Open Access. Powered by Scholars. Published by Universities.®
- Institution
-
- The Texas Medical Center Library (19192)
- TÜBİTAK (4871)
- Thomas Jefferson University (1684)
- University of Kentucky (1220)
- University of Alabama at Birmingham (1029)
-
- University of Nebraska - Lincoln (899)
- Chulalongkorn University (861)
- Western University (714)
- LSU Health New Orleans (640)
- Dartmouth College (637)
- University of Nebraska Medical Center (603)
- Touro College and University System (569)
- General Organization of Teaching Hospitals and Institutes (GOTHI) (510)
- Virginia Commonwealth University (472)
- Lehigh Valley Health Network (435)
- Chapman University (422)
- Marshall University (379)
- University of South Carolina (349)
- Edith Cowan University (344)
- Roseman University of Health Sciences (320)
- Wright State University (306)
- University of Tennessee Health Science Center (298)
- Zucker School of Medicine at Hofstra/Northwell (290)
- Himmelfarb Health Sciences Library, The George Washington University (273)
- Old Dominion University (263)
- Loma Linda University (262)
- Wayne State University (254)
- Marquette University (225)
- University of Texas Rio Grande Valley (221)
- Rowan University (214)
- Keyword
-
- Humans (12527)
- Female (5268)
- Male (4615)
- Animals (4402)
- Mice (3027)
-
- Adult (2465)
- Middle Aged (2321)
- Aged (1948)
- Child (1473)
- Retrospective Studies (1111)
- Adolescent (1064)
- Tumor (1026)
- Neoplasms (968)
- Doctor of Philosophy (PhD) Heersink School of Medicine (961)
- Mutation (891)
- Biomarkers (835)
- Cell Line (831)
- COVID-19 (811)
- Treatment Outcome (797)
- United States (773)
- Young Adult (760)
- Carcinoma (715)
- Cell Line, Tumor (701)
- Infant (699)
- Receptors (686)
- Risk Factors (652)
- Inflammation (643)
- Animal (632)
- Inbred C57BL (627)
- Mice, Inbred C57BL (622)
- Publication Year
- Publication
-
- Faculty, Staff and Student Publications (9634)
- Faculty, Staff and Students Publications (7832)
- Turkish Journal of Medical Sciences (4871)
- All ETDs from UAB (1022)
- Chulalongkorn University Theses and Dissertations (Chula ETD) (830)
-
- Dartmouth Scholarship (625)
- Journal of Medicine in Scientific Research (510)
- Theses and Dissertations (439)
- Children’s Nutrition Research Center Staff Publications (414)
- InTouch (406)
- Department of Medicine (383)
- Brain and Mind Institute Researchers' Publications (380)
- School of Medicine Faculty Publications (355)
- School of Veterinary and Biomedical Sciences: Faculty Publications (329)
- Annual Research Symposium (317)
- Department of Pathology, Anatomy, and Cell Biology Faculty Papers (300)
- Journal Articles (295)
- Center for Medical Ethics and Health Policy Staff Publications (294)
- Theses and Dissertations (ETD) (280)
- Nebraska Center for Virology: Faculty Publications (265)
- Duncan NRI Faculty and Staff Publications (259)
- Electronic Theses and Dissertations (253)
- Dissertations and Theses (Open Access) (251)
- Pharmacy Faculty Articles and Research (215)
- Department of Biochemistry and Molecular Biology Faculty Papers (211)
- BioMedicine (209)
- Loma Linda University Electronic Theses, Dissertations & Projects (206)
- Biomedical Sciences Faculty Research and Publications (193)
- Journal Articles: Biochemistry & Molecular Biology (188)
- Research outputs 2022 to 2026 (179)
- Publication Type
Articles 4351 - 4380 of 45396
Full-Text Articles in Entire DC Network
A Functional Perspective On Astrocyte Heterogeneity, Wookbong Kwon, Michael R Williamson, Benjamin Deneen
A Functional Perspective On Astrocyte Heterogeneity, Wookbong Kwon, Michael R Williamson, Benjamin Deneen
Faculty, Staff and Students Publications
Astrocytes are glial cells of the central nervous system (CNS) that perform an array of diverse functions that are essential for brain activity. Studies on the functional diversity of astrocytes suggest that such diversity may be derived from specialized populations. We provide an overview of the current state of research on astrocyte diversity and outline current challenges and knowledge gaps while also examining the developmental origins of these populations and how their interactions with neurons contribute to their functional heterogeneity. We highlight recent studies that provide evidence for functionally diverse astrocyte populations under homeostatic conditions and as an adaptive response …
Clinical Phenotype And Outcomes In Autoimmune Encephalitis After Herpes Simplex Virus Encephalitis: A Systematic Review And Meta-Analysis, Jonathan Cleaver, Renetta Chungath, Amy Gimson, Christine Strippel, Bryan Ceronie, Babak Soleimani, Thomas Johnson, Eyal Muscal, Kristen Fisher, Yike Jiang, Timothy A Erickson, Kristy O Murray, Siv Tonje Faret Hovet, Charlotte Aaberg Poulsen, Anna Søgaard Magnussen, Pauline Dumez, Shannon Ronca, Martin Häusler, Annegret Quade, Andrew Swayne, Morten Blaabjerg, Mette Nissen, Alexander J Sandweiss, Jerome Honnorat, Russell Dale, Ming Lim, Michael Eyre, Margherita Nosadini, Lahiru Handunnetthi, Sarosh R Irani, Adam E Handel
Clinical Phenotype And Outcomes In Autoimmune Encephalitis After Herpes Simplex Virus Encephalitis: A Systematic Review And Meta-Analysis, Jonathan Cleaver, Renetta Chungath, Amy Gimson, Christine Strippel, Bryan Ceronie, Babak Soleimani, Thomas Johnson, Eyal Muscal, Kristen Fisher, Yike Jiang, Timothy A Erickson, Kristy O Murray, Siv Tonje Faret Hovet, Charlotte Aaberg Poulsen, Anna Søgaard Magnussen, Pauline Dumez, Shannon Ronca, Martin Häusler, Annegret Quade, Andrew Swayne, Morten Blaabjerg, Mette Nissen, Alexander J Sandweiss, Jerome Honnorat, Russell Dale, Ming Lim, Michael Eyre, Margherita Nosadini, Lahiru Handunnetthi, Sarosh R Irani, Adam E Handel
Faculty, Staff and Students Publications
Background: Autoimmune encephalitis after herpes simplex virus encephalitis (HSVE-AE) represents the intersection of central nervous system infection and autoimmunity. Defining the phenotype and the safety and effectiveness of immunotherapy in HSVE-AE would help identify immunotherapy candidates, optimise therapeutic strategies, and improve patient outcomes.
