Medicine and Health Sciences Commons^™

Association Of Area Deprivation Index With Perinatal And Covid-19 Outcomes During The Early Pandemic: A Secondary Analysis Of A Prospective Cohort Study, Abigail Bell, Megan Foeller, Candice Woolfolk, Emily Diveley, Fan Zhang, Amy Scheffer, Ruizhi Huang, Daniel Jackson, Nandini Raghuraman, Ebony Carter, Indira U Mysorekar, Jeannie C Kelly

Center on Aging Staff Publications

Objective: We sought to evaluate the relationship between neighborhood-level deprivation and perinatal outcomes, particularly preterm birth, as well as COVID-19 outcomes among pregnant patients during the early pandemic.

Methods: We performed a secondary analysis of a prospective longitudinal cohort study that investigated the impact of prenatal COVID-19 exposure on perinatal outcomes. Pregnant patients were recruited 12/23/20-7/18/22 and serially assessed for COVID-19 exposure during pregnancy, with serum antibody testing, electronic medical record review, and patient report. For this secondary analysis, address at the time of delivery was used to categorize patients into low ADI (≤50th percentile Area Deprivation Index, indicating low …

From Molecules To Models: A Holistic Review Of Autism Spectrum Disorder Mechanisms And Research Tools, Sriya Gullapalli, Lois Baldado, Megan W. Szobody, Anesu K. Murambadoro, Kevin Garcia Valdez, Arjun Bellamkonda, Daniela Gonzalez, Usman Ghumman, Nikhilesh Anand, Kelsey A. Potter-Baker, Bharathi Gadad

School of Medicine Publications

Autism Spectrum Disorder (ASD) is a complex neurodevelopmental condition characterized by persistent deficits in social communication and interaction, as well as restricted, repetitive patterns of behavior, interests, or activities. These features are associated with atypical early brain development and connectivity. While ASD has been traditionally associated with molecular genetic alterations, recent research highlights the significant contribution of various environmental factors to the pathophysiology of the disorder. Pathogenic genetic variations in key regulatory genes remain central to ASD risk; however, environmental influences such as advanced maternal or paternal age, poor maternal health during pregnancy, gestational diabetes mellitus, alterations in the early-life …

Exploring Bone Oncology In A Medically Underserved Area: A Retrospective Cohort Of Bone Metastases And Malignant Bone Neoplasia In The Rio Grande Valley, Blake C. Martin, Juan Carlos Lopez Alvarenga, Michael Sander

School of Medicine Publications

Objectives: The Rio Grande Valley (RGV) is a developing clinical research region characterized by its distinctive demographic profile that offers an opportunity to investigate diverse health issues. This pilot investigation sought to evaluate the demographic and clinical characteristics linked to bone metastases and primary malignant bone neoplasms (PMBNs) in patients from the RGV and to compare the frequency of these conditions with the US general population.

Methods: This was a retrospective chart review in which data were gathered from the University of Texas Rio Grande Valley UTHealth electronic database from January 1, 2018 to September 4, 2024. Various statistical analyses …

Hypercalcemia Of Down Syndrome., Seth Lmb, Melissa Litao, Nasreen Talib, Jacob M. Redel

Manuscripts, Articles, Book Chapters and Other Papers

We present a case of hypercalcemia in a 12-month-old female with Down syndrome. The patient presented with significant weight loss (810 g since her 6-month visit) and severe growth failure (weight 5.8 kg, -4.5 SDs). Laboratory evaluation revealed severe hypercalcemia with appropriately suppressed PTH and 1,25-hydroxyvitamin D levels. Renal ultrasound confirmed medullary nephrocalcinosis. After excluding common etiologies, the patient was diagnosed with hypercalcemia of Down syndrome, also termed Abnormal Calcium, Calcinosis, Creatinine in Down syndrome. Treatment with intravenous fluids, calcitonin, and transition to a low-calcium formula (Calcilo XD) normalized serum calcium levels. The patient maintained normal calcium levels on restricted …

Categorizing Weight Growth Of Infants Born Before 32 Weeks' Gestation Using The 2023 Postnatal Growth Charts For Preterm Infants., Fu-Sheng Chou, Hung-Wen Yeh, Crystal Hsueh, Jing Zhang, Maria Fe B. Villosis, Karine Barseghyan, Ashwini Lakshmanan, Reese H. Clark

Manuscripts, Articles, Book Chapters and Other Papers

OBJECTIVE: To categorize growth and correlate growth categories with morbidities in infants born before 32 weeks of gestation.

