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Articles 4471 - 4500 of 45413
Full-Text Articles in Entire DC Network
Optimizing Motion Management And Baseline Shifts In Magnetic Resonance-Guided Spine Stereotactic Body Radiation Therapy, Yao Ding, Travis C Salzillo, Debra N Yeboa, Martin C Tom, Zhiheng Wang, Parmeswaran Diagaradjane, Ergys Subashi, Jinzhong Yang, Todd Swanson, Thomas Beckham, Chenyang Wang, Amol J Ghia, Tina Briere, Jihong Wang, Fabienne Lathuilière, Sneha Cloake, Eun Young Han
Optimizing Motion Management And Baseline Shifts In Magnetic Resonance-Guided Spine Stereotactic Body Radiation Therapy, Yao Ding, Travis C Salzillo, Debra N Yeboa, Martin C Tom, Zhiheng Wang, Parmeswaran Diagaradjane, Ergys Subashi, Jinzhong Yang, Todd Swanson, Thomas Beckham, Chenyang Wang, Amol J Ghia, Tina Briere, Jihong Wang, Fabienne Lathuilière, Sneha Cloake, Eun Young Han
Faculty, Staff and Student Publications
BACKGROUND: Stereotactic body radiation therapy (SBRT) has proven effective in controlling spinal lesions with minimal toxicity, primarily due to its ability to limit spinal cord dose. Recent advances in MR-linac (MRL) technology offer superior spinal cord visualization and real-time gating, which can facilitate dose escalation in spinal tumor treatment while maintaining safety.
PURPOSE: This study aimed to optimize motion management for spine SBRT on an MRL by analyzing patient-specific motion dynamics and evaluating the most effective registration structures. We hypothesized that baseline shifts (BLS) would improve delivery efficiency while maintaining spinal cord dose constraints. The goal was to establish displacement …
A Brief History Of Circadian Time In The Heart, Martin E Young, Vanya Khanna, Mallory Metcalfe, Niruththaan Rameshkumar, Sarah Harington, Leo H Li, Janan Shoja Doost, Heinrich Taegtmeyer, Tami A Martino
A Brief History Of Circadian Time In The Heart, Martin E Young, Vanya Khanna, Mallory Metcalfe, Niruththaan Rameshkumar, Sarah Harington, Leo H Li, Janan Shoja Doost, Heinrich Taegtmeyer, Tami A Martino
Faculty, Staff and Student Publications
This review tracks the discovery of circadian biology in cardiovascular science, starting with early clinical observations of daily changes in heart rate, blood pressure, and cardiovascular events. These patterns suggested that time of day matters, but it was not until the past two decades that the mechanisms and knowledge translation of these rhythms were uncovered. We describe the heart's intrinsic circadian properties and importantly how this leads to regulation of cardiac gene and protein expression, neuroendocrine and vascular rhythms, metabolism, cellular electrophysiology, and cell signaling pathways. Next, we explore emerging themes, including the impact of circadian timing on ischemic injury, …
Trpc4 Regulates Limbic Behavior And Neuronal Development By Stabilizing Dendrite Branches Through Actomyosin-Driven Integrin Activation, Jaepyo Jeon, Travis I Moore, Insuk So, Marc Freichel, Veit Flockerzi, Lutz Birnbaumer, Michael X Zhu
Trpc4 Regulates Limbic Behavior And Neuronal Development By Stabilizing Dendrite Branches Through Actomyosin-Driven Integrin Activation, Jaepyo Jeon, Travis I Moore, Insuk So, Marc Freichel, Veit Flockerzi, Lutz Birnbaumer, Michael X Zhu
Faculty, Staff and Student Publications
Transient Receptor Potential Canonical 4 (TRPC4) channels have been implicated in multiple neurological functions, including anxiety and sociability. TRPC4 variants were also found in patients with autism. However, the contributions of TRPC4 to neurodevelopment remain undefined. Here, we show that neurobehavioral deficits appear early in young TRPC4 knockout (Trpc4−/−) mice immediately after weaning, manifesting as alterations in multiple, limbic-related behaviors, such as nesting, marble burying, burrowing, self-grooming, and social interactions. Hippocampal neurons of Trpc4−/− mice exhibit reduced dendritic arborization both in vivo and in vitro. Mechanistically, we found that TRPC4 expression in dendrites surged at the …
Causes Of Symptoms And Symptom Persistence In Long Covid And Myalgic Encephalomyelitis/Chronic Fatigue Syndrome, Anthony L Komaroff, Robert Dantzer
Causes Of Symptoms And Symptom Persistence In Long Covid And Myalgic Encephalomyelitis/Chronic Fatigue Syndrome, Anthony L Komaroff, Robert Dantzer
Faculty, Staff and Student Publications
Debilitating symptoms for many years can follow acute COVID-19 ("long COVID"), myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS), and various post-acute infection syndromes (PAISs). Together, long COVID and ME/CFS affect 60-400 million individuals, globally. Many similar underlying biological abnormalities have been identified in both conditions including autoantibodies against neural targets, endothelial dysfunction, acquired mitochondrial dysfunction, and a pro-inflammatory gut microbiome. Each of these abnormalities may directly cause some of the symptoms. In addition, the symptoms also may be caused by ancient, evolutionarily conserved symptomatic and metabolic responses to vital threats-sickness behavior and torpor-responses mediated by specific, recently discovered neural circuits. These neural …