Methods: We systematically searched Embase, Medline, PubMed, and Web of Science (2007-2024) for cases meeting consensus criteria for AE after confirmed HSVE. Demographics, phenotype, treatment and outcome data were extracted. Dimensionality reduction, network analysis, and multivariate logistic regression was used to explore age- and diagnosis-specific patterns and outcome predictors.
Results: From 2259 articles screened, 78 studies (225 …
One-Year Outcomes From The Pivotal Trial Of A Four-Branch Off-The-Shelf Solution To Treat Pararenal And Extent Iv Thoracoabdominal Aortic Aneurysms, Mark A Farber, Sukgu Han, Michel S Makaroun, Jon S Matsumura, Bernardo C Mendes, Gustavo S Oderich, Luis A Sanchez, Bjoern D Suckow, Carlos H Timaran
One-Year Outcomes From The Pivotal Trial Of A Four-Branch Off-The-Shelf Solution To Treat Pararenal And Extent Iv Thoracoabdominal Aortic Aneurysms, Mark A Farber, Sukgu Han, Michel S Makaroun, Jon S Matsumura, Bernardo C Mendes, Gustavo S Oderich, Luis A Sanchez, Bjoern D Suckow, Carlos H Timaran
Faculty, Staff and Students Publications
Objective: To report 1-year primary-arm outcomes of the GORE EXCLUDER Thoracoabdominal Branch Endoprosthesis pivotal trial.
Methods: The multicenter, nonrandomized, prospective study included patients with extent IV thoracoabdominal aortic aneurysms (TAAAs) and pararenal aortic aneurysms (PRAAs). All-cause and adjudicated lesion-related mortality were assessed at 12 months. Core-lab-reported, imaging-dependent outcomes included aneurysm size, endoleaks assessed through 1-year follow-up window, and target vessel instability (defined as occlusion, stenosis, type Ic/IIIc endoleak, or reintervention) at 1 year.
Results: One hundred two patients were treated; 59 patients had an extent IV TAAA and 43 had a PRAA. The mean maximum aneurysm diameter was 59.4 ± …
A Prospective, Randomized, Controlled Clinical Trial Of High-Frequency Electromagnetic Coupling Powered Permanent Peripheral Nerve Stimulator For The Treatment Of Chronic Craniofacial Pain, Salim M Hayek, Nameer Haider, Ashwin Viswanathan, Mehul Desai, Jeffrey Rosenberg, Niek E Vanquathem
A Prospective, Randomized, Controlled Clinical Trial Of High-Frequency Electromagnetic Coupling Powered Permanent Peripheral Nerve Stimulator For The Treatment Of Chronic Craniofacial Pain, Salim M Hayek, Nameer Haider, Ashwin Viswanathan, Mehul Desai, Jeffrey Rosenberg, Niek E Vanquathem
Faculty, Staff and Students Publications
than one-fifth of the US population. While various medications and conservative treatment modalities are available for this condition, many patients have refractory symptoms. These patients suffer from social impairment, reduced quality of life, and increased financial burdens.
Objective: The objective of this study was to examine the clinical outcomes of patients receiving a permanent, high-frequency electromagnetic coupling (HF-EMC) powered peripheral nerve stimulator (PNS) system for the treatment of chronic craniofacial neuropathic pain.
Study design: This study was a multicenter, randomized, controlled clinical trial conducted under an investigational device exemption (IDE).
Setting: This study was conducted in 7 clinical sites in …
A Fascination With Gastrointestinal Viruses, Mary Kolb Estes
A Fascination With Gastrointestinal Viruses, Mary Kolb Estes
Faculty, Staff and Students Publications
My arrival into this world came quickly, according to my mother, and it feels like my life has mirrored that rapid beginning. I have enjoyed a rich, varied, and stimulating life and career that have gone through several phases. I credit genetics, my family, technological advances, and many environmental factors for shaping my career. Being a virologist allowed me to be curious and creative and to make several unexpected discoveries. This has been a fun and rewarding journey, but it wasn't always easy. I am not accustomed to talking about myself, but I am happy to share some scientific achievements …
Acute Loss Of Tactile Input Leads To General Compensatory Changes In Eye-Hand Coordination During Object Manipulation, Kevin Ung, John F Magnotti, Brandon Kim, Jeffrey M Yau, Per F Nordmark
Acute Loss Of Tactile Input Leads To General Compensatory Changes In Eye-Hand Coordination During Object Manipulation, Kevin Ung, John F Magnotti, Brandon Kim, Jeffrey M Yau, Per F Nordmark
Faculty, Staff and Students Publications
Current models of motor control emphasize the critical role of sensory feedback, as demonstrated by movement coordination deficits following sensory impairment. When both vision and touch are available for object-oriented manual behaviors, they serve distinct roles; vision guides the execution of planned movements, while touch provides more direct feedback on hand-object interactions. The impact of losing somatosensory feedback on eye-hand coordination during dexterous object manipulation tasks has not been thoroughly studied. Conceivably, vision is recruited to compensate for the feedback lost when touch is abolished based on the dexterity demands of the behavior. To investigate this, we tested healthy participants …
Treatment Of Cutaneous Collagenous Vasculopathy With Pulsed Dye Laser, Hannah L Hanania, Isabella Camacho-Hubbard, Zeena Y Nawas
Treatment Of Cutaneous Collagenous Vasculopathy With Pulsed Dye Laser, Hannah L Hanania, Isabella Camacho-Hubbard, Zeena Y Nawas
Faculty, Staff and Students Publications
Objectives: Cutaneous collagenous vasculopathy (CCV) is a rare, idiopathic microangiopathy marked by widespread telangiectasias and histologic vessel wall thickening. Due to its rarity and clinical overlap with other vascular conditions, CCV poses diagnostic and therapeutic challenges. This report highlights the successful use of pulsed dye laser (PDL) therapy in treating a case of extensive CCV.