STUDY DESIGN: This retrospective study categorized weight growth by correlating mean growth velocity (GV) with growth trajectory z-score changes (ΔGTZ ), as measured using 2023 Postnatal Growth Charts for Preterm Infants. The associations between weight categories and morbidities were assessed.

RESULTS: Weight gain of infants without morbidities was categorized into three groups based on correlating ΔGTZ with mean GV: slower ( ΔGTZ < -0.1), in-parallel ( ΔGTZ -0.1 to 0.3), and faster ( ΔGTZ > 0.3). The proportions of infants with and without morbidities in these categories were evaluated across two distinct cohorts, revealing similar …

Left And Right Ventricular Strain Mechanics In Fetal Tachyarrhythmia., Rukmini Komarlu, Janelle R. Noel-Macdonnell Phd, Neha Chellu, Geetha Haligheri

Manuscripts, Articles, Book Chapters and Other Papers

Introduction: Assessment of myocardial function in fetuses with supraventricular tachyarrhythmia is challenging. Speckle-tracking echocardiography (STE) is a newer sensitive method to assess ventricular systolic function. We sought to assess left (LV) and right (RV) ventricular myocardial strain mechanics in fetuses with tachyarrhythmia and hypothesized that strain mechanics are impaired in this patient population even after conversion to sinus rhythm.

METHODS: This was a single-center retrospective review. LV and RV strain parameters were assessed using STE in tachyarrhythmia and after conversion to sinus rhythm and, compared to gestational age (GA), matched control fetuses in sinus rhythm.

RESULTS: Eighteen fetuses with tachyarrhythmia …

Adenovirus Types In Us Children Hospitalized Or Seen In The Emergency Department With Acute Respiratory Illness, 2016-2019., Tess Stopczynski, Varvara Probst, Adam Gailani, Justin Z. Amarin, Olla Hamdan, Haya Hayek, Laura S. Stewart, Herdi K. Rahman, Rangaraj Selvarangan, Jennifer E. Schuster, Christopher J. Harrison, Mary E. Moffatt, Marian G. Michaels, John V. Williams, Julie A. Boom, Leila C. Sahni, Vasanthi Avadhanula, Mary Allen Staat, Elizabeth P. Schlaudecker, Christina Quigley, Geoffrey A. Weinberg, Peter G. Szilagyi, Janet A. Englund, Eileen J. Klein, Aaron T. Curns, Heidi L. Moline, Ariana P. Toepfer, James D. Chappell, Andrew J. Spieker, Natasha B. Halasa

Manuscripts, Articles, Book Chapters and Other Papers

BACKGROUND: Human adenovirus (HAdV) is a common cause of pediatric acute respiratory illness (ARI), contributing to 5-13% of cases worldwide. Clinical manifestations vary by HAdV species and type; therefore, delineating type-specific disease presentations and understanding severity of specific HAdV types' disease may help develop targeted interventions.

METHODS: We conducted a multicenter, prospective study within the New Vaccine Surveillance Network to characterize HAdV types. Children < 18 years old with ARI were enrolled in the emergency department or inpatient setting at 7 US children's hospitals from 1 December 2016 to 30 November 2019. Respiratory specimens were collected and tested for HAdV and other viruses. Subsequently, typing was conducted on HAdV specimens using single-plex real-time PCR assays targeting sequences in the hexon gene. Comparisons between HAdV types were performed to determine differences in characteristics and outcomes. Generalized linear mixed effects models were used to evaluate severity.