Dna Methylation Signatures Of Cardiovascular Health Provide Insights Into Diseases, Madeleine Carbonneau, Yi Li, Yishu Qu, Yinan Zheng, Alexis C Wood, Mengyao Wang, Chunyu Liu, Tianxiao Huan, Roby Joehanes, Xiuqing Guo, Jie Yao, Kent D Taylor, Russell P Tracy, Peter Durda, Yongmei Liu, W Craig Johnson, Wendy S Post, Tom Blackwell, Jerome I Rotter, Stephen S Rich, Susan Redline, Myriam Fornage, Jun Wang, Hongyan Ning, Lifang Hou, Donald Lloyd-Jones, Kendra Ferrier, Yuan-I Min, April P Carson, Laura M Raffield, Alexander Teumer, Hans J Grabe, Henry Völzke, Matthias Nauck, Marcus Dörr, Arce Domingo-Relloso, Amanda Fretts, Maria Tellez-Plaza, Shelley A Cole, Ana Navas-Acien, Meng Wang, Joanne M Murabito, Nancy L Heard-Costa, Brenton Prescott, Vanessa Xanthakis, Dariush Mozaffarian, Daniel Levy, Jiantao Ma
Dna Methylation Signatures Of Cardiovascular Health Provide Insights Into Diseases, Madeleine Carbonneau, Yi Li, Yishu Qu, Yinan Zheng, Alexis C Wood, Mengyao Wang, Chunyu Liu, Tianxiao Huan, Roby Joehanes, Xiuqing Guo, Jie Yao, Kent D Taylor, Russell P Tracy, Peter Durda, Yongmei Liu, W Craig Johnson, Wendy S Post, Tom Blackwell, Jerome I Rotter, Stephen S Rich, Susan Redline, Myriam Fornage, Jun Wang, Hongyan Ning, Lifang Hou, Donald Lloyd-Jones, Kendra Ferrier, Yuan-I Min, April P Carson, Laura M Raffield, Alexander Teumer, Hans J Grabe, Henry Völzke, Matthias Nauck, Marcus Dörr, Arce Domingo-Relloso, Amanda Fretts, Maria Tellez-Plaza, Shelley A Cole, Ana Navas-Acien, Meng Wang, Joanne M Murabito, Nancy L Heard-Costa, Brenton Prescott, Vanessa Xanthakis, Dariush Mozaffarian, Daniel Levy, Jiantao Ma
Faculty, Staff and Students Publications
Background: The association of overall cardiovascular health (CVH) with changes in DNA methylation (DNAm) has not been well characterized.
Methods: We calculated the American Heart Association's Life's Essential 8 score to reflect CVH in 5 cohorts with diverse backgrounds (mean age 54 years, 55% women, and enrollment year ranging from 1989 to 2012). Epigenome-wide association studies (EWAS) for Life's Essential 8 score were conducted, followed by bioinformatic analyses. DNAm loci significantly associated with Life's Essential 8 score were used to calculate a CVH DNAm score. We examined the association of the CVH DNAm score with incident cardiovascular disease (CVD), cardiovascular …
Current Practices In The Study Of Biomolecular Acondensates: A Community Comment, Simon Alberti, Paolo Arosio, Robert B Best, Steven Boeynaems, Danfeng Cai, Rosana Collepardo-Guevara, Gregory L Dignon, Rumiana Dimova, Shana Elbaum-Garfinkle, Nicolas L Fawzi, Monika Fuxreiter, Amy S Gladfelter, Alf Honigmann, Ankur Jain, Jerelle A Joseph, Tuomas P J Knowles, Keren Lasker, Edward A Lemke, Kresten Lindorff-Larsen, Reinhard Lipowsky, Jeetain Mittal, Samrat Mukhopadhyay, Sua Myong, Rohit V Pappu, Karsten Rippe, Tatyana A Shelkovnikova, Anthony G Vecchiarelli, Susanne Wegmann, Huaiying Zhang, Mingjie Zhang, Chloe Zubieta, Markus Zweckstetter, Dorothee Dormann, Tanja Mittag
Current Practices In The Study Of Biomolecular Acondensates: A Community Comment, Simon Alberti, Paolo Arosio, Robert B Best, Steven Boeynaems, Danfeng Cai, Rosana Collepardo-Guevara, Gregory L Dignon, Rumiana Dimova, Shana Elbaum-Garfinkle, Nicolas L Fawzi, Monika Fuxreiter, Amy S Gladfelter, Alf Honigmann, Ankur Jain, Jerelle A Joseph, Tuomas P J Knowles, Keren Lasker, Edward A Lemke, Kresten Lindorff-Larsen, Reinhard Lipowsky, Jeetain Mittal, Samrat Mukhopadhyay, Sua Myong, Rohit V Pappu, Karsten Rippe, Tatyana A Shelkovnikova, Anthony G Vecchiarelli, Susanne Wegmann, Huaiying Zhang, Mingjie Zhang, Chloe Zubieta, Markus Zweckstetter, Dorothee Dormann, Tanja Mittag
Duncan NRI Faculty and Staff Publications
The realization that the cell is abundantly compartmentalized into biomolecular condensates has opened new opportunities for understanding the physics and chemistry underlying many cellular processes, fundamentally changing the study of biology. The term biomolecular condensate refers to non-stoichiometric assemblies that are composed of multiple types of macromolecules in cells, occur through phase transitions, and can be investigated by using concepts from soft matter physics. As such, they are intimately related to aqueous two-phase systems and water-in-water emulsions. Condensates possess tunable emergent properties such as interfaces, interfacial tension, viscoelasticity, network structure, dielectric permittivity, and sometimes interphase pH gradients and electric potentials–. …
