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Lung Tissue Multilayer Network Analysis Uncovers The Molecular Heterogeneity Of Chronic Obstructive Pulmonary Disease, Joselyn Rojas-Quintero, Guillaume Noell, Sandra Casas-Recasens, Alen Faiz, Philip Hansbro, Angela Guirao, Rosalba Lepore, Davide Cirillo, Alvar Agustí, Francesca Polverino, Alfonso Valencia, Rosa Faner Nov 2024

Lung Tissue Multilayer Network Analysis Uncovers The Molecular Heterogeneity Of Chronic Obstructive Pulmonary Disease, Joselyn Rojas-Quintero, Guillaume Noell, Sandra Casas-Recasens, Alen Faiz, Philip Hansbro, Angela Guirao, Rosalba Lepore, Davide Cirillo, Alvar Agustí, Francesca Polverino, Alfonso Valencia, Rosa Faner

Faculty, Staff and Students Publications

Rationale: Chronic obstructive pulmonary disease (COPD) is a heterogeneous condition. Objectives: We hypothesized that the unbiased integration of different COPD lung omics using a novel multilayer approach might unravel mechanisms associated with clinical characteristics.

Methods: We profiled mRNA, microRNA and methylome in lung tissue samples from 135 former smokers with COPD. For each omic (layer), we built a patient network on the basis of molecular similarity. The three networks were used to build a multilayer network, and optimization of multiplex modularity was used to identify patient communities across the three distinct layers. Uncovered communities were related to clinical features.

Measurements …


What Do Cancer Genetic Providers Want Us To Know About Variant Reclassification And Recontact That We Are Not Asking? A Thematic Analysis Of Open-Ended Survey Responses, Kerri Brown, Marisel Ponton, Elenita Davidson, Banu Arun, Robert J Volk, Susan K Peterson Nov 2024

What Do Cancer Genetic Providers Want Us To Know About Variant Reclassification And Recontact That We Are Not Asking? A Thematic Analysis Of Open-Ended Survey Responses, Kerri Brown, Marisel Ponton, Elenita Davidson, Banu Arun, Robert J Volk, Susan K Peterson

Faculty, Staff and Student Publications

BACKGROUND: Accurate variant classification and relaying reclassified results to patients is critical for hereditary cancer care delivery. Over a 5- to 10-year period, 6%-15% of variants undergo reclassification. As the frequency of reclassifications increases, the issue of whether, how, when, and which providers should recontact patients becomes important but remains contentious.

METHODS: The authors used inductive thematic analysis to analyze open-ended comments offered by oncologists and genetic counselors (GCs) from a large national survey.

RESULTS: Of the 634 oncologists and cancer GCs, 126 (20%) offered substantive free-text comments. Four thematic areas emerged: 1) ambiguity over professional responsibility to recontact, 2) …


Low-Molecular Weight Cyclin E Confers A Vulnerability To Pkmyt1 Inhibition In Triple-Negative Breast Cancer, Mi Li, Amriti R Lulla, Yan Wang, Spyros Tsavaschidis, Fuchenchu Wang, Tuyen D T Nguyen, Marc A Pina, Mei-Kuang Chen, Sofia Mastoraki, Asha S Multani, Natalie W Fowlkes, Aysegul Sahin, C Gary Marshall, Kelly K Hunt, Khandan Keyomarsi Nov 2024

Low-Molecular Weight Cyclin E Confers A Vulnerability To Pkmyt1 Inhibition In Triple-Negative Breast Cancer, Mi Li, Amriti R Lulla, Yan Wang, Spyros Tsavaschidis, Fuchenchu Wang, Tuyen D T Nguyen, Marc A Pina, Mei-Kuang Chen, Sofia Mastoraki, Asha S Multani, Natalie W Fowlkes, Aysegul Sahin, C Gary Marshall, Kelly K Hunt, Khandan Keyomarsi

Faculty, Staff and Student Publications

Cyclin E is a regulatory subunit of CDK2 that mediates S phase entry and progression. The cleavage of full-length cyclin E (FL-cycE) to low-molecular weight isoforms (LMW-E) dramatically alters substrate specificity, promoting G1-S cell cycle transition and accelerating mitotic exit. Approximately 70% of triple-negative breast cancers (TNBC) express LMW-E, which correlates with poor prognosis. PKMYT1 also plays an important role in mitosis by inhibiting CDK1 to block premature mitotic entry, suggesting it could be a therapeutic target in TNBC expressing LMW-E. In this study, analysis of tumor samples of patients with TNBC revealed that coexpression of LMW-E and PKMYT1-catalyzed CDK1 …


Epigenome Reprogramming Through H3k27 And H3k4 Trimethylation As A Resistance Mechanism To Dna Methylation Inhibition In Brafv600e-Mutated Colorectal Cancer, Hey Min Lee, Ajay Kumar Saw, Van K Morris, Stefania Napolitano, Christopher Bristow, Micheal Peoples, Preeti Kanikarla Marie, Jonathan Schulz, Anand K Singh, Christopher Terranova, Oluwadara Coker, Abhinav Jain, Scott Kopetz, Kunal Rai Nov 2024

Epigenome Reprogramming Through H3k27 And H3k4 Trimethylation As A Resistance Mechanism To Dna Methylation Inhibition In Brafv600e-Mutated Colorectal Cancer, Hey Min Lee, Ajay Kumar Saw, Van K Morris, Stefania Napolitano, Christopher Bristow, Micheal Peoples, Preeti Kanikarla Marie, Jonathan Schulz, Anand K Singh, Christopher Terranova, Oluwadara Coker, Abhinav Jain, Scott Kopetz, Kunal Rai

Faculty, Staff and Student Publications

Purpose: BRAFV600E-mutated colorectal cancer exhibits a strong correlation with DNA hypermethylation, suggesting that this subgroup of tumors presents unique epigenomic phenotypes. Nonetheless, 5-azacitidine, which inhibits DNA methyltransferase activity, is not efficacious in BRAFV600E colorectal cancer in vivo.

