Open Access. Powered by Scholars. Published by Universities.®

Digital Commons Network™

Open Access. Powered by Scholars. Published by Universities.®

Articles 121 - 150 of 7383

Full-Text Articles in Entire DC Network

Generalizability Of An Ai-Based Mammogram Risk Score (Mrs) For Breast Cancer Among Diverse Populations Of Women, Shu Jiang, Debbie L Bennett, Peter Kraft, Graham A Colditz May 2026

Generalizability Of An Ai-Based Mammogram Risk Score (Mrs) For Breast Cancer Among Diverse Populations Of Women, Shu Jiang, Debbie L Bennett, Peter Kraft, Graham A Colditz

2020-Current year OA Pubs

Conventional prediction models incorporating genetic and clinical factors including breast density underperform in non-European populations. We investigated an artificial intelligence-derived mammogram risk score (MRS), a summary of texture features that captures intrinsic breast-tissue characteristics-the substrate for cancer development. This study leveraged data from two North American screening cohorts totaling >226,000 women, including non-Hispanic white, non-Hispanic Black, East Asian, South Asian, and Indigenous women. MRS distributions showed nonsignificant shifts (and similar SDs) between cohorts and across race and ethnic subgroups. MRS increased with age and was significantly associated with breast cancer risk, with hazard ratios per SD ranging from 2.24 [95% …


Co-Occurring Clonal Hematopoiesis Exhibits Strong Selection And High Leukemia Risk, Kara M Barnao, Irenaeus C C Chan, Duc Tran, Yin Cao, Kelly L Bolton, Et Al. May 2026

Co-Occurring Clonal Hematopoiesis Exhibits Strong Selection And High Leukemia Risk, Kara M Barnao, Irenaeus C C Chan, Duc Tran, Yin Cao, Kelly L Bolton, Et Al.

2020-Current year OA Pubs

Clonal hematopoiesis of indeterminate potential (CHIP) and mosaic chromosomal alterations (mCAs) are two types of clonal hematopoiesis (CH) associated with hematological parameters and malignancy risk. Here we show, in genomic data from 546,090 biobank participants, that co-occurring CH (≥2 CH mutations detected) is present in 1.6% of cancer-free individuals and shows strong evidence for selection (up to 804x enrichment). Co-occurrence is more frequent in those with a prior cancer (3.6%), suggesting treatment-induced selection. Acquisition of CHIP usually precedes mCAs with co-occurrences manifesting stronger phenotypic disruptions in telomere attrition and hematologic parameters than component CH events. Individuals with co-occurring CH have …


Target Ii Data Portal: A Multi-Omics Resource For Environmental Toxicant Studies In Mice, Prashant K Kuntala, Benpeng Miao, Deepak Purushotham, Bo Zhang, Daofeng Li, Ting Wang May 2026

Target Ii Data Portal: A Multi-Omics Resource For Environmental Toxicant Studies In Mice, Prashant K Kuntala, Benpeng Miao, Deepak Purushotham, Bo Zhang, Daofeng Li, Ting Wang

2020-Current year OA Pubs

The Toxicant Exposures and Responses by Genomic and Epigenomic Regulators of Transcription (TaRGET) program is a multiphase program that aims to understand how environmental factors contribute to disease susceptibility using toxicant-exposed mouse models. Here, we present the TaRGET II Data Portal ( https://data.targetepigenomics.org/ ), a comprehensive repository of multi-omics datasets generated from mice exposed to a range of environmental toxicants, including arsenic (As), lead (Pb), bisphenol A (BPA), tributyltin (TBT), di(2-ethylhexyl) phthalate (DEHP), tetrachlorodibenzo-p-dioxin (TCDD), and ambient air pollution (PM2.5). Epigenomic profiling assays capturing alterations in chromatin accessibility, DNA methylation, gene expression, and histone modifications were produced across multiple research …


Decoding Spatial Transcriptomics Across Multicellular And Subcellular Resolutions, Chongyue Zhao, Hanqiu Zhao, Zhiyu Dai, Et Al. May 2026

Decoding Spatial Transcriptomics Across Multicellular And Subcellular Resolutions, Chongyue Zhao, Hanqiu Zhao, Zhiyu Dai, Et Al.