Changes In Self-Reported Excessive Daytime Sleepiness Are Associated With 5-Year All-Cause Mortality Risk Among Veterans, Katherine G Bay, Arash Maghsoudi, Amin Ramezani, Drew A Helmer, Amir Sharafkhaneh, Javad Razjouyan
Changes In Self-Reported Excessive Daytime Sleepiness Are Associated With 5-Year All-Cause Mortality Risk Among Veterans, Katherine G Bay, Arash Maghsoudi, Amin Ramezani, Drew A Helmer, Amir Sharafkhaneh, Javad Razjouyan
Faculty, Staff and Students Publications
Excessive daytime sleepiness (EDS) is linked to adverse clinical outcomes. This study evaluated changes in a validated tool to assess EDS, the Epworth Sleepiness Scale (ESS) and mortality risk. This retrospective cohort study included Veterans receiving sleep-related services in the Department of Veterans Affairs (VA) from October 4, 1999 to August 18, 2018, with two qualifying ESS measures. ESS values were extracted from patient notes using a validated natural language processing (NLP) pipeline (96% accuracy). ESS scores were categorised as Normal (0-10) or Abnormal (11-24). Patients were grouped based on ESS changes: Normal-Normal, Normal-Abnormal, Abnormal-Abnormal and Abnormal-Normal. Cox proportional hazards …
Heart Failure And Death In Older Adults With Elevated Cardiac Biomarkers But Without Risk Factors: The Atherosclerosis Risk In Communities Study, Xiaoming Jia, Mahmoud Al Rifai, Chiadi Ndumele, Amil Shah, Elizabeth Selvin, Salim S Virani, Ron C Hoogeveen, Biykem Bozkurt, Christie M Ballantyne, Vijay Nambi
Heart Failure And Death In Older Adults With Elevated Cardiac Biomarkers But Without Risk Factors: The Atherosclerosis Risk In Communities Study, Xiaoming Jia, Mahmoud Al Rifai, Chiadi Ndumele, Amil Shah, Elizabeth Selvin, Salim S Virani, Ron C Hoogeveen, Biykem Bozkurt, Christie M Ballantyne, Vijay Nambi
Faculty, Staff and Students Publications
No abstract provided.
Ethical Considerations Of Deep Brain Stimulation For Treatment Refractory Schizophrenia: Surveying Stakeholders, Judith M Gault, Nicola Cascella, Nidal Moukaddam, Stephanie Lehto, Patrick Hosokawa, Paul S Appelbaum, Akira Sawa, Jocelyn Lippman-Bell, William S Anderson, Wayne Goodman, Sameer A Sheth, Daniel Kramer, John A Thompson, Elyn R Saks, Rachel A Davis
Ethical Considerations Of Deep Brain Stimulation For Treatment Refractory Schizophrenia: Surveying Stakeholders, Judith M Gault, Nicola Cascella, Nidal Moukaddam, Stephanie Lehto, Patrick Hosokawa, Paul S Appelbaum, Akira Sawa, Jocelyn Lippman-Bell, William S Anderson, Wayne Goodman, Sameer A Sheth, Daniel Kramer, John A Thompson, Elyn R Saks, Rachel A Davis
Faculty, Staff and Students Publications
Introduction: Ethical concerns have been raised by both current and historically controversial neurosurgical interventions for treatment-refractory schizophrenia and schizoaffective disorder (TR-SZ). Considering advances in next-generation deep brain stimulation (DBS), initial success in treating a few cases of TR-SZ, and how challenging trial enrollment is, transparency and disseminating knowledge about DBS is important, as is input from involved groups. Here information was presented about DBS as an experimental treatment option for TR-SZ to stakeholders to gauge enthusiasm after consideration of potential risks and benefits.
Methods: Stakeholders were presented with information about DBS (total n = 629). Opinions about whether DBS should …
Proteogenomic Characterization Unveils Biomarkers Associated With Chemoresistance In Muscle-Invasive Bladder Cancer, Matthew V Holt, Yongchao Dou, Meggie N Young, Alexander B Saltzman, Meenakshi Anurag, Jonathan T Lei, Antrix Jain, Mei Leng, Beom-Jun Kim, Lacey E Dobrolecki, Stefanie F Faucher, Sara Savage, Chenwei Wang, Zhiao Shi, Hugo Villanueva, Karoline Kremers, Kyle D Drinnon, Patricia D Castro, Michael M Ittmann, Mehak Mehboob Khatani, Sung Han Kim, Matthew J Ellis, Bing Zhang, Anna Malovannaya, Seth P Lerner
Proteogenomic Characterization Unveils Biomarkers Associated With Chemoresistance In Muscle-Invasive Bladder Cancer, Matthew V Holt, Yongchao Dou, Meggie N Young, Alexander B Saltzman, Meenakshi Anurag, Jonathan T Lei, Antrix Jain, Mei Leng, Beom-Jun Kim, Lacey E Dobrolecki, Stefanie F Faucher, Sara Savage, Chenwei Wang, Zhiao Shi, Hugo Villanueva, Karoline Kremers, Kyle D Drinnon, Patricia D Castro, Michael M Ittmann, Mehak Mehboob Khatani, Sung Han Kim, Matthew J Ellis, Bing Zhang, Anna Malovannaya, Seth P Lerner
Faculty, Staff and Students Publications
To explore potential chemoresistance mechanisms and identify therapeutic opportunities in muscle-invasive bladder cancer (MIBC), we conduct comprehensive proteogenomic characterization of 46 pre- and 14 post-treatment MIBC tumors incorporating genomics, transcriptomics, proteomics, and phosphoproteomics. Multi-omics clustering not only recapitulated established molecular subtypes but also revealed subtypes associated with chemotherapy sensitivity. Protein isoform level analysis identifies protein abundance of a short isoform of ATAD1 and RAF family proteins as biomarkers of chemosensitivity. Integration of proteomic and phosphoproteomic data reveals Wnt signaling via GSK3B-S9 phosphorylation and the JAK/STAT pathway as potential targets to overcome chemoresistance. Correlations between PD-L1 and TROP-2/NECTIN-4 indicate an additive …