Experimental design: We randomized and treated mice implanted with patient-derived tumor xenografts harboring BRAFV600E mutation with control, 5-azacitidine, vemurafenib (BRAF inhibitor), or the combination. Comprehensive epigenomic profiling was conducted on control and 5-azacitidine-treated tumor samples, including DNA methylation, histone modifications, chromatin accessibility, and gene expression. Combinations of epigenetic agents were explored in preclinical BRAFV600E colorectal cancer models.

Results: A profound reduction of DNA …


Driving Healthy Behaviors Through Social Support: The Role Of Co-Responsibility In Weight Loss And Maintenance, Melanie Knufinke-Meyfroyt, Carlo Lancia, Yentl Lodewijks, Simon Nienhuijs, Eva Deckers Nov 2024

Driving Healthy Behaviors Through Social Support: The Role Of Co-Responsibility In Weight Loss And Maintenance, Melanie Knufinke-Meyfroyt, Carlo Lancia, Yentl Lodewijks, Simon Nienhuijs, Eva Deckers

Patient Experience Journal

Objective: The effectiveness of out of hospital lifestyle interventions in healthcare is likely co-dependent on social support from involved one's. We sought to investigate the interrelationships between patient-partner Co-responsibility, Spousal Support, and Self-efficacy and the mechanisms through which they contribute to health behaviors and outcomes relevant to weight loss and maintenance. Methods: Co-responsibility, Spousal Support, self-efficacy, health outcomes and health behaviors like total weight loss, physical activity, OBESI-Q, and health satisfaction were assessed through a questionnaire among 868 individuals attempting to lose weight. Full and semi-partial correlations were used to understand the association between Co-responsibility, Spousal Support, Self-efficacy …


Conference Report: Review Of Clinical Implementation Of Advanced Quantitative Imaging Techniques For Personalized Radiotherapy, Yevgeniy Vinogradskiy, Houda Bahig, Nicholas Bucknell, Jeffrey Buchsbaum, Hui-Kuo George Shu Nov 2024

Conference Report: Review Of Clinical Implementation Of Advanced Quantitative Imaging Techniques For Personalized Radiotherapy, Yevgeniy Vinogradskiy, Houda Bahig, Nicholas Bucknell, Jeffrey Buchsbaum, Hui-Kuo George Shu

Department of Radiation Oncology Faculty Papers

The topic of quantitative imaging in radiation therapy was presented as a "Masterclass" at the 2023 annual meeting of the American Society of Radiation Oncology (ASTRO). Dual-energy computed tomography (CT) and single-positron computed tomography were reviewed in detail as the first portion of the meeting session, with data showing utility in many aspects of radiation oncology including treatment planning and dose response. Positron emission tomography/CT scans evaluating the functional volume of lung tissue so as to provide optimal avoidance of healthy lungs were presented second. Advanced brain imaging was then discussed in the context of different forms of magnetic resonance …


A Novel Machine Learning Model To Predict Revision Acl Reconstruction Failure In The Mars Cohort, Kinjal Vasavada, Vrinda Vasavada, Jay Moran, Sai Devana, Changhee Lee, Sharon L. Hame, Laith M. Jazrawi, Orrin H. Sherman, Laura J. Huston, Amanda K. Haas, Christina R. Allen, Daniel E. Cooper, Thomas M. Deberardino, Kurt P. Spindler, Michael J. Stuart, Annunziato Ned Amendola, Christopher C. Annunziata, Robert A. Arciero, Bernard R. Bach, Champ L. Baker, Arthur R. Bartolozzi, Keith M. Baumgarten, Jeffrey H. Berg, Geoffrey A. Bernas, Stephen F. Brockmeier, Robert H. Brophy, Charles A. Bush-Joseph, J. Brad Butler V, James L. Carey, James E. Carpenter, Brian J. Cole, Jonathan M. Cooper, Charles L. Cox, R. Alexander Creighton, Tal S. David, Warren R. Dunn, David C. Flanigan, Robert W. Frederick, Theodore J. Ganley, Charles J. Gatt, Steven R. Gecha, James Robert Giffin, Jo A. Hannafin, Norman Lindsay Harris, Keith S. Hechtman, Elliott B. Hershman, Rudolf G. Hoellrich, David C. Johnson, Timothy S. Johnson, Morgan H. Jones, Christopher C. Kaeding, Ganesh V. Kamath, Thomas E. Klootwyk, Bruce A. Levy, C. Benjamin Ma, G. Peter Maiers, Robert G. Marx, Matthew J. Matava, Gregory M. Mathien, David R. Mcallister, Eric C. Mccarty, Robert G. Mccormack, Bruce S. Miller, Carl W. Nissen, Daniel F. O'Neill, Brett D. Owens, Richard D. Parker, Mark L. Purnell, Arun J. Ramappa, Michael A. Rauh, Arthur C. Rettig, Jon K. Sekiya, Kevin G. Shea, James R. Slauterbeck, Matthew V. Smith, Jeffrey T. Spang, Steven J. Svoboda, Timothy N. Taft, Joachim J. Tenuta, Edwin M. Tingstad, Armando F. Vidal, Darius G. Viskontas, Richard A. White, James S. Williams, Michelle L. Wolcott, Brian R. Wolf, Rick W. Wright, James J. York Nov 2024