RESULTS: Among the 1843 HAdV-positive cases, 1402 specimens (76%) were typed. The most common types detected were HAdV-C1 (n = 439), HAdV-C2 (n = 393), and HAdV-B3 (n = 221). Children with HAdV-B7 (n = 78) …

Elevated Serum Bile Acids Predict Poor Liver Outcomes In Children With Alagille Syndrome: Results From The Gala Study Group., Carla Fiorella Murillo Perez, Shannon M. Vandriel, Emmanuel M. Gonzales, Jian-She Wang, Li-Ting Li, Huiyu She, Irena Jankowska, Piotr Czubkowski, Dorota Gliwicz-Miedzińska, Emmanuel Jacquemin, Jérôme Bouligand, Lorenzo D'Antiga, Emanuele Nicastro, Björn Fischler, Henrik Arnell, Susan M. Siew, Michael Stormon, Kathleen M. Loomes, David A. Piccoli, Elizabeth B. Rand, James E. Squires, Saul J. Karpen, Rene Romero, Mureo Kasahara, Zerrin Önal, Étienne Sokal, Tanguy Demaret, Sabina Wiecek, Florence Lacaille, Dominique Debray, Winita Hardikar, Sahana Shankar, Pamela L. Valentino, Shikha S. Sundaram, Noelle H. Ebel, Jeffrey A. Feinstein, Orith Waisbourd-Zinman, Henry C. Lin, Nathalie Rock, Henkjan J. Verkade, M Kyle Jensen, Catalina Jaramillo, Kyung Mo Kim, Seak Hee Oh, Jernej Brecemiclj, Seema Alam, Giuseppe Indolfi, Niviann Blondet, Rima Fawaz, Silvia Nastasio, Pier Luigi Calvo, Gabriella Nebbia, Cigdem Arikan, Catherine Larson-Nath, Andréanne N. Zizzo, Thomas Damgaard Sandahl, Christos Tzivinikos, Nehal M. El-Koofy, Mohamed A. Elmonem, Amal A. Aqul, Wikrom Karnsakul, Pinar Bulut, Nanda Kerkar, Victorien M. Wolters, Amin J. Roberts, Helen M. Evans, Maria Camila Sanchez, Maria Lorena Cavalieri, Deirdre A. Kelly, Jane Hartley, Way Seah Lee, Christina Hajinicolaou, Chatmanee Lertudomphonwanit, Ryan T. Fischer, Jesus Quintero Bernabeu, Ruben E. Quiros-Tejeira, Cristina Targa Ferreira, Elisa Carvalho, John Eshun, Aglaia Zellos, Antal Dezsőfi, Raquel Borges Pinto, Kathleen Schwarz, Maria Rogalidou, Jennifer Garcia, María Legarda Tamara, Marisa Beretta, Quais Mujawar, Ermelinda Santos-Silva, Cristina Molera Busoms, Eberhard Lurz, Cristina Gonçalves, Carolina Jimenez-Rivera, Jesus M. Banales, Richard J. Thompson, Bettina E. Hansen, Binita M. Kamath, Global Alagille Alliance (Gala) Study Group

Manuscripts, Articles, Book Chapters and Other Papers

BACKGROUND AND AIM: Alagille syndrome (ALGS) is a rare disorder characterised by cholestasis and extrahepatic manifestations. Given the current era of ileal bile acid transporter (IBAT) inhibitor therapies that reduce serum bile acid (SBA) levels, we evaluated whether SBA predicts liver disease outcomes in ALGS.

METHODS: Patients were ascertained from the Global ALagille Alliance (GALA) cohort. A prognostic threshold of SBA 102 μmol/L was assessed as a time-dependent covariate in Cox regression analyses for native liver survival (NLS) and event-free survival (EFS), while adjusting for total bilirubin (TB) levels.

RESULTS: 570 GALA patients were included (348 [61%] male). There was …

Halo Gravity Traction And Temporary Internal Distraction, Nicholas D. Fletcher, Anson G. Bautista, Joshua S. Murphy, K Aaron Shaw

Manuscripts, Articles, Book Chapters and Other Papers

Severe pediatric spinal deformities may require staged correction strategies to mitigate neurologic risk and optimize cardiopulmonary outcomes. This paper reviews two adjunctive techniques—halo gravity traction (HGT) and temporary internal distraction (TID)—used in the management of rigid scoliosis. HGT enables gradual preoperative spinal elongation and coronal/sagittal realignment, improving pulmonary function and nutritional status while reducing the need for three-column osteotomies. TID offers an internal, staged distraction approach for patients contraindicated for external traction, allowing incremental correction via posterior instrumentation followed by definitive fusion. Clinical studies report Cobb angle reductions of 30–80 %, with low rates of neurologic complications when neuromonitoring and …