Extraction-Free Rt-Rpa Assay For Detection Of Hpv16, Hpv18, And Hpv45 Mrna Expression, Emilie Newsham Novak, Ariel Ma, Kathryn A Kundrod, Megan M Chang, Cannon J Hansen, Jane Richards Montealegre, Michael E Scheurer, Philip E Castle, Ming Guo, Mila P Salcedo, Kathleen Schmeler, Rebecca Richards-Kortum
Extraction-Free Rt-Rpa Assay For Detection Of Hpv16, Hpv18, And Hpv45 Mrna Expression, Emilie Newsham Novak, Ariel Ma, Kathryn A Kundrod, Megan M Chang, Cannon J Hansen, Jane Richards Montealegre, Michael E Scheurer, Philip E Castle, Ming Guo, Mila P Salcedo, Kathleen Schmeler, Rebecca Richards-Kortum
Faculty, Staff and Students Publications
Messenger RNA (mRNA) from high-risk genotypes of human papillomavirus (hrHPV) is a more specific biomarker for cervical cancer risk than hrHPV DNA due to its ability to differentiate clinically significant infections from transient ones. Detecting mRNA from exfoliated cervical cells, however, is a complex, expensive, and equipment-intensive process, making it infeasible in resource-limited settings. Here we describe a sensitive, specific, and minimally instrumented method to detect HPV16, HPV18, and HPV45 mRNA in exfoliated cervical cells. First, reverse transcription recombinase polymerase amplification (RT-RPA) exo assays were designed to amplify and detect HPV16, HPV18, and HPV45 E7 mRNA ≥100 copies per reaction …
Anti-Inflammatory Diet And Probiotic Supplementation As Strategies To Modulate Immune Dysregulation In Autism Spectrum Disorder, Carlos Andrés Naranjo-Galvis, Diana María Trejos-Gallego, Cristina Correa-Salazar, Jessica Triviño-Valencia, Marysol Valencia-Buitrago, Andrés Felipe Ruiz-Pulecio, Luisa Fernanda Méndez-Ramírez, Jovanny Zabaleta, Miguel Andres Meñaca-Puentes, Carlos Alberto Ruiz-Villa, Marcela Orjuela-Rodriguez, Juan Carlos Carmona-Hernández, Luisa Matilde Salamanca-Duque
Anti-Inflammatory Diet And Probiotic Supplementation As Strategies To Modulate Immune Dysregulation In Autism Spectrum Disorder, Carlos Andrés Naranjo-Galvis, Diana María Trejos-Gallego, Cristina Correa-Salazar, Jessica Triviño-Valencia, Marysol Valencia-Buitrago, Andrés Felipe Ruiz-Pulecio, Luisa Fernanda Méndez-Ramírez, Jovanny Zabaleta, Miguel Andres Meñaca-Puentes, Carlos Alberto Ruiz-Villa, Marcela Orjuela-Rodriguez, Juan Carlos Carmona-Hernández, Luisa Matilde Salamanca-Duque
School of Medicine Faculty Publications
Background/Objectives: Autism spectrum disorder (ASD) is a neurodevelopmental condition associated with behavioral and cognitive impairments. Increasing evidence also links ASD with systemic immune dysregulation, including abnormal cytokine profiles and chronic low-grade inflammation. Emerging evidence suggests that targeted dietary strategies and probiotic supplementation may modulate immune responses and gut–brain interactions in patients with ASD. This study aimed to evaluate the immunomodulatory effects of a structured anti-inflammatory diet (NeuroGutPlus) compared to multi-strain probiotics in children with ASD. NeuroGutPlus is a nutritionally complete anti-inflammatory dietary protocol that targets gut integrity, inflammation, and mitochondrial function. It includes a diet low in gluten, FODMAPs, casein, …
Anti-Tumor Activity Of Camptothecin Analog Conjugate Of An Rspo4-Based Peptibody Targeting Lgr4/5/6 In Preclinical Models Of Colorectal Cancer, Yukimatsu Toh, Ling Wu, Jianghua Tu, Zhengdong Liang, Adela M Aldana, Jake J Wen, Li Li, Sheng Pan, Julie H Rowe, Martha E Hensel, Carolyn L Hodo, Rick A Finch, Kendra S Carmon, Qingyun J Liu
Anti-Tumor Activity Of Camptothecin Analog Conjugate Of An Rspo4-Based Peptibody Targeting Lgr4/5/6 In Preclinical Models Of Colorectal Cancer, Yukimatsu Toh, Ling Wu, Jianghua Tu, Zhengdong Liang, Adela M Aldana, Jake J Wen, Li Li, Sheng Pan, Julie H Rowe, Martha E Hensel, Carolyn L Hodo, Rick A Finch, Kendra S Carmon, Qingyun J Liu
The Brown Foundation: Institute of Molecular Medicine
Background: Antibody-drug conjugates (ADCs) are a significant advancement in targeted cancer therapy, but none are approved for colorectal cancer (CRC). LGR4/5/6, highly expressed in most CRCs, are promising targets. While LGR5-targeting ADCs show strong anti-tumor effects, their efficacy is limited by LGR5 loss in some CRC cells. RSPO4, a natural ligand for LGR4/5/6, binds all three receptors with high affinity. This research develops RSPO4-based peptibody drug-conjugates (PDCs) to simultaneously target LGR4/5/6, offering a novel therapeutic approach for CRC.