A Novel Machine Learning Model To Predict Revision Acl Reconstruction Failure In The Mars Cohort, Kinjal Vasavada, Vrinda Vasavada, Jay Moran, Sai Devana, Changhee Lee, Sharon L. Hame, Laith M. Jazrawi, Orrin H. Sherman, Laura J. Huston, Amanda K. Haas, Christina R. Allen, Daniel E. Cooper, Thomas M. Deberardino, Kurt P. Spindler, Michael J. Stuart, Annunziato Ned Amendola, Christopher C. Annunziata, Robert A. Arciero, Bernard R. Bach, Champ L. Baker, Arthur R. Bartolozzi, Keith M. Baumgarten, Jeffrey H. Berg, Geoffrey A. Bernas, Stephen F. Brockmeier, Robert H. Brophy, Charles A. Bush-Joseph, J. Brad Butler V, James L. Carey, James E. Carpenter, Brian J. Cole, Jonathan M. Cooper, Charles L. Cox, R. Alexander Creighton, Tal S. David, Warren R. Dunn, David C. Flanigan, Robert W. Frederick, Theodore J. Ganley, Charles J. Gatt, Steven R. Gecha, James Robert Giffin, Jo A. Hannafin, Norman Lindsay Harris, Keith S. Hechtman, Elliott B. Hershman, Rudolf G. Hoellrich, David C. Johnson, Timothy S. Johnson, Morgan H. Jones, Christopher C. Kaeding, Ganesh V. Kamath, Thomas E. Klootwyk, Bruce A. Levy, C. Benjamin Ma, G. Peter Maiers, Robert G. Marx, Matthew J. Matava, Gregory M. Mathien, David R. Mcallister, Eric C. Mccarty, Robert G. Mccormack, Bruce S. Miller, Carl W. Nissen, Daniel F. O'Neill, Brett D. Owens, Richard D. Parker, Mark L. Purnell, Arun J. Ramappa, Michael A. Rauh, Arthur C. Rettig, Jon K. Sekiya, Kevin G. Shea, James R. Slauterbeck, Matthew V. Smith, Jeffrey T. Spang, Steven J. Svoboda, Timothy N. Taft, Joachim J. Tenuta, Edwin M. Tingstad, Armando F. Vidal, Darius G. Viskontas, Richard A. White, James S. Williams, Michelle L. Wolcott, Brian R. Wolf, Rick W. Wright, James J. York

Rothman Institute Papers

BACKGROUND: As machine learning becomes increasingly utilized in orthopaedic clinical research, the application of machine learning methodology to cohort data from the Multicenter ACL Revision Study (MARS) presents a valuable opportunity to translate data into patient-specific insights.

PURPOSE: To apply novel machine learning methodology to MARS cohort data to determine a predictive model of revision anterior cruciate ligament reconstruction (rACLR) graft failure and features most predictive of failure.

STUDY DESIGN: Cohort study; Level of evidence, 3.

METHODS: The authors prospectively recruited patients undergoing rACLR from the MARS cohort and obtained preoperative radiographs, surgeon-reported intraoperative findings, and 2- and 6-year follow-up …


Structural Proteomics Defines A Sequential Priming Mechanism For The Progesterone Receptor, Josephine Ferreon, Michael Suess, Antrix Jain, Anna Malovannaya, Roberto Vera Alvarez, Bruce Pascal, Raj Kumar, Dean Edwards Nov 2024

Structural Proteomics Defines A Sequential Priming Mechanism For The Progesterone Receptor, Josephine Ferreon, Michael Suess, Antrix Jain, Anna Malovannaya, Roberto Vera Alvarez, Bruce Pascal, Raj Kumar, Dean Edwards

Faculty, Staff and Students Publications

The progesterone receptor (PR) is a steroid-responsive nuclear receptor with two isoforms: PR-A and PR-B. Disruption of PR-A:PR-B signaling is associated with breast cancer through interactions with oncogenic co-regulatory proteins (CoRs). However, molecular details of isoform-specific PR-CoR interactions remain poorly understood. Using structural mass spectrometry, we investigate the sequential binding mechanism of purified full-length PR and intact CoRs, steroid receptor coactivator 3 (SRC3) and p300, as complexes on target DNA. Our findings reveal selective CoR NR-box binding by PR and unique interaction surfaces between PR and CoRs during complex assembly, providing a structural basis for CoR sequential binding on PR. …


Phosphoglycerate Dehydrogenase Regulated By The Mitogen-Activated Protein Kinase Pathway Is An Actionable Vulnerability In Cutaneous Melanoma, Neel Jasani Nov 2024

Phosphoglycerate Dehydrogenase Regulated By The Mitogen-Activated Protein Kinase Pathway Is An Actionable Vulnerability In Cutaneous Melanoma, Neel Jasani

USF Tampa Graduate Theses and Dissertations

Metabolic alterations play a critical role in shaping tumor growth and development. Many metabolic enzymes are shown to play an important role in different aspects of tumor development, growth, and metastasis. One such enzyme that we are investigating in this project is the Phosphoglycerate Dehydrogenase (PHGDH). The PHGDH gene, encoding the rate-limiting enzyme of the serine synthesis pathway, is located at chromosome locus 1p12 and frequently amplified in melanoma. PHGDH is required for the proliferation of melanoma cells with chromosome 1p12 amplification. However, the role of PHGDH in chromosome 1p12 non-amplified melanoma is poorly understood. In this project, we sought …


Hypothermia In Patients With Traumatic Injuries: An Integrative Review, Andrew P. Gribble, David J. Saucedo Nov 2024

Hypothermia In Patients With Traumatic Injuries: An Integrative Review, Andrew P. Gribble, David J. Saucedo

Master's Projects

Abstract

Background: An estimated 30-50% of severely injured patients with traumatic injuries will experience hypothermia. As a result of hypothermia, several clinical manifestations such as impaired coagulation, dissociation of the oxygen curve, cardiac arrhythmias, reduced cardiac output and death. Little evidence has been published promoting specific patient re-warming protocols and the best rewarming methods, active versus passive. Few studies have focused on the pre-hospitalization treatment for hypothermia and the overall effectiveness of interventions to mitigate hypothermia to reduce morbidity and mortality. Given this knowledge, the aim of this integrative review (IR) is to research and evaluate current practices regarding hypothermia …


