Elimination Of Pseudo-Hfos In Ieeg Using Sparse Representation And Random Forest Classifier, Behrang Fazli Besheli, Zhiyi Sha, Thomas Henry, Jay R Gavvala, Candan Gurses, Sacit Karamursel, Nuri F Ince

Faculty, Staff and Student Publications

High-Frequency Oscillation (HFO) is a promising biomarker of the epileptogenic zone. However, sharp artifacts might easily pass the conventional HFO detectors as real HFOs and reduce the seizure onset zone (SOZ) localization. We hypothesize that, unlike pseudo-HFOs, which originates from artifacts with sharp changes or arbitrary waveform characteristic, real HFOs could be represented by a limited number of oscillatory waveforms. Accordingly, to distinguish true ones from pseudo-HFOs, we established a new classification method based on sparse representation of candidate events that passed an initial detector with high sensitivity but low specificity. Specifically, using the Orthogonal Matching Pursuit (OMP) and a …

Biological Treatment Usage In Patients With Hiv And Rheumatic Disease, 2003-2021: Long-Term Safety And Follow-Up, Benjamin Sornrung Naovarat, Gloria Salazar, Mariko Ishimori, Francis M Williams, John D Reveille

Faculty, Staff and Student Publications

OBJECTIVE: This study examined the safety and efficacy of biological agents, especially tumour necrosis factor (TNF) inhibitors, for HIV-positive rheumatology patients refractory to standard therapy.

METHODS: This study is a retrospective case series including patients derived from a community HIV clinic as well as from two academic centres. Initial visit data collected included: sociodemographic characteristics, CD4 counts, HIV viral load and medication use. Patients with persistent disease activity despite standard conservative therapy were begun on biological agents.The main outcomes were patient and physician global assessment of treatment response and medication side effects in patients with rheumatological disorders treated with biological …