Methods: A 40-year-old woman with a decade-long history of progressive telangiectasias involving the extremities, trunk, and forearms underwent treatment with a 595-nm PDL. Six treatment sessions were conducted over 14 months.
Results: The patient experienced significant improvement in erythema, telangiectasias, and associated discomfort, with sustained …
Patient-Centered Management Of Heavy Menstrual Bleeding While On Anticoagulation: A Survey Study, Benjamin Barnett, Rushad Patell, Dana Angelini, Leben Tefera, Jordan K Schaefer, Ang Li, Alejandra Gutierrez Bernal, Shruti Chaturvedi, Anjlee Mahajan, Leslie Lake, Jori May, Anna L Parks
Patient-Centered Management Of Heavy Menstrual Bleeding While On Anticoagulation: A Survey Study, Benjamin Barnett, Rushad Patell, Dana Angelini, Leben Tefera, Jordan K Schaefer, Ang Li, Alejandra Gutierrez Bernal, Shruti Chaturvedi, Anjlee Mahajan, Leslie Lake, Jori May, Anna L Parks
Faculty, Staff and Students Publications
Background: Nearly three-quarters of women experience heavy menstrual bleeding (HMB) during anticoagulation treatment for venous thromboembolism (VTE). HMB can lead to medical interventions, impact school or work and diminish quality of life (QOL). While there are several management options for HMB in patients with VTE, we lack information on how patients approach HMB treatment decisions.
Objectives: We examined patients' experience with, perceptions of, and preferences for treatment of HMB while on anticoagulation.
Methods: Clinicians and patient advocates developed a web-based survey that was distributed via patient advocacy organizations and social media between May and June 2024, targeting participants 18 years …
Elephant Endotheliotropic Herpesvirus 2 Infection In 5 African Elephants (Loxodonta Africana) At Multiple North American Zoological Institutions, Taylor J Willis, Anne Burgdorf-Moisuk, Maren Connolly, Jan Raines, Cameron Ratliff, Zoltan S Gyimesi, Erica Lipanovich, Genevive A Dumonceaux, Kathryn L Perrin, Lauren L Howard, Matthew E Kinney, Kirk Suedmeyer, Erin Latimer, Tiffany L Kim, Jessica R Watts, Jie Tan, Paul Ling
Elephant Endotheliotropic Herpesvirus 2 Infection In 5 African Elephants (Loxodonta Africana) At Multiple North American Zoological Institutions, Taylor J Willis, Anne Burgdorf-Moisuk, Maren Connolly, Jan Raines, Cameron Ratliff, Zoltan S Gyimesi, Erica Lipanovich, Genevive A Dumonceaux, Kathryn L Perrin, Lauren L Howard, Matthew E Kinney, Kirk Suedmeyer, Erin Latimer, Tiffany L Kim, Jessica R Watts, Jie Tan, Paul Ling
Faculty, Staff and Students Publications
Objective: To acknowledge that elephant endotheliotropic herpesvirus (EEHV) is a well-recognized major threat to Asian elephants (Elephas maximus) and can cause acute and often fatal hemorrhagic disease (HD). Historically, EEHV-HD has been less frequently identified in African elephants (Loxodonta africana). This case series describes 5 recent cases of EEHV2 infection in African elephants within managed care at 5 North American institutions.
Animals: 5 African elephants (L africana).
Clinical presentation: The cases involved 4-, 7-, and 10-year-old males that died despite receiving aggressive medical therapy and 4- and 14-year-old females that survived. Clinical signs included lethargy, decreased appetite, lameness, changes in …
High-Resolution Mapping Of Alcohol-Related Brain Connectivity In Adults Using 7t Fmri And Multivoxel Pattern Classification, Alan N. Francis, Ihsan Salloum
High-Resolution Mapping Of Alcohol-Related Brain Connectivity In Adults Using 7t Fmri And Multivoxel Pattern Classification, Alan N. Francis, Ihsan Salloum
School of Medicine Publications
Background: Emerging evidence suggests that alcohol use disrupts large-scale brain network interactions, particularly within the triple network model-comprising the Salience Network (SN), Default Mode Network (DMN), and Frontoparietal Network (FPN). However, few studies have examined how these connectivity alterations vary across the full spectrum of alcohol consumption, especially using ultra-high-field imaging and data-driven approaches. This study leverages 7 Tesla resting-state fMRI and multivariate pattern analysis (MVPA) to characterize distinct brain connectivity patterns across heavy, moderate, and non-drinking adults, aiming to identify neural signatures that differentiate alcohol use severity levels.