Dna Methylation Classifier To Diagnose Pancreatic Ductal Adenocarcinoma Metastases From Different Anatomical Sites, Teodor G Calina, Eilís Perez, Elena Grafenhorst, Jamal Benhamida, Simon Schallenberg, Ines Koch, Baoqing Chen, Jana Ihlow, Stephanie Roessler, Benjamin Goeppert, Bruno Sinn, Marcus Bahra, George A Calin, Eliane T Taube, Uwe Pelzer, Christopher C M Neumann, David Horst, Erik Knutsen, David Capper, Mihnea P Dragomir Nov 2024

Dna Methylation Classifier To Diagnose Pancreatic Ductal Adenocarcinoma Metastases From Different Anatomical Sites, Teodor G Calina, Eilís Perez, Elena Grafenhorst, Jamal Benhamida, Simon Schallenberg, Ines Koch, Baoqing Chen, Jana Ihlow, Stephanie Roessler, Benjamin Goeppert, Bruno Sinn, Marcus Bahra, George A Calin, Eliane T Taube, Uwe Pelzer, Christopher C M Neumann, David Horst, Erik Knutsen, David Capper, Mihnea P Dragomir

Faculty, Staff and Student Publications

Background: We have recently constructed a DNA methylation classifier that can discriminate between pancreatic ductal adenocarcinoma (PAAD) liver metastasis and intrahepatic cholangiocarcinoma (iCCA) with high accuracy (PAAD-iCCA-Classifier). PAAD is one of the leading causes of cancer of unknown primary and diagnosis is based on exclusion of other malignancies. Therefore, our focus was to investigate whether the PAAD-iCCA-Classifier can be used to diagnose PAAD metastases from other sites.

Methods: For this scope, the anomaly detection filter of the initial classifier was expanded by 8 additional mimicker carcinomas, amounting to a total of 10 carcinomas in the negative class. We validated the …


Modeling Antisense Oligonucleotide Therapy In Mecp2 Duplication Syndrome Human Ipsc-Derived Neurons Reveals Gene Expression Programs Responsive To Mecp2 Levels, Harini P Tirumala, Ying-Wooi Wan, Caroline L Harrop, Jesse D Bengtsson, Claudia M B Carvalho, Davut Pehlivan, Bernhard Suter, Jeffrey L Neul, Zhandong Liu, Paymaan Jafar-Nejad, Frank Rigo, Huda Y Zoghbi Nov 2024

Modeling Antisense Oligonucleotide Therapy In Mecp2 Duplication Syndrome Human Ipsc-Derived Neurons Reveals Gene Expression Programs Responsive To Mecp2 Levels, Harini P Tirumala, Ying-Wooi Wan, Caroline L Harrop, Jesse D Bengtsson, Claudia M B Carvalho, Davut Pehlivan, Bernhard Suter, Jeffrey L Neul, Zhandong Liu, Paymaan Jafar-Nejad, Frank Rigo, Huda Y Zoghbi

Faculty, Staff and Students Publications

Genomic copy-number variations (CNVs) that can cause neurodevelopmental disorders often encompass many genes, which complicates our understanding of how individual genes within a CNV contribute to pathology. MECP2 duplication syndrome (MDS or MRXSL in OMIM; OMIM#300260) is one such CNV disorder caused by duplications spanning methyl CpG-binding protein 2 (MECP2) and other genes on Xq28. Using an antisense oligonucleotide (ASO) to normalize MECP2 dosage is sufficient to rescue abnormal neurological phenotypes in mouse models overexpressing MECP2 alone, implicating the importance of increased MECP2 dosage within CNVs of Xq28. However, because MDS CNVs span MECP2 and additional genes, we generated human …


Daily Diagnostic Quality Computed Tomography-On-Rails (Ctor) Image Guidance For Abdominal Stereotactic Body Radiation Therapy (Sbrt), Rachael M Martin-Paulpeter, P James Jensen, Luis A Perles, Gabriel O Sawakuchi, Prajnan Das, Albert C Koong, Joshua S Niedzielski, Sam Beddar Nov 2024

Daily Diagnostic Quality Computed Tomography-On-Rails (Ctor) Image Guidance For Abdominal Stereotactic Body Radiation Therapy (Sbrt), Rachael M Martin-Paulpeter, P James Jensen, Luis A Perles, Gabriel O Sawakuchi, Prajnan Das, Albert C Koong, Joshua S Niedzielski, Sam Beddar

Faculty, Staff and Student Publications

BACKGROUND/OBJECTIVES: Stereotactic body radiation therapy (SBRT) for abdominal targets faces a variety of challenges, including motion caused by the respiration and digestion and a relatively poor level of contrast between the tumor and the surrounding tissues. Breath-hold treatments with computed tomography-on-rails (CTOR) image guidance is one way of addressing these challenges, allowing for both the tumor and normal tissues to be well-visualized. Using isodose lines (IDLs) from CT simulations as a guide, the anatomical information can be used to shift the alignment or trigger a replan, such that normal tissues receive acceptable doses of radiation.

METHODS: This study aims to …


Gender Representation Of Presenters At American Academy Of Ophthalmology Conferences From 2004-2019, Eleanor Burton, Chase Paulson, Ayesha Patil, Ruby Garcia, Sydni Johnson, Josie White, Adriana Rush, Devin Eddington, Jeff H. Pettey, Rachel G. Simpson Nov 2024

Gender Representation Of Presenters At American Academy Of Ophthalmology Conferences From 2004-2019, Eleanor Burton, Chase Paulson, Ayesha Patil, Ruby Garcia, Sydni Johnson, Josie White, Adriana Rush, Devin Eddington, Jeff H. Pettey, Rachel G. Simpson

Journal of Academic Ophthalmology

Importance: Gender equity is an important topic in medicine and accurate trends are essential to evaluate historical, current, and future trends.

Objective: To describe changes in gender representation at American Academy of Ophthalmology (AAO) meetings from 2004 to 2019.

Participants: Presenters at the American Academy of Ophthalmology meetings from 2004 to 2019.