Pengaruh Aerobic Low Impact Exercise Terhadap Fungsi Kognitif Lansia Dengan Risiko Demensia Di Sasana Tresna Werdha Cibubur Tahun 2025, Nur Achirda, Liza Laela Abida, Kania Annisa Zahra

Jurnal Fisioterapi Terapan Indonesia

Background: Entering old age, the elderly often face various problems, one of which is impaired cognitive function. Some factors that influence the decline in cognitive abilities in the elderly include gender, education level, occupation, nutritional status, and comorbidities that can interfere with the nervous system, such as dementia and Alzheimer's disease. The problem of dementia in the elderly is an important concern that requires effective prevention and treatment. Dementia in the elderly can include several aspects, such as orientation, registration, attention and calculation, memory, and language. Physiotherapy has an important role in maintaining and improving body movement function, so that …

Pengaruh Deep Neck Flexor Exercise Terhadap Neck Pain Non-Specific Pada Penjahit, Salwa Maylani, Fendy Nugroho, Yoni Rustiana

Jurnal Fisioterapi Terapan Indonesia

Background: tailors tend to bow for a long time which results in excessive activation of the postural muscles in maintaining the position of the neck which causes weakness, decreased activity, and muscle imbalance which results in pain in the neck area. In overcoming these disorders, the intervention that can be given is deep neck flexor exercise. Objective: to determine the effect of deep neck flexor exercise on non-specific neck pain in tailors. Methods: this study used an experimental one group pre and post test with control design which was carried out in May-July 2024 at PT. Iskandar Indah Printing Textile …

Kecemasan Orang Tua Yang Memiliki Anak Disabilitas Intelektual Di Slbn 4 Jakarta, Hermito Gidion, Purnama Betty Sitorus, Zahrah Nabila Humayrah

Jurnal Fisioterapi Terapan Indonesia

Anxiety is a common mental condition characterized by feelings of nervousness, fear, and restlessness that can interfere with daily life. Parents who have children with intellectual disabilities often experience anxiety due to various factors, including psychological pressure and high emotional burdens. The aim of this study was to analyze the level of anxiety among parents who have children with intellectual disabilities at SLBN 4 Jakarta and to identify the relationship between predisposing and precipitating factors and the level of anxiety. This research employed a quantitative descriptive approach with a cross-sectional design. The sample consisted of 81 parents at SLBN 4 …

Hubungan Alignment Knee Joint Terhadap Kecepatan Berlari Pada Anak Usia 4-6 Tahun, Rifka Alifia Haura, Miranti Yolanda Anggita, Abdul Chalik Meidian

Jurnal Fisioterapi Terapan Indonesia

Alignment Knee joint alignment is a critical component in the biomechanical analysis of the body, particularly in locomotor activities such as running. Imbalance or malalignment in the knee joint can disrupt movement patterns and increase the risk of musculoskeletal injuries. In pediatric physiotherapy, early identification of lower limb posture is essential to support optimal gross motor development. This study aims to examine the relationship between knee joint alignment and running speed in children aged 4–6 years. A crosssectional design was used, involving 45 children who met the inclusion criteria. Measurement of knee alignment was performed using a goniometer to assess …

Pengaruh Biofeedback Terhadap Program Peningkatan Kekuatan Otot, Aditya Johan Romadhon, Fendy Nugroho, Pajar Haryatno

Jurnal Fisioterapi Terapan Indonesia

Background: In sport the muscle fiber composition surely affect athlete performances, selective training technic and using advance technology may improve and set a new standards for athlete optimal performances, technology innovation such as computer simulator has been use to generate realistic match simulation in several sport, but the technology is not cheap that many sport clubs can afford, so biofeedback may become innovation to improve athletes performance by monitoring muscle activation to achieve selective muscle contraction in muscle strengthening programs. Objective: The objective of this study was to evaluate whether auditory feedback as biofeedback can improve muscle activation in a …

Stage- And Smoking-Associated Microrna Expression In Lung Adenocarcinoma, Min Huang, Yimin Ge, Huiqin Chen, Caimiao Wei, David Cogdell, Cristina Ivan, Meng Chen, Wei Zhang, George A Calin, Ming Guo

Faculty, Staff and Student Publications

Background: Altered expression of microRNAs (miRNAs) is implicated in lung carcinogenesis, but little research has investigated the association of miRNA alterations with lung cancer stage or smoking status. To identify such alterations in lung adenocarcinoma, we conducted miRNA profiling.