Methods: We analyzed resting-state functional connectivity data from 69 adults (Mean …
A Large-Scale Multi-Centre Study Characterising Atrophy Heterogeneity In Alzheimer's Disease, Vikram Venkatraghavan, Damiano Archetti, Pierrick Bourgeat, Chenyang Jiang, Mara Ten Kate, Anna C. Van Loenhoud, Rik Ossenkoppele, Charlotte E. Teunissen, Elsmarieke Van De Giessen, Yolande A.L. Pijnenburg, Giovanni B. Frisoni, Béla Weiss, Zoltán Vidnyánszky, Tibor Auer, Stanley Durrleman, Alberto Redolfi, Simon M. Laws, Paul Maruff, Neil P. Oxtoby, Andre Altmann, Daniel C. Alexander, Wiesje M. Van Der Flier, Frederik Barkhof, Betty M. Tijms
A Large-Scale Multi-Centre Study Characterising Atrophy Heterogeneity In Alzheimer's Disease, Vikram Venkatraghavan, Damiano Archetti, Pierrick Bourgeat, Chenyang Jiang, Mara Ten Kate, Anna C. Van Loenhoud, Rik Ossenkoppele, Charlotte E. Teunissen, Elsmarieke Van De Giessen, Yolande A.L. Pijnenburg, Giovanni B. Frisoni, Béla Weiss, Zoltán Vidnyánszky, Tibor Auer, Stanley Durrleman, Alberto Redolfi, Simon M. Laws, Paul Maruff, Neil P. Oxtoby, Andre Altmann, Daniel C. Alexander, Wiesje M. Van Der Flier, Frederik Barkhof, Betty M. Tijms
Research outputs 2022 to 2026
Previous studies identified atrophy-based Alzheimer's disease(AD) subtypes linked to distinct clinical symptoms, but their consistency across subtyping approaches remains unclear. This large-scale study evaluates subtype concordance using two data-driven approaches. In this work, we analyzed data from n=10,011 patients across 10 AD cohorts spanning Europe, the US, and Australia, extracting regional volumes using Freesurfer. To characterize atrophy heterogeneity in the AD continuum, we developed a two-step approach, Snowphlake (Staging NeurOdegeneration With PHenotype informed progression timeLine of biomarKErs), to identify subtypes and atrophy-event sequences within each subtype. Results were compared with SuStaIn (Subtype and Stage Inference), which jointly estimates subtypes and …
Combining Lumipulse P-Tau217 And Aβ42/40 As Confirmatory Tests For Aβ Positivity Prior To Disease-Modifying Therapy, James D. Doecke, Ahmed Chenna, Mintzu Lo, Youssouf Badal, Brandon Yee, Robert Martone, Christos Petropoulos, Christopher J. Fowler, Simon Laws, Stephanie R. Rainey-Smith, Ralph N. Martins, Christopher C. Rowe, Colin L. Masters, John Winslow
Combining Lumipulse P-Tau217 And Aβ42/40 As Confirmatory Tests For Aβ Positivity Prior To Disease-Modifying Therapy, James D. Doecke, Ahmed Chenna, Mintzu Lo, Youssouf Badal, Brandon Yee, Robert Martone, Christos Petropoulos, Christopher J. Fowler, Simon Laws, Stephanie R. Rainey-Smith, Ralph N. Martins, Christopher C. Rowe, Colin L. Masters, John Winslow
Research outputs 2022 to 2026
Introduction: For a blood-based biomarker to be considered a confirmatory test for the detection of abnormal amyloid beta (Aβ) levels, the sensitivity and specificity must be equivalent to that of current cerebrospinal fluid tests. Methods: In the current study we assessed the ability of phosphorylated tau (p-tau)217 and Aβ42/40 from the Lumipulse G p-tau217 and β-amyloid ratio (1-42/1-40) tests, individually and combined, to predict Aβ positron emission tomography status in two sub-cohorts from the Australian Imaging, Biomarkers, and Lifestyle Study of Ageing. Results: Testing an Alzheimer's disease continuum cohort, the area under the curve (AUC), sensitivity, specificity, and accuracy for …
Risk Factors Of Acute Gastroenteritis And The Implementation Of Community-Based Total Sanitation In Banyuwangi, Indonesia: A Cross-Sectional Study, Citra Al Karina, Juniastuti Juniastuti, Budi Utomo, I Made Dwi Mertha Adnyana
Risk Factors Of Acute Gastroenteritis And The Implementation Of Community-Based Total Sanitation In Banyuwangi, Indonesia: A Cross-Sectional Study, Citra Al Karina, Juniastuti Juniastuti, Budi Utomo, I Made Dwi Mertha Adnyana
Makara Journal of Health Research
Background: In Banyuwangi Regency, Indonesia, diarrhea remains a major health problem, even though the community-based total sanitation (CBTS) program has been implemented for ten years. This household survey study aimed to identify the risk factors of acute gastroenteritis (AGE) and to evaluate the implementation of CBTS in Banyuwangi Regency.