Design & Setting: This is a retrospective cross-sectional study. Data was extracted using AAO annual and subspecialty meeting archives for every third year between 2004 and 2019. Sessions were stratified by category and subspecialty. Poster sessions were excluded. Gender was considered binary and determined …


Community Outreach Vision Screenings With Student-Led Eye Health Education Improves Student Eye Health Knowledge And Ophthalmic Health Disparities Awareness, Tannia M. Rodriguez, Karim Dirani, Samantha M. Arsenault, Ryan Lee Freedman, John-Michael Guest, Kathleen George, Collin Richards, Leo Hall, Mark S. Juzych, Anju Goyal Nov 2024

Community Outreach Vision Screenings With Student-Led Eye Health Education Improves Student Eye Health Knowledge And Ophthalmic Health Disparities Awareness, Tannia M. Rodriguez, Karim Dirani, Samantha M. Arsenault, Ryan Lee Freedman, John-Michael Guest, Kathleen George, Collin Richards, Leo Hall, Mark S. Juzych, Anju Goyal

Journal of Academic Ophthalmology

BACKGROUND: The high prevalence of vision impairment and discordant lack of eye care utilization makes it essential to develop effective avenues to educate the future physician work force regarding basic eye health knowledge and ophthalmic health disparities. The public is often not aware that blinding eye diseases can begin asymptomatically. It is important for medical students to understand basic eye health knowledge, such as blinding eye diseases can begin asymptomatically. The purpose of this study was to assess the impact of an eye health knowledge 5-Point Teaching Intervention (5PTI) and structured patient intake form on student eye health knowledge and …


Commentary: Obstructive Sleep Apnea In The Hemodialysis Population: Are Clinicians Putting Existing Scientific Evidence Into Practice?, Aleena Jamal, Som Singh, Fawad Qureshi Nov 2024

Commentary: Obstructive Sleep Apnea In The Hemodialysis Population: Are Clinicians Putting Existing Scientific Evidence Into Practice?, Aleena Jamal, Som Singh, Fawad Qureshi

SKMC Student Presentations and Publications

No abstract provided.


Large-Scale Application Of Clingen-Insight Apc-Specific Acmg/Amp Variant Classification Criteria Leads To Substantial Reduction In Vus, Xuemei Shi, Elisabet Ognedal, Valeria Vasta, Thomas V O Hansen, Marta Pineda, Deborah Ritter, Johan De Dunnen, Emadeldin Hassanin, Wencong Lyman Lin, Ester Borras, Karl Krahn, Margareta Nordling, Alexandra Martins, Khalid Mahmood, Emily Nadeau, Victoria Beshay, Carli Tops, Maurizio Genuardi, Tina Pesaran, Ian M Frayling, Gabriel Capellá, Andrew Latchford, Sean V Tavtigian, Carlo Maj, Sharon E Plon, Marc S Greenblatt, Finlay A Macrae, Isabel Spier, Stefan Aretz Nov 2024

Large-Scale Application Of Clingen-Insight Apc-Specific Acmg/Amp Variant Classification Criteria Leads To Substantial Reduction In Vus, Xuemei Shi, Elisabet Ognedal, Valeria Vasta, Thomas V O Hansen, Marta Pineda, Deborah Ritter, Johan De Dunnen, Emadeldin Hassanin, Wencong Lyman Lin, Ester Borras, Karl Krahn, Margareta Nordling, Alexandra Martins, Khalid Mahmood, Emily Nadeau, Victoria Beshay, Carli Tops, Maurizio Genuardi, Tina Pesaran, Ian M Frayling, Gabriel Capellá, Andrew Latchford, Sean V Tavtigian, Carlo Maj, Sharon E Plon, Marc S Greenblatt, Finlay A Macrae, Isabel Spier, Stefan Aretz

Faculty, Staff and Students Publications

Pathogenic constitutional APC variants underlie familial adenomatous polyposis, the most common hereditary gastrointestinal polyposis syndrome. To improve variant classification and resolve the interpretative challenges of variants of uncertain significance (VUSs), APC-specific variant classification criteria were developed by the ClinGen-InSiGHT Hereditary Colorectal Cancer/Polyposis Variant Curation Expert Panel (VCEP) based on the criteria of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology (ACMG/AMP). A streamlined algorithm using the APC-specific criteria was developed and applied to assess all APC variants in ClinVar and the International Society for Gastrointestinal Hereditary Tumours (InSiGHT) international reference APC Leiden Open Variation …


Probabilistic Presurgical Language Fmri Atlas Of Patients With Brain Tumors, Jian Ming Teo, Vinodh A Kumar, Jina Lee, Rami W Eldaya, Ping Hou, Kyle R Noll, Sherise D Ferguson, Sujit S Prabhu, Max Wintermark, Ho-Ling Liu Nov 2024

Probabilistic Presurgical Language Fmri Atlas Of Patients With Brain Tumors, Jian Ming Teo, Vinodh A Kumar, Jina Lee, Rami W Eldaya, Ping Hou, Kyle R Noll, Sherise D Ferguson, Sujit S Prabhu, Max Wintermark, Ho-Ling Liu

Faculty, Staff and Student Publications

Background and purpose: Patients with brain tumors have high intersubject variation in putative language regions, which may limit the utility of straightforward application of healthy subject brain atlases in clinical scenarios. The purpose of this study was to develop a probabilistic functional brain atlas that consolidates language functional activations of sentence completion and Silent Word Generation language paradigms using a large sample of patients with brain tumors.