Methods: Lung adenocarcinoma specimens and paired nonneoplastic lung tissues from 58 patients who had received no preoperative therapy and underwent tumor resection from 1991 to 2006 were collected from tumor tissue banks. Thirty (52%) of the tumors were stage I and 28 (48%) stage II or higher. Twenty-five (43%) patients were nonsmokers and 33 (57%) were smokers. To identify miRNAs of …

Assessing Hesitancy Towards Paediatric Vaccines Among Healthcare Professionals: A Descriptive Cross-Sectional Study From The United Arab Emirates, Drishti D. Kampani, Kamel A. Samara, Mohammed Mahfouz, Ahmad Hisham Al-Anoud, Amna Basel Al-Beer, Humaid Altaheri, Hiba Jawdat Barqawi, Eman Abu-Gharbieh

Abington Jefferson Health Papers

BACKGROUND: Vaccination is one of the most effective public health interventions, preventing millions of deaths globally. However, vaccine hesitancy persists, not only among the public, but also among healthcare professionals (HCPs), who serve as key sources of vaccine information. This study assesses HCPs' vaccination attitudes and estimates the prevalence and determinants of vaccine hesitancy in the UAE.

DESIGN AND METHODS: This cross-sectional, descriptive study surveyed HCPs across the UAE from March to October 2024 using a 57-item questionnaire adapted from previous literature. Univariate, bivariate (chi-squared test), and multivariate (logistic regression) analyses were conducted.

RESULTS: HCPs demonstrated generally positive attitudes towards …

Application Of The Surgical Apgar Score To Predict Intensive Care Unit Admission And Post-Operative Outcomes In Cesarean Hysterectomy For Placenta Accreta Spectrum, Emily Root, Jacqueline Curbelo, Patrick Ramsey, Jessian L Munoz

Faculty, Staff and Students Publications

Background and Objective: Placenta Accreta Spectrum (PAS) encompasses a continuum of abnormal placentation conditions associated with significant maternal and fetal morbidity. Management of PAS requires coordinated cesarean hysterectomy. Associated morbidities include blood transfusion, coagulopathy, and intensive care unit (ICU) admission. Accurate prediction of ICU admission allows for enhanced multidisciplinary management, coordination of care and utilization of resources. Scoring systems exist in other surgical specialties that can predict the likelihood of ICU admission, but these have not been applied to an obstetric population. The SAS is a 10-point scale that has been validated for the prediction of ICU-level care requirements within …

Emergent Bedside Re-Sternotomy: An Innovative Simulation Model For Training Pediatric Cardiac Intensive Care Teams, Toluwani Akinpelu, Nikhil R. Shah, Mohammed Alhendy, Malarvizhi Thangavelu, Karen Weaver, Nicole Muller, James Mcelroy, Utpal Bhalala

School of Medicine Publications

Introduction: Cardiac tamponade after cardiac surgery is a life-threatening event that requires simultaneous resuscitation and emergent re-sternotomy by the intensive care team. A simulated scenario using an innovative mannequin with sternotomy wound has the capability of reproducing cardiac arrest associated with postoperative tamponade. We evaluated the validity of this mannequin to investigate the confidence level and crisis resource management skills of the team during bedside re-sternotomy to manage postoperative cardiac tamponade.