Methods: LGR4/5/6 expression in CRCs was analysed using RNA-seq datasets and Western blot. Peptibody binding affinities were measured, conjugated to camptothecin analog, …
Mechano-Signal Transduction Pathways Of The Diaphragmatic Muscle And Role Of Cytoskeleton, Junaith S Mohamed, Patricia S Pardo, Aladin M Boriek
Mechano-Signal Transduction Pathways Of The Diaphragmatic Muscle And Role Of Cytoskeleton, Junaith S Mohamed, Patricia S Pardo, Aladin M Boriek
Faculty, Staff and Students Publications
Mechanotransduction, also referred to as mechano-signal transduction, is a biophysical process wherein cells perceive and respond to mechanical stimuli by converting them into biochemical signals that initiate specific cellular responses. This mechanism is fundamental to the development and growth, and proper functioning of mechanically active tissues, such as the diaphragm-a respiratory muscle vital for breathing in mammals. In vivo, the diaphragm is subjected to transdiaphragmatic pressure, and therefore, its muscle fibers are subjected to mechanical forces not only in the direction of the muscle fibers but also in the direction transverse to the fibers. Previous research conducted in our laboratory …
High-Grade Glioma With Pleomorphic And Pseudopapillary Features: A Single-Institution Series Of Three Cases, Eric A Goethe, Rasha Alfattal, Subhiksha Srinivasan, Pushan Dasgupta, Vinay Puduvalli, Shiao-Pei Weathers, Leomar Y Ballester, Jeffrey S Weinberg, Sujit Prabhu, Sherise D Ferguson, Maria A Gubbiotti
High-Grade Glioma With Pleomorphic And Pseudopapillary Features: A Single-Institution Series Of Three Cases, Eric A Goethe, Rasha Alfattal, Subhiksha Srinivasan, Pushan Dasgupta, Vinay Puduvalli, Shiao-Pei Weathers, Leomar Y Ballester, Jeffrey S Weinberg, Sujit Prabhu, Sherise D Ferguson, Maria A Gubbiotti
Faculty, Staff and Students Publications
Introduction: Modern molecular diagnostic techniques such as DNA methylation profiling are leading to the reclassification of several central nervous system malignancies and discovery of novel diagnostic entities, such as high-grade glioma with pleomorphic and pseudopapillary features (HPAP).
Methods: We performed a retrospective chart review of all patients with HPAP confirmed with methylation profiling at a single institution between 2023 and 2025. Demographic, radiographic, surgical, and outcome data were collected.
Results: Three patients were identified: two females and one male with a mean age of 49.7 years (range 25-62). No patients had a prior cancer history. One patient had an incidentally …
Improving Automated Deep Phenotyping Through Large Language Models Using Retrieval-Augmented Generation, Brandon T Garcia, Lauren Westerfield, Priya Yelemali, Nikhita Gogate, E Andres Rivera-Munoz, Haowei Du, Moez Dawood, Angad Jolly, James R Lupski, Jennifer E Posey
Improving Automated Deep Phenotyping Through Large Language Models Using Retrieval-Augmented Generation, Brandon T Garcia, Lauren Westerfield, Priya Yelemali, Nikhita Gogate, E Andres Rivera-Munoz, Haowei Du, Moez Dawood, Angad Jolly, James R Lupski, Jennifer E Posey
Faculty, Staff and Students Publications
Background: Diagnosing rare genetic disorders relies on precise phenotypic and genotypic analysis, with the Human Phenotype Ontology (HPO) providing a standardized language for capturing clinical phenotypes. Rule-based HPO extraction tools use concept recognition to automatically identify phenotypes, but they often struggle with incomplete phenotype assignment, requiring significant manual review. While large language models (LLMs) hold promise for more context-driven phenotype extraction, they are prone to errors and "hallucinations," making them less reliable without further refinement. We present RAG-HPO, a Python-based tool that leverages retrieval-augmented generation (RAG) to elevate accuracy of HPO term assignment by LLM. This approach bypasses the limitations …
Extended Survival With Pancreatic Carcinosarcoma: A Case Report And Literature Review, Tian Xiao, Claire Browne, Morgan Black, Celia Marginean, Elena Tsvetkova
Extended Survival With Pancreatic Carcinosarcoma: A Case Report And Literature Review, Tian Xiao, Claire Browne, Morgan Black, Celia Marginean, Elena Tsvetkova
Faculty, Staff and Students Publications
Pancreatic carcinosarcoma is a rare and aggressive malignancy that can mimic pancreatic adenocarcinomas in presentation but often has different disease biology and different responses to conventional treatment for pancreatic adenocarcinoma. Case reports have documented a 5-year overall survival of approximately 13% only if the disease is caught at an earlier stage and is amenable to multi-modality treatment, including surgery, chemotherapy, and radiation. In the advanced stage, treatments do not often provide benefit, and patients may decline rapidly. There are currently no studies demonstrating survival benefits with chemotherapy in patients with metastatic carcinosarcoma, owing to both the rarity and the often …