Materials and methods: The atlas was developed using retrospectively collected fMRI data from patients with brain tumors who underwent their first standard-of-care presurgical language fMRI scan at our institution between July 18, 2015, …


Estimating The Number Of Polygenic Diseases Among Six Mutually Exclusive Entities Of Non-Tumors And Cancer, C I Edvard Smith, Jan A Burger, Rula Zain Nov 2024

Estimating The Number Of Polygenic Diseases Among Six Mutually Exclusive Entities Of Non-Tumors And Cancer, C I Edvard Smith, Jan A Burger, Rula Zain

Faculty, Staff and Student Publications

In the era of precision medicine with increasing amounts of sequenced cancer and non-cancer genomes of different ancestries, we here enumerate the resulting polygenic disease entities. Based on the cell number status, we first identified six fundamental types of polygenic illnesses, five of which are non-cancerous. Like complex, non-tumor disorders, neoplasms normally carry alterations in multiple genes, including in 'Drivers' and 'Passengers'. However, tumors also lack certain genetic alterations/epigenetic changes, recently named 'Goners', which are toxic for the neoplasm and potentially constitute therapeutic targets. Drivers are considered essential for malignant transformation, whereas environmental influences vary considerably among both types of …


Endovascular Treatment Of Patients With Acute Ischemic Stroke With Tandem Lesions Presenting With Low Alberta Stroke Program Early Computed Tomography Score, Milagros Galecio-Castillo, Mudassir Farooqui, Waldo R. Guerrero, Marc Ribo, Ameer E. Hassan, Mouhammad A. Jumaa, Afshin A. Divani, Michael G. Abraham, Nils Petersen, Johanna T. Fifi Nov 2024

Endovascular Treatment Of Patients With Acute Ischemic Stroke With Tandem Lesions Presenting With Low Alberta Stroke Program Early Computed Tomography Score, Milagros Galecio-Castillo, Mudassir Farooqui, Waldo R. Guerrero, Marc Ribo, Ameer E. Hassan, Mouhammad A. Jumaa, Afshin A. Divani, Michael G. Abraham, Nils Petersen, Johanna T. Fifi

School of Medicine Publications

Background: Recent trials confirmed the efficacy and safety of endovascular thrombectomy in patients with low Alberta Stroke Program Early Computed Tomography Score (ASPECTS); however, evidence in tandem lesions is limited. This study evaluates endovascular thrombectomy safety and efficacy in patients with acute large-vessel occlusion with tandem lesions, stratified by baseline ASPECTS.

Methods and results: We conducted a retrospective analysis of data from 16 centers. Inclusion criteria included the following: age ≥18 years, anterior circulation tandem lesions, endovascular thrombectomy onset, and ≥70% internal carotid artery stenosis/occlusion. Patients were categorized into low (0-5) and high (6-10) ASPECTS. Inverse probability of treatment weighting …


Identifying Subsets Of Cancer Patients With An Increased Risk Of Developing Cutaneous Melanoma: A Surveillance, Epidemiology, And End Results-Based Analysis, Thomas Z. Rohan, Jenna L. Mandel, Henry Y. Yang, Lauren Banner, Daniel Joffe, Rachel Zachian, Jaanvi Mehta, Safiyyah Bhatti, Tingting Zhan, Neda Nikbakht Nov 2024

Identifying Subsets Of Cancer Patients With An Increased Risk Of Developing Cutaneous Melanoma: A Surveillance, Epidemiology, And End Results-Based Analysis, Thomas Z. Rohan, Jenna L. Mandel, Henry Y. Yang, Lauren Banner, Daniel Joffe, Rachel Zachian, Jaanvi Mehta, Safiyyah Bhatti, Tingting Zhan, Neda Nikbakht

SKMC Student Presentations and Publications

Cancer survivors have an increased risk of developing second primary malignancies. We aimed to identify whether certain cancers lead to an increased risk of developing melanoma among cancer survivors. We evaluated the risk of developing cutaneous melanoma after the 20 most common cancers in the United States through the Surveillance, Epidemiology, and End Results database. We identified 9 primary cancers linked to increased risk of developing a subsequent cutaneous melanoma: cutaneous melanoma (standardized incidence ratio [SIR] = 9.65), leukemia (SIR = 1.76), non-Hodgkin lymphoma (SIR = 1.33), thyroid cancer (SIR = 1.32), brain and nervous system cancer (SIR = 1.31), …


Skn-1 Activation During Infection Of Caenorhabditis Elegans Requires Cdc-48 And Endoplasmic Reticulum Proteostasis, Carolaing Gabaldón, Ozgur Karakuzu, Danielle A Garsin Nov 2024

Skn-1 Activation During Infection Of Caenorhabditis Elegans Requires Cdc-48 And Endoplasmic Reticulum Proteostasis, Carolaing Gabaldón, Ozgur Karakuzu, Danielle A Garsin

Faculty, Staff and Student Publications

During challenge of Caenorhabditis elegans with human bacterial pathogens such as Pseudomonas aeruginosa and Enterococcus faecalis, the elicited host response can be damaging if not properly controlled. The activation of Nrf (nuclear factor erythroid-related factor)/CNC (Cap-n-collar) transcriptional regulators modulates the response by upregulating genes that neutralize damaging molecules and promote repair processes. Activation of the C. elegans Nrf ortholog, SKN-1, is tightly controlled by a myriad of regulatory mechanisms, but a central feature is an activating phosphorylation accomplished by the p38 mitogen-activated kinase (MAPK) cascade. In this work, loss of CDC-48, an AAA+ ATPase, was observed to severely compromise SKN-1 …


Trends In Transcatheter Versus Surgical Aortic Valve Replacement Outcomes In Patients With Low-Surgical Risk: A Systematic Review And Meta-Analysis Of Randomized Trials, Negin Sadat Hosseini Mohammadi, Hamidreza Soleimani, Arman Soltani Moghadam, Elaheh Karimi, Yaser Sattar, Yaser Jenab, Mehdi Mehrani, Alimohammad Hajizeinali, Mina Iskander, Mehrshad Fathian Sabet, Negar Salehi, Karim Al-Azizi, Diaa Hakim, Mahboob Alam, Kaveh Hosseini Nov 2024

Trends In Transcatheter Versus Surgical Aortic Valve Replacement Outcomes In Patients With Low-Surgical Risk: A Systematic Review And Meta-Analysis Of Randomized Trials, Negin Sadat Hosseini Mohammadi, Hamidreza Soleimani, Arman Soltani Moghadam, Elaheh Karimi, Yaser Sattar, Yaser Jenab, Mehdi Mehrani, Alimohammad Hajizeinali, Mina Iskander, Mehrshad Fathian Sabet, Negar Salehi, Karim Al-Azizi, Diaa Hakim, Mahboob Alam, Kaveh Hosseini

Faculty, Staff and Students Publications

Background: Limited data exist on long-term outcomes after transcatheter aortic valve replacement (TAVR) and surgical aortic valve replacement (SAVR). This meta-analysis aims to elucidate outcome trends following TAVR versus SAVR in patients with severe aortic stenosis and low-surgical risk.