Methods: A cross-sectional study was conducted in Banyuwangi Regency. Characteristic data from patients with AGE were collected from the two primary healthcare working areas, followed by collecting data of their family members and CBTS in their houses. Data were obtained through interviews and direct observation. The CBTS evaluation results …
Identifying Novel Fibrotic Mechanisms Underlying Treatment-Resistant Lower Urinary Tract Dysfunction, Quentin Darcy
Identifying Novel Fibrotic Mechanisms Underlying Treatment-Resistant Lower Urinary Tract Dysfunction, Quentin Darcy
Graduate Doctoral Dissertations
ABSTRACT
IDENTIFYING NOVEL FIBROTIC MECHANISMS UNDERLYING TREATMENT-RESISTANT LOWER URINARY TRACT DYSFUNCTION
August 2025
Quentin D’Arcy, B.S., University of Massachusetts Amherst
Ph.D., University of Massachusetts Boston
Directed by Dr. Jill Macoska
Lower urinary tract dysfunction (LUTD) is a common, age-related disease that affects millions of men over the age of 50. Current treatment for this and other related prostate diseases concentrate on decreasing benign prostate growth and relaxing smooth muscle contractions to alleviate urinary voiding symptoms. However, up to 45% of patients with LUTD are treatment-resistant and require surgical intervention to resolve prostate issues. By focusing on the contribution of inflammation-derived …
Biomarkers For The Diagnosis Of Indeterminate Pulmonary Nodules: Are We There Yet?, Kevin C Mcgann, Timothy A Khalil, Michael N Kammer, Edwin J Ostrin, Harvey I Pass, Jun-Chieh James Tsay, Leopoldo N Segal, Melissa Potter, Stephen A Deppen, Fabien Maldonado, Eric L Grogan
Biomarkers For The Diagnosis Of Indeterminate Pulmonary Nodules: Are We There Yet?, Kevin C Mcgann, Timothy A Khalil, Michael N Kammer, Edwin J Ostrin, Harvey I Pass, Jun-Chieh James Tsay, Leopoldo N Segal, Melissa Potter, Stephen A Deppen, Fabien Maldonado, Eric L Grogan
Faculty, Staff and Student Publications
Indeterminate pulmonary nodules (IPNs), which are nodules that cannot be classified as definitively benign or malignant at the time of detection, are now diagnosed on the order of millions per year. Management of IPNs remains heavily debated, and routine practice ultimately involves some balance of overall clinical risk assessment and additional diagnostic tests or procedures which may generate significant risk, cost, and worry. Biomarkers are biologically based tests or indicators capable of accurately characterizing the physiologic properties of homeostasis and disease that are not otherwise easily evaluated by the clinician. Accurate biomarkers thereby serve as reliable surrogates for biological aberrancy, …
Expression Graph Network Framework For Biomarker Discovery, Yang Liu, Jason Huse, Kasthuri Kannan
Expression Graph Network Framework For Biomarker Discovery, Yang Liu, Jason Huse, Kasthuri Kannan
Faculty, Staff and Student Publications
Biomarker discovery for complex diseases, such as cancer, hinges on uncovering molecular signatures that capture intricate, interconnected relationships within biological data-a challenge that traditional statistical and machine learning methods often fail to meet due to the complexity of high-dimensional gene expression profiles. To overcome this, we introduce the expression graph network framework (EGNF). This cutting-edge graph-based approach integrates graph neural networks with network-based feature engineering to enhance the predictive identification of biomarkers. EGNF constructs biologically informed networks by combining gene expression data and clinical attributes within a graph database, utilizing hierarchical clustering to generate dynamic, patient-specific representations of molecular interactions. …
Auprc: A Metric For Evaluating The Performance Of In-Silico Perturbation Methods In Identifying Differentially Expressed Genes, Hongxu Zhu, Amir Asiaee, Leila Azinfar, Jun Li, Han Liang, Ehsan Irajizad, Kim-Anh Do, James P Long
Auprc: A Metric For Evaluating The Performance Of In-Silico Perturbation Methods In Identifying Differentially Expressed Genes, Hongxu Zhu, Amir Asiaee, Leila Azinfar, Jun Li, Han Liang, Ehsan Irajizad, Kim-Anh Do, James P Long
Faculty, Staff and Student Publications
In silico perturbation models, computational methods that can predict cellular responses to perturbations, present an opportunity to reduce the need for costly and time-intensive in vitro experiments. Many recently proposed models predict high-dimensional cellular responses, such as gene or protein expression to perturbations such as gene knockout or drugs. However, evaluating in silico performance has largely relied on metrics such as $R^{2}$, which assess overall prediction accuracy but fail to capture biologically significant outcomes like the identification of differentially expressed (DE) genes. In this study, we present a novel evaluation framework that introduces the AUPRC metric to assess the precision …
Whole-Genome Sequence-Based Association Analysis Of African American Individuals With Bipolar Disorder And Schizophrenia, Runjia Li, Sarah A Gagliano Taliun, Kevin Liao, Matthew Flickinger, Janet L Sobell, Giulio Genovese, Adam E Locke, Rebeca Rothwell Chiu, Jonathon Lefaive, Jiongming Wang, Taylor Martins, Sinéad Chapman, Anna Neumann, Robert E Handsaker, Donna K Arnett, Kathleen C Barnes, Eric Boerwinkle, David Braff, Brian E Cade, Myriam Fornage, Richard A Gibbs, Karin F Hoth, Lifang Hou, Charles Kooperberg, Ruth J F Loos, Ginger A Metcalf, Courtney G Montgomery, Alanna C Morrison, Zhaohui S Qin, Susan Redline, Alexander P Reiner, Stephen S Rich, Jerome I Rotter, Kent D Taylor, Karine A Viaud-Martinez, Tim B Bigdeli, Stacey Gabriel, Sebastian Zollner, Albert V Smith, Goncalo Abecasis, Steve A Mccarroll, Michele T Pato, Carlos N Pato, Michael Boehnke, James Knowles, Hyun Min Kang, Roel A Ophoff, Jason Ernst, Laura J Scott
Whole-Genome Sequence-Based Association Analysis Of African American Individuals With Bipolar Disorder And Schizophrenia, Runjia Li, Sarah A Gagliano Taliun, Kevin Liao, Matthew Flickinger, Janet L Sobell, Giulio Genovese, Adam E Locke, Rebeca Rothwell Chiu, Jonathon Lefaive, Jiongming Wang, Taylor Martins, Sinéad Chapman, Anna Neumann, Robert E Handsaker, Donna K Arnett, Kathleen C Barnes, Eric Boerwinkle, David Braff, Brian E Cade, Myriam Fornage, Richard A Gibbs, Karin F Hoth, Lifang Hou, Charles Kooperberg, Ruth J F Loos, Ginger A Metcalf, Courtney G Montgomery, Alanna C Morrison, Zhaohui S Qin, Susan Redline, Alexander P Reiner, Stephen S Rich, Jerome I Rotter, Kent D Taylor, Karine A Viaud-Martinez, Tim B Bigdeli, Stacey Gabriel, Sebastian Zollner, Albert V Smith, Goncalo Abecasis, Steve A Mccarroll, Michele T Pato, Carlos N Pato, Michael Boehnke, James Knowles, Hyun Min Kang, Roel A Ophoff, Jason Ernst, Laura J Scott
Faculty, Staff and Student Publications
In studies of individuals of primarily European genetic ancestry, common and low-frequency variants and rare coding variants have been found to be associated with the risk of bipolar disorder (BD) and schizophrenia (SZ). However, less is known for individuals of other genetic ancestries or the role of rare non-coding variants in BD and SZ risk. We performed whole-genome sequencing (∼27X) of African American individuals: 1,598 with BD, 3,295 with SZ, and 2,651 unaffected controls (InPSYght study). We increased power by incorporating 14,812 jointly called psychiatrically unscreened ancestry-matched controls from the Trans-Omics for Precision Medicine (TOPMed) Program for a total of …
Cross-Platform Transcriptomic Data Integration Identifies An Overactive Neuro-Immune Signature In Human Osteoarthritis Synovium, Michael D Newton, Hannah Swahn, Dana E Orange, Joseph B Lesnak, Theodore J Price, Anne-Marie Malfait, Rachel E Miller, Martin K Lotz, Tristan Maerz
Cross-Platform Transcriptomic Data Integration Identifies An Overactive Neuro-Immune Signature In Human Osteoarthritis Synovium, Michael D Newton, Hannah Swahn, Dana E Orange, Joseph B Lesnak, Theodore J Price, Anne-Marie Malfait, Rachel E Miller, Martin K Lotz, Tristan Maerz
Faculty, Staff and Student Publications
Objective: Chronic synovitis is associated with osteoarthritis (OA) pain, but the molecular underpinnings remain unclear. Our objective was to characterize the transcriptional phenotype of OA synovium with a focus on signaling relevant to pain.