Prior Adolescent Oxycodone Exposure Enhances Pain Sensitivity Following Chronic Intermittent Ethanol In Adult Female Mice, Lisa L. Wilson, Lucas Albrechet-Souza, Linh Ha, Nicholas W. Gilpin, Tiffany A. Wills
Prior Adolescent Oxycodone Exposure Enhances Pain Sensitivity Following Chronic Intermittent Ethanol In Adult Female Mice, Lisa L. Wilson, Lucas Albrechet-Souza, Linh Ha, Nicholas W. Gilpin, Tiffany A. Wills
School of Graduate Studies Faculty Publications
The opioid crisis remains a critical public health concern, with rising rates of overdose and opioid use disorder. While opioids are effective for managing pain, both chronic use and withdrawal are associated with increased pain sensitivity. Although most prior research has focused on adults, opioid use during adolescence is common and linked to a heightened risk for developing alcohol use disorder and other forms of substance misuse. Like opioids, acute alcohol use can be analgesic, but chronic alcohol exposure and withdrawal lead to increased pain sensitivity. However, the interactive effects of adolescent opioid and adult alcohol exposure on pain remain …
Newly Diagnosed Acute Myeloid Leukemia In Unfit Patients: 2026 Treatment Algorithms, Naseema Gangat, Courtney D Dinardo
Newly Diagnosed Acute Myeloid Leukemia In Unfit Patients: 2026 Treatment Algorithms, Naseema Gangat, Courtney D Dinardo
Faculty, Staff and Student Publications
Management paradigms for newly-diagnosed acute myeloid leukemia (ND-AML) in patients considered unfit to receive intensive chemotherapy have evolved with improved understanding of disease biology. In this setting, management requires clear delineation of goals of therapy that should include preservation of quality-of-life (QoL). Combination of venetoclax (Ven) and a hypomethylating agent (HMA) is the current standard-of-care in most circumstances with flexible options in regard to drug dose and duration of treatment as well as the addition (triplet combinations) or alternative use of targeted therapies, such as inhibitors of FLT3, IDH1, IDH2, or menin for patients with NPM1MUT …
Kdm2b Variants In The Cxxc Domain Impair Its Dna-Binding Ability And Cause A Distinct Neurodevelopmental Syndrome, Amber S E Van Oirsouw, Michael A Hadders, Martijn Koetsier, Edith D J Peters, Nurit Assia Batzir, Tahsin Stefan Barakat, Diana Baralle, Adelyn Beil, Marie-Noëlle Bonnet-Dupeyron, Philip M Boone, Arjan Bouman, Deanna Alexis Carere, Benjamin Cogne, Leslie Dunnington, Laura S Farach, Casie A Genetti, Bertrand Isidor, Louis Januel, Aakash Joshi, Nayana Lahiri, Kristen N Lee, Idit Maya, Meriel Mcentagart, Hope Northrup, Mathilde Pujalte, Kate Richardson, Susan Walker, Bobby P C Koeleman, Mariëlle Alders, Richard H Van Jaarsveld, Renske Oegema
Kdm2b Variants In The Cxxc Domain Impair Its Dna-Binding Ability And Cause A Distinct Neurodevelopmental Syndrome, Amber S E Van Oirsouw, Michael A Hadders, Martijn Koetsier, Edith D J Peters, Nurit Assia Batzir, Tahsin Stefan Barakat, Diana Baralle, Adelyn Beil, Marie-Noëlle Bonnet-Dupeyron, Philip M Boone, Arjan Bouman, Deanna Alexis Carere, Benjamin Cogne, Leslie Dunnington, Laura S Farach, Casie A Genetti, Bertrand Isidor, Louis Januel, Aakash Joshi, Nayana Lahiri, Kristen N Lee, Idit Maya, Meriel Mcentagart, Hope Northrup, Mathilde Pujalte, Kate Richardson, Susan Walker, Bobby P C Koeleman, Mariëlle Alders, Richard H Van Jaarsveld, Renske Oegema
Faculty, Staff and Student Publications
Rare variants affecting the epigenetic regulator KDM2B cause a recently delineated neurodevelopmental disorder. Interestingly, we previously identified both a general KDM2B-associated episignature and a subsignature specific to variants in the DNA-binding CxxC domain. In light of the existence of a distinct subsignature, we set out to determine if KDM2B CxxC variants are associated with a unique phenotype and disease mechanism. We recruited individuals with heterozygous CxxC variants and assessed the variants' effect on protein expression and DNA-binding ability. We analyzed clinical data from 19 individuals, including ten previously undescribed individuals with seven novel CxxC variants. The core phenotype of the …
Single Balloon Enteroscopy In The Elderly, Marc J Zuckerman, Majd Michael, Mohammad Bashashati, Alok K Dwivedi, Nancy A Casner, Mohamed O Othman, Sherif E Elhanafi
Single Balloon Enteroscopy In The Elderly, Marc J Zuckerman, Majd Michael, Mohammad Bashashati, Alok K Dwivedi, Nancy A Casner, Mohamed O Othman, Sherif E Elhanafi
Faculty, Staff and Students Publications
Background: Single-balloon enteroscopy (SBE) is a minimally invasive procedure to assess and treat small bowel pathologies. The most common use is to detect suspected small bowel bleeding: Insignificant gastrointestinal (GI) bleeding or iron deficiency anaemia (IDA). The safety and feasibility of SBE in the elderly has not been adequately studied.
Aim: To assess the safety and feasibility of both antegrade and retrograde SBE in elderly patients.