Methods and results: A systematic search was conducted in PubMed, Embase, Scopus, and the Cochrane Library databases from inception until May 2024, to identify studies comparing TAVR versus SAVR in patients with low-surgical risk (Society of Thoracic Surgeons predicted risk of mortality score < 4%). The primary outcome was all-cause mortality. Secondary outcomes included cardiovascular mortality, stroke, disabling stroke, rehospitalization, myocardial infarction, aortic valve reintervention, permanent pacemaker implantation, and new-onset atrial fibrillation. Binary random-effects models were used to compare the risk of each outcome across various follow-up intervals and the risk of bias was assessed using the Cochrane Collaboration's Risk of Bias-2 tool. The meta-analysis included 6 randomized trials including 4682 patients. TAVR was associated with a lower risk of all-cause mortality than SAVR in the 30-day (hazard ratio [HR: 0.45] [95% CI: 0.26-0.77], I2: 0%) and 30-day to 1-year (HR: 0.55 [95% CI: 0.37-0.81], I2: 16%) follow-ups. However, the …


Activation Of A Gpcr, Orl1 Receptor: A Novel Therapy To Prevent Heart Failure Progression, Theodore G Wensel, Todd K Rosengart, Megumi Mathison Nov 2024

Activation Of A Gpcr, Orl1 Receptor: A Novel Therapy To Prevent Heart Failure Progression, Theodore G Wensel, Todd K Rosengart, Megumi Mathison

Faculty, Staff and Students Publications

The number of ischemic heart failure (HF) patients is growing dramatically worldwide. However, there are at present no preventive treatments for HF. Our previous study showed that Gata4 overexpression improved cardiac function after myocardial infarction in rat hearts. We also found that Gata4 overexpression significantly increased the expression of a Pnoc gene, an endogenous ligand for the cell membrane receptor ORL1. We hypothesized that the activation of the ORL1 receptor would suppress HF in a rat ischemic heart model. Adult Sprague Dawley rats (8 weeks old, six males and six females) underwent left anterior descending coronary artery ligation. Three weeks …


Mitral Annular Disjunction In Heritable Thoracic Aortic Disease: Insights From The Montalcino Aortic Consortium, Kishan L Asokan, Jennifer R Landes, Wannes Renders, Laura Muiño Mosquera, Julie De Backer, Anji T Yetman, Arturo Evangelista, Richmond Jeremy, Edward G Jones, Shaine Morris, Tam Doan, Maral Ouzonian, Alan Braverman, Guillaume Jondeau, Olivier Milleron, Dianna M Milewicz, Siddharth K Prakash Nov 2024

Mitral Annular Disjunction In Heritable Thoracic Aortic Disease: Insights From The Montalcino Aortic Consortium, Kishan L Asokan, Jennifer R Landes, Wannes Renders, Laura Muiño Mosquera, Julie De Backer, Anji T Yetman, Arturo Evangelista, Richmond Jeremy, Edward G Jones, Shaine Morris, Tam Doan, Maral Ouzonian, Alan Braverman, Guillaume Jondeau, Olivier Milleron, Dianna M Milewicz, Siddharth K Prakash

Faculty, Staff and Student Publications

Background: Mitral annular disjunction (MAD), posterior displacement of the mitral valve leaflet hinge point, predisposes to arrhythmias or sudden cardiac death. We evaluated the burden of MAD, mitral valve prolapse (MVP), and mitral regurgitation (MR) by heritable thoracic aortic disease gene in a cross-sectional analysis of 2014-2023 data in the Montalcino Aortic Consortium registry.

Methods and results: MAD was determined by direct measurement of echocardiographic images. MR and MVP were defined according to current clinical guidelines. Associations were evaluated using χ2 or Fisher exact tests. MR and MVP were enriched in Montalcino Aortic Consortium participants (672) with pathogenic variants (PV) …


How Did Dat Happen? A Coombs Negative Delayed Hemolytic Transfusion Reaction In A Patient With Myelodysplastic Syndrome: A Case Report, Aniket Vijay Rao Dr, Aditya Sanjeevi, Daniel Jose Idoate, Nagesh Jadhav, Basil Verghese, Himal Kharel Nov 2024

How Did Dat Happen? A Coombs Negative Delayed Hemolytic Transfusion Reaction In A Patient With Myelodysplastic Syndrome: A Case Report, Aniket Vijay Rao Dr, Aditya Sanjeevi, Daniel Jose Idoate, Nagesh Jadhav, Basil Verghese, Himal Kharel

Advances in Clinical Medical Research and Healthcare Delivery

Delayed hemolytic transfusion reactions (DHTRs) present significant challenges in diagnosis and management despite advancements in pre-transfusion testing. We report a case of a 76-year-old female with myelodysplastic syndrome (MDS) who developed severe hemolytic anemia following a seemingly compatible blood transfusion and appropriate pretransfusion testing. Evaluation revealed characteristics consistent with DHTR. Diagnostic uncertainty arose due to a negative Direct Antiglobulin Test (DAT) in the setting of a concomitant Vitamin B-12 deficiency. She was supported with prednisone and B12 supplementation. We discuss challenges in diagnosis, including the limitation of DAT, and propose strategies for comprehensive antibody identification. The case underscores the importance …