Methods: The simulation scenario was developed using the sternotomy mannequin for a pediatric cardiac intensive care unit (CICU) team. The case involved a 3-year-old male, intubated, mechanically ventilated after …

The Gut Microbiome In Stevens-Johnson Syndrome And Sjögren's Disease: Correlations With Dry Eye, Luciana Frizon, Talita Trevizani Rocchetti, André Frizon, Rafael Jorge Alves De Alcântara, Cintia S De Paiva, José Álvaro Pereira Gomes

Faculty, Staff and Students Publications

Changes in gut microbial composition may influence mucosal immune responses and contribute to systemic autoimmune manifestations. In this pilot exploratory study, we investigated and compared the gut microbiome in patients with Stevens–Johnson syndrome (SJS), patients with Sjögren’s disease (SjD), and healthy controls, using next-generation sequencing (NGS), and assessed correlations with dry eye parameters. The study included 10 patients with SJS matched by age and sex to 10 healthy controls, and 10 patients with SjD matched to an additional set of 10 healthy controls. Dry eye parameters were employed to evaluate dry eye disease (DED). Microbiome profiles were determined using next-generation …

The Intersection Of Near-Death Experiences (Ndes) And Traumatic Brain Injury (Tbi): Neurobiological, Phenomenological, And Creative Implications, Diego Iacono, Gloria C Feltis

Department of Neurology Faculty Papers

Traumatic brain injury (TBI) and near-death experiences (NDEs) represent profound disruptions in brain function, often associated with dramatic changes in consciousness, self-perception, and behavior. While these events are typically studied for their pathological consequences, a growing body of evidence suggests they may also trigger unexpected cognitive and creative enhancements in a subset of individuals. We explore the intersection between TBI, NDEs, and the emergence of heightened artistic expression, integrating findings from neuroanatomy, neuropathology, genetics, and phenomenology. We examine how alterations in key brain networks - such as the default mode network, frontoparietal circuits, and limbic regions - may underpin shifts …

The Impact Of Extramedullary And Paraskeletal Plasmacytomas On Treatment Outcomes In Multiple Myeloma Treated With Teclistamab: U.S. Myeloma Immunotherapy Consortium Real-World Experience, Aimaz Afrough, Danai Dima, Beatrice Razzo, Utkarsh Goel, Aishwarya Sannareddy, Oren Pasvolsky, Mariola Vazquez-Martinez, Christopher Ferreri, Rahul Banerjee, Jack Khouri, James Davis, Mahmoud Gaballa, Alex Lieberman-Cribbin, Masooma Rana, Kelley Julian, Faiz Anwer, Leyla Shune, Shaun Dejarnette, Ariel Grajales-Cruz, Evguenia Ouchveridze, Gabriel De Avila, Sandra Susanibar-Adaniya, Andrew Portuguese, Daniel Schrum, Erin Eberwein, Hitomi Hosoya, Lekha Mikkilineni, Gurbakhash Kaur, Joseph Mcguirk, Adriana Rossi, Megan Herr, Omar Castaneda, Frederick Locke, Shahzad Raza, Yi Lin, Shebli Atrash, Douglas Sborov, Peter Voorhees, Shambavi Richard, Alfred Garfall, Surbhi Sidana, Krina Patel, Doris Hansen, Andrew Cowan, Larry Anderson, Hans Lee

Department of Medical Oncology Faculty Papers

Teclistamab, a bispecific antibody targeting B-cell maturation antigen (BCMA), is effective in relapsed or refractory multiple myeloma (RRMM), but its impact on patients with soft tissue plasmacytomas is unclear. We studied 385 RRMM patients treated with teclistamab at 13 U.S. centers through September 2023, with follow-up to April 2024. Soft tissue plasmacytomas were classified as true extramedullary disease (EMD; not contiguous with bone) or paraskeletal plasmacytomas (PSK; contiguous with bone). Patients with the simultaneous presence of both were classified as true-EMD, reflecting its adverse prognosis. Of those, 109 (28%) had true EMD, 33 (9%) had PSK, and 243 (63%) had …

Developmental Stage-Dependent Transcriptomic Responses To Neonatal Intraventricular Hemorrhage, Elizabeth Wallace-Anthony, Miriam Zamorano, Hemendra J Vekaria, Braden B Oldham, Kiara P Umpornpun, Scott D Olson, Stefano Berto, Brandon A Miller

Faculty, Staff and Student Publications

Neonatal intraventricular hemorrhage (IVH) is a major complication of preterm birth, yet how developmental stage influences the brain's response to injury remains unclear. We performed single-nucleus RNA sequencing on rat brains 24 h after IVH at postnatal day 2 (PND2) or day 5 (PND5) to define transcriptional responses across cell types. We identified 42 distinct cell populations and found that PND5 brains exhibited a markedly stronger immune and inflammatory response to IVH, with a threefold increase in differentially expressed genes compared to PND2. Microglia were the most perturbed cell type at both stages, showing increased oxidative stress and polarization toward …