Design: Eight publicly-available microarray and RNA-sequencing GEO datasets from human non-OA and OA subjects underwent quality control and re-analysis for differentially-expressed genes (DEGs). Cross-platform statistical integration was performed via a weighted Z-test to combine detection power across datasets. Gene set enrichment, cell type enrichment, and regulon analyses were performed. Human single-cell RNA sequencing data was used to map gene expression to cell types. Ligand-receptor interactions were …
Deciphering Transcriptomic Changes In Chemobrain: A Comprehensive Review, Tusar Kanta Acharya, Yuan Pan, Peter M Grace, Cobi J Heijnen, Rajasekaran Mahalingam
Deciphering Transcriptomic Changes In Chemobrain: A Comprehensive Review, Tusar Kanta Acharya, Yuan Pan, Peter M Grace, Cobi J Heijnen, Rajasekaran Mahalingam
Faculty, Staff and Student Publications
Chemotherapy-induced cognitive impairments (CICI), colloquially known as "chemobrain," represents a profound and debilitating side effect experienced by a significant number of cancer survivors, impacting their memory, multitasking, and quality of life. This review critically evaluates the molecular mechanisms underlying CICI, with a particular focus on the insights gained from transcriptomic analyses. As cancer incidence rises globally, understanding the complex interplay between chemotherapy agents and their cognitive repercussions becomes increasingly vital. Key mechanisms implicated in CICI include blood-brain barrier disruption, neuroinflammation, and oxidative stress as a result of various chemotherapy treatments, such as doxorubicin, cisplatin, and paclitaxel. We delve into advanced …
Longitudinal Meta-Cohort Study Protocol Using Systems Biology To Identify Vaccine Safety Biomarkers, Joann Diray-Arce, Ana C Chang, Sara Moradipoor, Donato Amodio, Bruce Carleton, Wan-Chun Chang, Nigel W Crawford, Meagan Karoly, Annmarie Hoch, Kerry Mcenaney, Tahir S Kafil, Mahitha Donthireddy, Sarah K Steltz, Simon D Van Haren, Asimenia Angelidou, Kinga K Smolen, Hanno Steen, Jessica Lasky-Su, Huyen Tran, Peter Liu, C Buddy Creech, Clare L Cutland, Helen Petousis-Harris, Ishac Nazy, Rae S M Yeung, Sonali Kochhar, Steve Black, Nicholas Wood, Dale Nordenberg, Paolo Palma, Inna G Ovsyannikova, Richard B Kennedy, Gregory A Poland, Al Ozonoff, Robert T Chen, Ofer Levy, Karina A Top, International Network Of Special Immunization Services (Insis) Members
Longitudinal Meta-Cohort Study Protocol Using Systems Biology To Identify Vaccine Safety Biomarkers, Joann Diray-Arce, Ana C Chang, Sara Moradipoor, Donato Amodio, Bruce Carleton, Wan-Chun Chang, Nigel W Crawford, Meagan Karoly, Annmarie Hoch, Kerry Mcenaney, Tahir S Kafil, Mahitha Donthireddy, Sarah K Steltz, Simon D Van Haren, Asimenia Angelidou, Kinga K Smolen, Hanno Steen, Jessica Lasky-Su, Huyen Tran, Peter Liu, C Buddy Creech, Clare L Cutland, Helen Petousis-Harris, Ishac Nazy, Rae S M Yeung, Sonali Kochhar, Steve Black, Nicholas Wood, Dale Nordenberg, Paolo Palma, Inna G Ovsyannikova, Richard B Kennedy, Gregory A Poland, Al Ozonoff, Robert T Chen, Ofer Levy, Karina A Top, International Network Of Special Immunization Services (Insis) Members
Faculty, Staff and Students Publications
The International Network of Special Immunization Services (INSIS) was established to investigate the causes and risk factors of rare adverse events following immunizations (AEFIs) and develop immunization strategies for mitigating or preventing risk for individuals with prior AEFIs or at risk of AEFIs. INSIS integrates clinical data with multi-omic technologies (e.g., transcriptomics, proteomics, metabolomics) through a global consortium of clinical networks, leading immunology, pharmacogenomics teams to uncover the molecular mechanisms behind AEFIs. The network ensures accurate and standardized data collection and analysis through rigorous data management and quality assurance processes. INSIS also implements harmonized case definitions and protocols for collecting …
Whole-Genome Sequence-Based Association Analysis Of African American Individuals With Bipolar Disorder And Schizophrenia, Runjia Li, Sarah A Gagliano Taliun, Kevin Liao, Matthew Flickinger, Janet L Sobell, Giulio Genovese, Adam E Locke, Rebeca Rothwell Chiu, Jonathon Lefaive, Jiongming Wang, Taylor Martins, Sinéad Chapman, Anna Neumann, Robert E Handsaker, Donna K Arnett, Kathleen C Barnes, Eric Boerwinkle, David Braff, Brian E Cade, Myriam Fornage, Richard A Gibbs, Karin F Hoth, Lifang Hou, Charles Kooperberg, Ruth J F Loos, Ginger A Metcalf, Courtney G Montgomery, Alanna C Morrison, Zhaohui S Qin, Susan Redline, Alexander P Reiner, Stephen S Rich, Jerome I Rotter, Kent D Taylor, Karine A Viaud-Martinez, National Heart, Lung, And Blood Institute Trans-Omics For Precision Medicine (Topmed) Consortium;, Genomic Psychiatry Cohort Investigators, Tim B Bigdeli, Stacey Gabriel, Sebastian Zollner, Albert V Smith, Goncalo Abecasis, Steve A Mccarroll, Michele T Pato, Carlos N Pato, Michael Boehnke, James Knowles, Hyun Min Kang, Roel A Ophoff, Jason Ernst, Laura J Scott