2020-Current year OA Pubs

Current whole-genome spatial transcriptomics (ST) platforms, which range from multicellular (e.g., Visium) to subcellular resolution (e.g., Visium HD, Stereo-seq), face significant challenges in accurately decomposing or aggregating spots into single cells-the fundamental units of biological activity. To date, most existing computational methods operate at the spot level, and no method has effectively reconstructed transcriptomes at single-cell resolution. In this study, we present STARS (Spatial Transcriptomics across Resolutions for Single Cells). Leveraging Vision Transformer model and contrastive learning, STARS combines high-resolution histology images with spot-level transcriptomics data to reconstruct single-cell-level gene expression from multicellular and subcellular platforms. We demonstrate the advantage …


Longitudinal Changes In Cognition And Brain Imaging In Persons With Human Immunodeficiency Virus, James Kennedy, Sarah A Cooley, June Roman Fox, Kalen J Petersen, Elizabeth Westerhaus, Pat Reid, Linet Lopez, Beau M Ances May 2026

Longitudinal Changes In Cognition And Brain Imaging In Persons With Human Immunodeficiency Virus, James Kennedy, Sarah A Cooley, June Roman Fox, Kalen J Petersen, Elizabeth Westerhaus, Pat Reid, Linet Lopez, Beau M Ances

2020-Current year OA Pubs

BACKGROUND: As persons with human immunodeficiency virus (PWH) live longer, interactions between human immunodeficiency virus (HIV), aging, and structural brain integrity become increasingly vital for understanding cognitive disorders. This study analyzed the effects of aging, HIV serostatus, and viral load on cognition and brain volumes in a large cohort of persons without HIV (PWOH), PWH with undetectable virus (PWHU) (HIV RNA ≤50 copies/mL), and PWH with detectable virus (PHWD) (HIV RNA >50 copies/mL). Cross-sectional and longitudinal data were included.

METHODS: Cognitive composites (NPZ4) and brain volumes were obtained from 259 PWOH, 264 PWHU, and 84 PWHD with a total of …


Quantification Of Sarm1 Nadase Activity In Human Peripheral Blood Mononuclear Cells, Lila F Dabill, Ivana R Shen, Jennifer M Brazill, Alicia Neiner, Yo Sasaki, Erica L Scheller May 2026

Quantification Of Sarm1 Nadase Activity In Human Peripheral Blood Mononuclear Cells, Lila F Dabill, Ivana R Shen, Jennifer M Brazill, Alicia Neiner, Yo Sasaki, Erica L Scheller

2020-Current year OA Pubs

SARM1 (sterile α and TIR motif-containing protein-1) is an NADase enzyme that serves as the central executioner of Wallerian axon degeneration. Given this, SARM1 is of high interest as a candidate therapeutic target, and SARM1 inhibitors are currently in clinical trials for treatment of neurodegeneration. Beyond neuroscience, emerging studies reveal that SARM1 may also drive aspects of bone fragility, liver pathology, adipose expansion, and insulin resistance in metabolic disease. However, we lack methods to quantify SARM1 activation in humans to better define patients at high risk of SARM1-mediated tissue damage. Unlike neurons, peripheral blood mononuclear cells (PBMCs) represent an easily …


Subclinical Neuropsychiatric Trait Variation In Parents Of Children With Autism Spectrum Disorder: A Cohort Study, Lindsay J Mullin, Carolyn Lasch, Natasha Marrus, Et Al. May 2026

Subclinical Neuropsychiatric Trait Variation In Parents Of Children With Autism Spectrum Disorder: A Cohort Study, Lindsay J Mullin, Carolyn Lasch, Natasha Marrus, Et Al.

2020-Current year OA Pubs

BACKGROUND: Many neuropsychiatric conditions share overlapping features underpinned by shared genetics. In this study, we examined the co-aggregation of sub-threshold variation in neuropsychiatric phenotypes in biological parents of autistic children to provide insights into the intergenerational transmission of genetic liability for autism.

METHODS: Autistic, neuropsychiatric (i.e., anxiety, depression, ADHD), and cognitive traits were characterized in biological parents of children enrolled in a longitudinal developmental study: 189 families of autistic children and 100 families with no autistic children were included. Families were further characterized as having only one (simplex) or more than one (multiplex) autistic child. Maternal and paternal traits were …


Hierarchical Small Molecule Inhibition Of Myst Acetyltransferases, Xuemin Chen, Alexandra Castroverde, Minervo Perez, Ronald Holewinski, Kiall F Suazo, Rashmi Karki, Thorkell Andresson, Benjamin A Garcia, Jordan L Meier May 2026

Hierarchical Small Molecule Inhibition Of Myst Acetyltransferases, Xuemin Chen, Alexandra Castroverde, Minervo Perez, Ronald Holewinski, Kiall F Suazo, Rashmi Karki, Thorkell Andresson, Benjamin A Garcia, Jordan L Meier

2020-Current year OA Pubs

MYST lysine acetyltransferases (KATs) are a class of epigenetic enzymes critical for cellular function that constitute an emerging therapeutic target in cancer. Recently, several drug-like MYST inhibitors have been reported that show promise in preclinical models as well as in clinical trials of breast cancer. Understanding the specificity of these molecules is critical for their effective use as chemical probes. Here we apply an integrated profiling strategy to systematically define the potency and selectivity of drug-like MYST KAT inhibitors. First, we use optimized chemoproteomic profiling and histone acetylation biormarkers to study the industry-developed KAT inhibitor PF-9363. This reveals dose-dependent engagement …