Benchmarking Dna Foundation Models For Genomic And Genetic Tasks, Haonan Feng, Lang Wu, Bingxin Zhao, Chad Huff, Jianjun Zhang, Jia Wu, Lifeng Lin, Peng Wei, Chong Wu

Faculty, Staff and Student Publications

The rapid evolution of DNA foundation models promises to revolutionize genomics, yet comprehensive evaluations are lacking. Here, we present a comprehensive, unbiased benchmark of five models (DNABERT-2, Nucleotide Transformer V2, HyenaDNA, Caduceus-Ph, and GROVER) across diverse genomic and genetic tasks including sequence classification, gene expression prediction, variant effect quantification, and topologically associating domain (TAD) region recognition, using zero-shot embeddings. Our analysis reveals that mean token embedding consistently and significantly improves sequence classification performance, outperforming other pooling strategies. Model performance varies among tasks and datasets; while general purpose DNA foundation models showed competitive performance in pathogenic variant identification, they were less …

Radiologist-Validated Automatic Lumbar T1-Weighted Spinal Mri Segmentation Tool Via An Attention U-Net Algorithm, Aryan Kalluvila, Ethan Wang, Michael C Hurley, Colbey Freeman, Jason M Johnson

Faculty, Staff and Student Publications

Background/Objectives: Spinal MRI segmentation has become increasingly important with the prevalence of disc herniation and vertebral injuries. Artificial intelligence can help orthopedic surgeons and radiologists automate the process of segmentation. Currently, there are few tools for T1-weighted spinal MRI segmentation, with most focusing on T2-weighted imaging. This paper focuses on creating an automatic lumbar spinal MRI segmentation tool for T1-weighted images using deep learning.

Methods: An Attention U-Net was employed as the main algorithm because the architecture has shown success in other segmentation applications. Segmentation loss functions were compared, focusing on the difference between BCE and MSE loss. Two board-certified …

Gender Differences In Healthy Eating Index As Informed By The Awareness Of Diagnosis Of Metabolic Dysfunction-Associated Steatotic Liver Disease, Wei Ting Lin, Madeline Novack, Suthat Liangpunsakul, Chiung Kuei Huang, Hui Yi Lin, Po Hung Chen, Tung Sung Tseng, Peng Sheng Ting

School of Public Health Faculty Publications

Background/Objectives: Dietary quality is a driver of metabolic dysfunction-associated steatotic liver disease (MASLD). Men and women often have different levels of adherence to medical advice, but the effect of gender on adherence to dietary advice as a function of awareness of MASLD is understudied. We aim to investigate the differences in diet quality between men and women who are aware of their diagnosis of MASLD compared to their undiagnosed counterparts. Methods: We utilized the National Health and Nutrition Examination Survey 2017–2020 to identify a nationally representative sample of subjects with MASLD, 127 of whom reported a diagnosis of MASLD (diagnosed …

Microbial Associations And Viruses On The Risk Of Celiac Disease (Mavric): A Longitudinal Post-Hoc Case-Cohort Study, Kristian F Lynch, Eric W Triplett, Heikki Hyöty, Angelica P Ahrens, Jutta E Laiho, Joseph F Petrosino, Richard E Lloyd, Daniel Agardh

Faculty, Staff and Students Publications

Celiac disease etiopathogenesis requires genetic predisposition and exposure to gluten, yet these factors alone are not sufficient. Larger longitudinal studies are needed to determine the role of time-varying infections and gut microorganisms. The aim was to design a celiac disease case-cohort longitudinal study using The Environmental Determinants of Diabetes in the Young (TEDDY) study. By age 3-years, persistent tissue transglutaminase autoantibodies (tTGA), i.e., celiac disease autoimmunity (CDA), was confirmed in 704 of the 6132 genetically at-risk TEDDY children. Celiac disease onset (CD-onset) was defined as the age CDA developed when followed by a biopsy-proven diagnosis. A competing risk analysis on …