Whole-Genome Sequence-Based Association Analysis Of African American Individuals With Bipolar Disorder And Schizophrenia, Runjia Li, Sarah A Gagliano Taliun, Kevin Liao, Matthew Flickinger, Janet L Sobell, Giulio Genovese, Adam E Locke, Rebeca Rothwell Chiu, Jonathon Lefaive, Jiongming Wang, Taylor Martins, Sinéad Chapman, Anna Neumann, Robert E Handsaker, Donna K Arnett, Kathleen C Barnes, Eric Boerwinkle, David Braff, Brian E Cade, Myriam Fornage, Richard A Gibbs, Karin F Hoth, Lifang Hou, Charles Kooperberg, Ruth J F Loos, Ginger A Metcalf, Courtney G Montgomery, Alanna C Morrison, Zhaohui S Qin, Susan Redline, Alexander P Reiner, Stephen S Rich, Jerome I Rotter, Kent D Taylor, Karine A Viaud-Martinez, National Heart, Lung, And Blood Institute Trans-Omics For Precision Medicine (Topmed) Consortium;, Genomic Psychiatry Cohort Investigators, Tim B Bigdeli, Stacey Gabriel, Sebastian Zollner, Albert V Smith, Goncalo Abecasis, Steve A Mccarroll, Michele T Pato, Carlos N Pato, Michael Boehnke, James Knowles, Hyun Min Kang, Roel A Ophoff, Jason Ernst, Laura J Scott
Faculty, Staff and Students Publications
In studies of individuals of primarily European genetic ancestry, common and low-frequency variants and rare coding variants have been found to be associated with the risk of bipolar disorder (BD) and schizophrenia (SZ). However, less is known for individuals of other genetic ancestries or the role of rare non-coding variants in BD and SZ risk. We performed whole-genome sequencing (∼27X) of African American individuals: 1,598 with BD, 3,295 with SZ, and 2,651 unaffected controls (InPSYght study). We increased power by incorporating 14,812 jointly called psychiatrically unscreened ancestry-matched controls from the Trans-Omics for Precision Medicine (TOPMed) Program for a total of …
Covered Stent Salvage For Iatrogenic Vertebral Artery Injury In Traumatic Cervical Spine Injury: A Case Report And Literature Review, Tzu-Hao Yen, Wei-Liang Chen, Ying-Lin Tseng, You-Pen Chiu, Hui-Ru Ji, Jeng-Hung Guo, Cheng-Di Chiu
Covered Stent Salvage For Iatrogenic Vertebral Artery Injury In Traumatic Cervical Spine Injury: A Case Report And Literature Review, Tzu-Hao Yen, Wei-Liang Chen, Ying-Lin Tseng, You-Pen Chiu, Hui-Ru Ji, Jeng-Hung Guo, Cheng-Di Chiu
BioMedicine
We report the case of a 70-year-old woman who sustained complex traumatic injuries in a motor vehicle accident, including cervical spine fractures and a high suspicion of traumatic vertebral artery injury (VAI). Initial digital subtraction angiography (DSA) revealed no evidence of vertebral artery (VA) involvement. She subsequently underwent anterior cervical discectomy and fusion (ACDF); however, an iatrogenic injury to the right VA occurred intraoperatively, necessitating emergent endovascular stenting for vascular repair. This case underscores the importance of comprehensive preoperative imaging, intraoperative vigilance, and coordinated multidisciplinary management in cervical spine trauma with potential vascular involvement.
Endoscopic Management Of Ureteric Stenosis And Calculi In Bilateral Incomplete Renal Duplication: A Case Study, Hafeez Sohaib Ahmad Warraich, Zirwa Younis, Jawairia Warraich, Khizra Warraich
Endoscopic Management Of Ureteric Stenosis And Calculi In Bilateral Incomplete Renal Duplication: A Case Study, Hafeez Sohaib Ahmad Warraich, Zirwa Younis, Jawairia Warraich, Khizra Warraich
BioMedicine
Renal duplication anomalies are one of the most frequent congenital urological conditions in the general population all over the world. Bilateral incomplete duplication, however, is exceedingly rare. We present a case of a 29-year-old female with bilateral incomplete duplex kidneys complicated by mid-ureteric stenosis on the right side and calculi in the left ureter and upper moiety of the left duplex kidney. Diagnostic imaging, including ultrasound, computed tomography (CT), and intravenous urography (IVU) confirmed these findings. The patient underwent successful bilateral ureteroscopy (URS) and left-sided retrograde intra-renal surgery (RIRS) for management of the above mentioned complications related to the duplex …
Effect Of Garcinol Against Arsenic-Induced Neurobehavioral Alterations And Liver And Kidney Dysfunction In Albino Mice, Abdulmohsen I. Algefare
Effect Of Garcinol Against Arsenic-Induced Neurobehavioral Alterations And Liver And Kidney Dysfunction In Albino Mice, Abdulmohsen I. Algefare
BioMedicine
The extended exposure to inorganic arsenic is commonly linked to brain damage through oxidative and apoptotic processes. The compound known as Garcinol (GCL) has garnered significant interest due to its potential advantages for human well-being. Nevertheless, the ability of GCL to protect against toxicity generated by arsenic in the brain has not yet been investigated. Hence, our study aimed to examine the neuroprotective effectiveness of GCL in mitigating the detrimental impacts of sodium arsenite (SA) on behavioral patterns, the molecular mechanisms, apoptotic markers, and oxidative stress parameters in the brain, liver, and kidney of mice. The mice were categorized into …
Investigating The Association Between Hyperthyroidism And The Risk Of Herpes Zoster In A Cohort Study In Taiwan, Shih-Wei Lai, Yu-Hung Kuo, Kuan-Fu Liao
Investigating The Association Between Hyperthyroidism And The Risk Of Herpes Zoster In A Cohort Study In Taiwan, Shih-Wei Lai, Yu-Hung Kuo, Kuan-Fu Liao
BioMedicine
Background: The aim of this cohort study was to investigate the association between hyperthyroidism and the likelihood of developing herpes zoster in Taiwan.