Methods: We performed a retrospective cohort study of all antegrade and retrograde SBE done at our center from March 2011 through May 2020. We collected patient's data including demographics, indications, findings, therapeutic interventions, and …
Bioinspired Ruthenium-Manganese-Oxygen Complex For Biocatalytic And Radiosensitization Therapies To Eradicate Primary And Metastatic Tumors, Ruidan Li, Ting Wang, Shengdong Mu, Zhenyu Xing, Zhiying Ding, Qinlong Wen, Zhigong Wei, Xiaolin Wang, Mohsen Adeli, Shuang Li, Chong Cheng, Xingchen Peng
Bioinspired Ruthenium-Manganese-Oxygen Complex For Biocatalytic And Radiosensitization Therapies To Eradicate Primary And Metastatic Tumors, Ruidan Li, Ting Wang, Shengdong Mu, Zhenyu Xing, Zhiying Ding, Qinlong Wen, Zhigong Wei, Xiaolin Wang, Mohsen Adeli, Shuang Li, Chong Cheng, Xingchen Peng
Faculty, Staff and Students Publications
Designing efficient, biocompatible radiation-sensitive materials to activate systemic immune responses can maximize tumoricidal effects against malignant tumors. Here, inspired by natural Mn-peroxidase, we propose the de novo design of the RuMn-oxygen complex (MnBTC-Ru) for biocatalytic and radiosensitization therapies to eradicate primary and metastatic tumors. Our results reveal that Mn-organic ligands can enhance the electron density of Ru clusters, thereby optimizing their binding to oxygen species and resulting in high reactive oxygen species and oxygen generation. Accordingly, MnBTC-Ru with radiation can enhance cell membrane and DNA damage, triggering apoptosis though oxidative damage, heightening radiosensitization, and activating CD8
Comparison Of Scoring Systems For Bleeding In Open Cardiac Surgery Patients, İpek Yakin, Çağri Düzyol, İlke Dolğun, Ahmet Yüksek, Kemal Tolga Saraçoğlu
Comparison Of Scoring Systems For Bleeding In Open Cardiac Surgery Patients, İpek Yakin, Çağri Düzyol, İlke Dolğun, Ahmet Yüksek, Kemal Tolga Saraçoğlu
Turkish Journal of Medical Sciences
Background/aim: The aim of our study was to determine which preoperative bleeding risk scoring system is more sensitive in predicting perioperative transfusion requirement in patients undergoing open-heart surgery.
Materials and methods: This is a retrospective single-center cohort study. Seven scoring systems (TRACK, PAPWORTH, WILL-BLEED, CRUSADE, ACTION, TRUST, ACTA-PORT) were used to predict the likelihood of perioperative erythrocyte suspension (ES) transfusion requirement.
Results: Four hundred patients were enrolled in the study. Age, creatinine level, and diagnoses of diabetes mellitus and hypertension were significantly higher in patients who required ES (p ˂ 0.05). In addition, ejection fraction percentages and hemoglobin and hematocrit …
The Role Of Carbon Dioxide Angiography In Reducing Contrast-Induced Nephropathy In Diabetic Foot Patients Undergoing Endovascular Treatment, Sadik Ahmet Uyanik, Erdem Bi̇rgi̇, Saffet Öztürk, Umut Asfuroğlu, Erdi̇ Tangobay, Hi̇kmet Erhan Güven
The Role Of Carbon Dioxide Angiography In Reducing Contrast-Induced Nephropathy In Diabetic Foot Patients Undergoing Endovascular Treatment, Sadik Ahmet Uyanik, Erdem Bi̇rgi̇, Saffet Öztürk, Umut Asfuroğlu, Erdi̇ Tangobay, Hi̇kmet Erhan Güven
Turkish Journal of Medical Sciences
Background/aim: This study investigates the role of carbon dioxide (CO2) angiography, delivered with an automated CO2 delivery system, in decreasing the amount of iodinated contrast and preventing contrast-induced nephropathy (CIN) in diabetic foot patients who underwent endovascular revascularization.
Materials and methods: A total of 272 diabetic foot patients who underwent endovascular treatment for infrainguinal chronic peripheral arterial disease (PAD) were included in the study. Of these, 64 patients underwent endovascular intervention using CO2 angiography (study group), while 208 patients underwent endovascular intervention using only contrast media (control group). The rates of CIN and the amount of contrast used during interventions …
Management Of Critically Ill Patients Following Earthquake Disasters, Esat Kivanç Kaya, Burçi̇n Halaçli, Mehmet Yildirim, Arzu Topeli̇
Management Of Critically Ill Patients Following Earthquake Disasters, Esat Kivanç Kaya, Burçi̇n Halaçli, Mehmet Yildirim, Arzu Topeli̇
Turkish Journal of Medical Sciences
The devastating earthquakes that struck southeastern Turkiye on February 6, 2023, emphasized the profound societal and healthcare challenges posed by natural disasters. These events highlighted the essential need for healthcare professionals to be well-prepared and equipped with the expertise to manage such crises effectively. Earthquake-induced trauma presents a wide array of medical and surgical complications, frequently requiring urgent hospitalization and specialized management for critically ill patients. However, the limited availability of comprehensive data and evidence-based guidelines complicates optimal care delivery in these scenarios. This review outlines current recommendations for the multidisciplinary management of critically ill patients with earthquake-related trauma. It …
Evaluation Of Rheumatic Etiologies Underlying Childhood-Onset Arthritis, Seher Şener, Erdal Atalay, Ezgi̇ Deni̇z Batu, Cansu Ayten Tatar, Özge Başaran, Yelda Bi̇lgi̇ner, Seza Özen
Evaluation Of Rheumatic Etiologies Underlying Childhood-Onset Arthritis, Seher Şener, Erdal Atalay, Ezgi̇ Deni̇z Batu, Cansu Ayten Tatar, Özge Başaran, Yelda Bi̇lgi̇ner, Seza Özen
Turkish Journal of Medical Sciences
Background/aim: Childhood-onset arthritis may result from various rheumatic diseases. This study aimed to systematically evaluate their distribution and characteristics in a large pediatric cohort.
Materials and methods: We retrospectively analyzed all pediatric patients who presented with arthritis to the pediatric rheumatology clinic between January 2000 and January 2023.