Mecp2 Interacts With The Super Elongation Complex To Regulate Transcription, Jun Young Sonn, Wonho Kim, Marta Iwanaszko, Yuki Aoi, Yan Li, Guantong Qi, Luke Parkitny, Janice L Brissette, Lorin Weiner, Juan Botas, Ismael Al-Ramahi, Ali Shilatifard, Huda Y Zoghbi

Faculty, Staff and Students Publications

Loss-of-function mutations in methyl-CpG binding protein 2 (MECP2) cause Rett syndrome. While we know that MeCP2 binds to methylated cytosines on DNA, the full breadth of the molecular mechanisms by which MeCP2 regulates gene expression remains incompletely understood. Here, using a genetic modifier screen, we identify the super elongation complex, a P-TEFb–containing elongation factor that releases promoter-proximally paused RNA polymerase II, as a genetic interactor of MECP2. MeCP2 physically interacts with SEC subunits and directly binds AFF4, the scaffold of the SEC, via the transcriptional repression domain. Furthermore, MeCP2 facilitates the binding of AFF4 on a subset …

Mucosal Melanoma: Mechanisms Of Its Etiology, Progression, Resistance And Therapy, Sofie-Yasmin Hassan, Thomas W. Flanagan, Sarah-Lilly Hassan, Sybille Facca, Youssef Haikel, Mohamed Hassan

School of Graduate Studies Faculty Publications

Mucosal melanoma (MM) is a rare, aggressive cancer whose incidence has increased continuously over the years. This subtype of melanoma arises from melanocytes on hairless surfaces, typically in the respiratory tract, gastrointestinal (GI) tract, and urogenital tract. The most common sites of occurrence include the head and neck, the anorectal region, and the vulvovaginal region, while the rare sites of MM are the urinary tract and the upper and lower GI tract, including the esophagus, duodenum and the gallbladder. MM arises in melanocytes of the ectodermal mucosa that originate from neural crest cells and migrate through embryonic mesenchyme to their …

“I Missed My Other Oncologist”: Established Relationships As Barriers And Facilitators To Accessing Car-T And Autologous Transplantation, Zachary A. K. Frosch, Clark Meshack, Caitlin Meeker, Asya Varshavsky-Yanovsky, Rashmi Khanal, Michael Bromberg, Ashwin Chandar, Emmanuel Quien, Jordan Carter, Shazia K. Nakhoda, Marcus Messmer, Charissa Montgomery, Jason A. Incorvati, Nadia D. Ali, Michael J. Styler, Carolyn Y. Fang

Division of Gastroenterology and Hepatology Faculty Papers

BACKGROUND: Autologous stem cell transplantation (ASCT) and chimeric antigen receptor T-cell therapy (CAR-T) can provide significant clinical benefit, but are not equally available to all patients. Oncologist continuity and trust are important to patients, and may act as barriers to receipt of therapy. However, detailed data are lacking on the mechanism by which these might affect receipt of therapy, or how this barrier may be overcome.

METHODS: We conducted a qualitative interview study with patients with non-Hodgkin lymphoma (NHL), classic Hodgkin lymphoma (cHL) or multiple myeloma (MM) eligible for or treated with ASCT/CAR-T. Participants were recruited from a multi-site academic …

The Mechanism Of Action Of Remote Electrical Neuromodulation (Ren) In Treating Migraine And Potentially Other Idiopathic Pain Conditions, Marius Birlea, Christopher L. Robinson, Eden Mama, Alit Stark-Inbar, Alon Ironi, Daniel Atashsokhan, Thomas Berk

College of Nursing Faculty Papers & Presentations

Purpose of Review

This review provides evidence for the mechanism of action (MOA) of Remote Electrical Neuromodulation (REN), a non-pharmacological therapeutic technology for treating migraine and other symptoms manifested by certain idiopathic pain diseases. It discusses the main physiological and anatomical aspects associated with conditioned pain modulation (CPM), and how REN is applied for the treatment of migraine pain and other symptoms.

Recent Findings

The REN wearable device (Nerivio®) is FDA cleared for acute and preventive treatment of migraine in patients aged 8 years and above, and CE marked in patients aged 12 and above. In brief, the REN MOA …