Methods: Using the National Health Insurance Research Database (NHIRD) in Taiwan, we selected individuals aged 20-84 who were newly diagnosed with hyperthyroidism between 2013 and 2020 as the hyperthyroidism group. These individuals were then matched with a control group without hyperthyroidism in a 1:1 propensity score matching for sex, age, and baseline comorbidities. The occurrence of herpes zoster was tracked in both groups until the end of the study period or until a diagnosis of herpes zoster …
An Investigation Into The Potent Anticancer, Antimicrobial, And Anti-Inflammatory Activities Of A Punica Granatum Nanoemulgel, Ahmad M Eid, Murad Abualhasan, Yara Khaliliya, Zeina Sinan, Aya Khaliliya
An Investigation Into The Potent Anticancer, Antimicrobial, And Anti-Inflammatory Activities Of A Punica Granatum Nanoemulgel, Ahmad M Eid, Murad Abualhasan, Yara Khaliliya, Zeina Sinan, Aya Khaliliya
BioMedicine
Purpose: The objective of this study is to formulate a nanoemulgel using Punica granatum (P. granatum) seed oil and study the antibacterial, anticancer, and anti-inflammatory properties. Methods: The process to formulate a nanoemulsion from P. granatum seed oil involved using the self-nanoemulsifying technique, with Span 80 and Tween 80 serving as the emulsifying agents. Carbopol hydrogel was combined with the nanoemulsion to produce the nanoemulgel. The particle size, polydispersity index (PDI), rheological behavior, antibacterial, cytotoxic, and anti-inflammatory properties were subsequently examined.
Results: The nanoemulsion formulation with a PDI of 0.229 and a particle size of 189.44 nm was …
Metabolomics In Cancer Detection: A Review Of Techniques, Biomarkers, And Clinical Utility, Kavitha Liegelin Bernhardt, Janita R. T. Pinto
Metabolomics In Cancer Detection: A Review Of Techniques, Biomarkers, And Clinical Utility, Kavitha Liegelin Bernhardt, Janita R. T. Pinto
BioMedicine
Cancer poses a significant burden on global public health, contributing to high mortality rates worldwide. Ongoing diagnostic strategies have predominantly relied on imaging techniques, histopathological examination and molecular analyses which have limitations in sensitivity, and specificity. Early cancer detection is a pivotal determinant of successful treatment and patient survival rates. Metabolomic applications involve the comprehensive analysis of metabolites to understand the metabolic profile of an organism, tissue, or cell under different conditions such as lack of oxygen in tumors. The aim of this review is to provide an extensive approach of metabolomic applications in early cancer detection and to provide …
A Hard Problem: Managing Constipation In The Geriatric Population, William G. Jones, Veeraen Jonnalagadda, Alexandra E. Thomson, Victoria Grumbles, Chase Cottle, Christian Robertson, Maulikkumar Patel
A Hard Problem: Managing Constipation In The Geriatric Population, William G. Jones, Veeraen Jonnalagadda, Alexandra E. Thomson, Victoria Grumbles, Chase Cottle, Christian Robertson, Maulikkumar Patel
HCA Healthcare Journal of Medicine
Constipation is a common condition among geriatric patients with different presenting symptoms and potential serious complications. Additionally, the condition causes a significant burden on our healthcare system. Here, we summarized recommendations from several societies, including the American College of Gastroenterology, American Geriatrics Society, and American Academy of Family Physicians to provide guidance on managing constipation with geriatric patients. Our aim was to emphasize the importance of prevention of constipation in this population and methods to do so. We also give recommendations on how to manage constipation when it does develop and how to manage it across different healthcare settings. These …
Risk Of Major Depression In Partners Of People With Alzheimer's Disease: A National Cohort Study, Casey Crump, Jingkai Wei, Barbara G Vickrey, Alexis C Edwards, Paul E Schulz, Weiva Sieh, Jan Sundquist, Kristina Sundquist
Risk Of Major Depression In Partners Of People With Alzheimer's Disease: A National Cohort Study, Casey Crump, Jingkai Wei, Barbara G Vickrey, Alexis C Edwards, Paul E Schulz, Weiva Sieh, Jan Sundquist, Kristina Sundquist
Faculty, Staff and Student Publications
Background: Alzheimer's disease (AD) may cause significant psychosocial distress not only in the patient but also their partner. However, long-term risks of major depression in partners of AD patients are largely unknown.
Methods: A national cohort study was conducted of all 145 289 partners of people diagnosed with all-cause dementia, including 57 113 partners of people diagnosed with AD, in Sweden during 1998-2017, and 1 300 561 population-based controls. Cox regression was used to compute hazard ratios (HRs) for subsequent risk of major depression identified from nationwide outpatient and inpatient diagnoses through 2018, adjusting for sociodemographic factors and prior mental …