Results: A total of 1713 pediatric patients who presented with arthritis were included in this study (median age at diagnosis: 6.8 years; F/M = 1.2). Most of the patients (n = 859, 50.1%) had juvenile idiopathic arthritis (JIA) (especially oligoarticular JIA). Patients with familial Mediterranean fever, comprising 277 individuals (16.2%) presented with …
Discontinuation Of Hydroxychloroquine Due To Suspected Retinal Toxicity In Systemic Lupus Erythematosus And The Role Of Multimodal Imaging, Burak İnce, Mehmet Bedi̇i̇ Oğurel, Zafer Cebeci̇, Yavuz Burak Tor, Yasemi̇n Yalçinkaya, Ahmet Gül, Murat İnanç, Bahar Artim Esen
Discontinuation Of Hydroxychloroquine Due To Suspected Retinal Toxicity In Systemic Lupus Erythematosus And The Role Of Multimodal Imaging, Burak İnce, Mehmet Bedi̇i̇ Oğurel, Zafer Cebeci̇, Yavuz Burak Tor, Yasemi̇n Yalçinkaya, Ahmet Gül, Murat İnanç, Bahar Artim Esen
Turkish Journal of Medical Sciences
Background/aim: To evaluate the effect of hydroxychloroquine (HCQ) on disease activity and damage in patients with systemic lupus erythematosus (SLE) in whom HCQ had previously been discontinued due to retinal toxicity, and to examine and reevaluate toxicity findings through a detailed ophthalmological examination.
Materials and methods: Patients with SLE who had been on HCQ for at least 3 years after achieving lupus low disease activity state (LLDAS) following remission induction, and were followed up for at least 3 years after HCQ discontinuation due to retinal toxicity diagnosed by visual field testing, were analysed. Disease activity, the number and severity of …
Evaluation Of Metabolic Uptake In Gynecological Organs Using Fdg-Pet In Women Diagnosed With Non-Gynecological Malignancies, Funda Atalay, Uğurcan Zorlu, Koray Aslan, Fatma Batak, Tuba Zengi̇n Aksel, Güli̇n Uçmak
Evaluation Of Metabolic Uptake In Gynecological Organs Using Fdg-Pet In Women Diagnosed With Non-Gynecological Malignancies, Funda Atalay, Uğurcan Zorlu, Koray Aslan, Fatma Batak, Tuba Zengi̇n Aksel, Güli̇n Uçmak
Turkish Journal of Medical Sciences
Background/aim: Gynecological malignancies, including those affecting the uterus, cervix, vagina, vulva, and adnexa, pose significant physical and psychosocial burdens. Early detection and effective management of these malignancies are critical for improving outcomes. This study aims to evaluate metabolic uptake patterns in gynecological organs using fluorodeoxyglucose positron emission tomography (FDG-PET) and to analyze their malignancy potential in women with nongynecological cancers.
Materials and methods: A retrospective analysis was conducted on 221 women with nongynecological malignancies who exhibited pathological FDG uptake in gynecological organs on FDG-PET/CT imaging. Lesions were evaluated based on the standardized uptake value maximum (SUVmax), morphological characteristics on contrast-enhanced …
Diagnostic Accuracy And Potential Triage Utility Of The Shetty Test In Foot And Ankle Trauma: A Cross-Sectional Study, Burcu Doğan, Seval Komut, Erdal Komut, Nezi̇h Kavak, Osmancan Güneş, Anilcan Tahsi̇n Karahan
Diagnostic Accuracy And Potential Triage Utility Of The Shetty Test In Foot And Ankle Trauma: A Cross-Sectional Study, Burcu Doğan, Seval Komut, Erdal Komut, Nezi̇h Kavak, Osmancan Güneş, Anilcan Tahsi̇n Karahan
Turkish Journal of Medical Sciences
Background/aim: Foot and ankle trauma represents a common reason for emergency department visits. While the majority of cases involve soft tissue injuries, radiographic imaging is frequently overutilized due to concerns about missed fractures, leading to increased costs and emergency department crowding. The Shetty test, a recently introduced clinical decision rule, may serve as a simpler alternative to established tools such as the Ottawa ankle rules. This study aimed to assess the diagnostic accuracy of the Shetty test and its potential role as a supportive tool within existing triage systems for patients presenting with foot and ankle trauma.
Materials and methods: …
Ultrasonographic And Elastographic Evaluation Of Plantar Fascia And Achilles Tendon Alterations In Type 2 Diabetes Mellitus, Rifat Bozkuş, İhsani̇ye Süer Doğan, Berna Turhan, Sümeyya Duran Kaymak, Mustafa Hulusi̇ Kurt, Rasi̇me Peli̇n Kavak
Ultrasonographic And Elastographic Evaluation Of Plantar Fascia And Achilles Tendon Alterations In Type 2 Diabetes Mellitus, Rifat Bozkuş, İhsani̇ye Süer Doğan, Berna Turhan, Sümeyya Duran Kaymak, Mustafa Hulusi̇ Kurt, Rasi̇me Peli̇n Kavak
Turkish Journal of Medical Sciences
Background/aim: The primary aim of this study is to compare the thickness and stiffness of the PF and AT between healthy volunteers and patients with type 2 diabetes mellitus (T2DM). A secondary objective is to explore the correlations between the thickness and stiffness of the PF and AT with diabetes duration (in months) and hemoglobin A1c (HbA1c) levels in T2DM patients without peripheral neuropathy or foot ulcers, with peripheral neuropathy or with foot ulcers.Material and Methods: A total of 289 participants, including 117 healthy volunteers (Group A) and 172 T2DM patients (59.5%), matched for age, sex, and body mass index, …