Recurrent Deep Vein Thrombosis In May Thurner Syndrome Precipitated By Heparin Induced Thrombocytopenia: A Case Report And Review Of Literature, Abhishek Bhandari, Chengu Niu Nov 2024

Recurrent Deep Vein Thrombosis In May Thurner Syndrome Precipitated By Heparin Induced Thrombocytopenia: A Case Report And Review Of Literature, Abhishek Bhandari, Chengu Niu

Advances in Clinical Medical Research and Healthcare Delivery

May Thurner Syndrome involves the extrinsic compression of the left common iliac vein by the right common iliac artery, which predisposes to venous thrombosis. This case report and review of literature details a complex instance of recurrent Deep Vein Thrombosis (DVT) in a 58-year-old female patient with May Thurner Syndrome (MTS), exacerbated by Heparin-Induced Thrombocytopenia (HIT). The patient, post Coronary Artery Bypass Graft surgery, developed leg symptoms leading to the discovery of an extensive DVT from the calf veins to the external iliac vein. She was initially treated with heparin, which was switched to bivalirudin following a significant drop in …


Prevalence Of Serious Diagnoses And Disposition Among Older Adults Presenting With A Chief Complaint Of Constipation, A Retrospective Repeated Cross-Sectional Study, Ari B. Friedman, Michael N. Adjei-Poku, Rachel Gonzales, Rachel Kelz, Rachel R. Wu, Anne R. Cappola Nov 2024

Prevalence Of Serious Diagnoses And Disposition Among Older Adults Presenting With A Chief Complaint Of Constipation, A Retrospective Repeated Cross-Sectional Study, Ari B. Friedman, Michael N. Adjei-Poku, Rachel Gonzales, Rachel Kelz, Rachel R. Wu, Anne R. Cappola

Journal of Geriatric Emergency Medicine

A chief complaint of “constipation” in the emergency department (ED) is generally considered low-risk, and potentially suitable for lower acuity care. However, it may also indicate abdominal pain perceived as lower severity by triage staff, despite being relatively high-risk. We hypothesized that ED visits for constipation in older adults would more frequently result in the diagnosis of serious, treatable conditions compared to younger adults. We analyzed data from the National Hospital Ambulatory Medical Care Survey (NHAMCS) over an 8-year period (2013-2020). Older adults with constipation were more likely to be non-Hispanic White. Among adults with constipation, 25.6% (95% CI: 22.8-28.4) …


Health Outcomes Reported By Healthcare Providers And Clients Of A Community-Based Medically Tailored Meal Program, Jessica M. Sautter, Jule Anne Henstenburg, Adrian Glass Crafford, Ian Rowe-Nicholls, Victor S. Diaz, Kaitlyn Ann Bartholomew, Julia S. Evans, Maria R. Johnson, Jeffrey Zhou, Deeksha Ajeya Nov 2024

Health Outcomes Reported By Healthcare Providers And Clients Of A Community-Based Medically Tailored Meal Program, Jessica M. Sautter, Jule Anne Henstenburg, Adrian Glass Crafford, Ian Rowe-Nicholls, Victor S. Diaz, Kaitlyn Ann Bartholomew, Julia S. Evans, Maria R. Johnson, Jeffrey Zhou, Deeksha Ajeya

Department of Family & Community Medicine Faculty Papers

BACKGROUND: Medically tailored meal (MTM) programs provide home-delivered meals to people living with serious illness and poor nutritional status. Client outcome studies have found evidence of decreased healthcare utilization and cost savings associated with MTM program participation, and inconclusive evidence of change in health measures. The purpose of this study was to use a novel observational framework to describe the client profile and change in health outcomes using routinely collected health and program data from a community-based MTM program at MANNA (Philadelphia, PA).

METHODS: Clients reported their self-rated health and experiences of food insecurity and malnutrition. Healthcare providers reported clients' …


Differences In Brain Volume In Military Service Members And Veterans After Blast-Related Mild Tbi: A Limbic-Cenc Study, Nicholas J Tustison, Mary R Newsome, Elizabeth S Hovenden, Brian B Avants, Jessica Gill, Sidney R Hinds, Kimbra Kenney, Hannah M Lindsey, Sarah L Martindale, Mary Jo Pugh, Randall S Scheibel, Pashtun-Poh Shahim, Robert Shih, James R Stone, Maya Troyanskaya, William C Walker, Kent Werner, Gerald E York, David X Cifu, David F Tate, Elisabeth A Wilde Nov 2024

Differences In Brain Volume In Military Service Members And Veterans After Blast-Related Mild Tbi: A Limbic-Cenc Study, Nicholas J Tustison, Mary R Newsome, Elizabeth S Hovenden, Brian B Avants, Jessica Gill, Sidney R Hinds, Kimbra Kenney, Hannah M Lindsey, Sarah L Martindale, Mary Jo Pugh, Randall S Scheibel, Pashtun-Poh Shahim, Robert Shih, James R Stone, Maya Troyanskaya, William C Walker, Kent Werner, Gerald E York, David X Cifu, David F Tate, Elisabeth A Wilde

Faculty, Staff and Students Publications

Importance: Blast-related mild traumatic brain injuries (TBIs), the "signature injury" of post-9/11 conflicts, are associated with clinically relevant, long-term cognitive, psychological, and behavioral dysfunction and disability; however, the underlying neural mechanisms remain unclear.

Objective: To investigate associations between a history of remote blast-related mild TBI and regional brain volume in a sample of US veterans and active duty service members.

Design, setting, and participants: Prospective cohort study of US veterans and active duty service members from the Long-Term Impact of Military-Relevant Brain Injury Consortium-Chronic Effects of Neurotrauma Consortium (LIMBIC-CENC), which enrolled more than 1500 participants at 5 sites used in …