Abl Kinases Regulate Fgf Signaling Independent Of Crk Phosphorylation To Prevent Peters Anomaly Type Ii, Hao Wu, Yingyu Mao, Qian Wang, Honglian Yu, Michael Bouaziz, Neoklis Makrides, Enpeng Wang, Zhipeng Ding, Anthony J Koleske, Glenn L Radice, Jerry Hsu, Xin Zhang May 2026

Abl Kinases Regulate Fgf Signaling Independent Of Crk Phosphorylation To Prevent Peters Anomaly Type Ii, Hao Wu, Yingyu Mao, Qian Wang, Honglian Yu, Michael Bouaziz, Neoklis Makrides, Enpeng Wang, Zhipeng Ding, Anthony J Koleske, Glenn L Radice, Jerry Hsu, Xin Zhang

2020-Current year OA Pubs

Peters anomaly is an anterior segment dysgenesis and a leading cause of congenital corneal opacity. Here, we show that loss of ABL kinases restores lens induction in the absence of FGF signaling but induces Peters anomaly type II independently of ERK signaling, a phenotype also observed with elevated FGF-Ras activity. This defect is rescued by allelic deletion of the ABL substrates CRK and CRKL. Contrary to prevailing models, ABL kinases do not act through direct phosphorylation of CRK proteins; instead, they phosphorylate PTPN12, suppressing p130CAS phosphorylation and CRK recruitment required for RHO GTPase activation. ABL kinase deficiency reduces actomyosin contractility …


Mosunetuzumab Monotherapy Is Active And Tolerable In Patients With Relapsed/Refractory Richter Transformation, Katharine L Lewis, Nancy L Bartlett, Et Al. May 2026

Mosunetuzumab Monotherapy Is Active And Tolerable In Patients With Relapsed/Refractory Richter Transformation, Katharine L Lewis, Nancy L Bartlett, Et Al.

2020-Current year OA Pubs

Richter transformation (RT) to diffuse large B-cell lymphoma is an aggressive lymphoma that arises from underlying chronic lymphocytic leukemia or small lymphocytic lymphoma. RT is often chemorefractory, resulting in poor clinical outcomes with standard chemoimmunotherapy. Mosunetuzumab, a bispecific CD20/CD3 T-cell-engaging antibody, was investigated in a cohort of 20 patients with relapsed/refractory RT. Cytokine release syndrome occurred in 65% of patients, almost exclusively grade 1 (20%) or grade 2 (40%), and occurring during the first treatment cycle. Other adverse events included infections, neutropenia, thrombocytopenia, tumor flare, and low-grade neurotoxicity, with no adverse events leading to treatment discontinuation. Mosunetuzumab resulted in an …


Simultaneous Multielectrode Recordings Along The Human Scala Tympani: Evidence For Level-Dependent Place Coding, Amit Walia, Matthew A Shew, Shannon M Lefler, Amanda J Ortmann, Patrick Ioerger, Jordan Varghese, Jacques A Herzog, Craig A Buchman May 2026

Simultaneous Multielectrode Recordings Along The Human Scala Tympani: Evidence For Level-Dependent Place Coding, Amit Walia, Matthew A Shew, Shannon M Lefler, Amanda J Ortmann, Patrick Ioerger, Jordan Varghese, Jacques A Herzog, Craig A Buchman

2020-Current year OA Pubs

The cochlea systematically encodes sound frequency and intensity via a precisely organized tonotopic map, in which traveling waves peak at specific cochlear locations. A fundamental but incompletely understood aspect of auditory coding involves how stimulus intensity shapes this tonotopic organization. In animal models, increasing intensity shifts the cochlear traveling wave peak basally; however, physiological evidence for such intensity-dependent shifts in human cochlear processing is limited. Here, we performed simultaneous multielectrode electrocochleography recordings along the human scala tympani to characterize how cochlear place coding varies as a function of stimulus intensity. In subjects with preserved cochlear mechanics, including individuals with auditory …


Making Process Evaluations More Explanatory - Key Opportunities To Advance Implementation Research, Michel Wensing, Elvin H Geng May 2026

Making Process Evaluations More Explanatory - Key Opportunities To Advance Implementation Research, Michel Wensing, Elvin H Geng

2020-Current year OA Pubs

Process evaluation of implementation strategies is increasingly common, but a review by Bracci et al. showed that room for improvement exists. In this contribution, we complement their recommendations by ideas on the design of process evaluations. Process evaluations are meant to provide explanations for why implementation strategies were effective, or not effective. Therefore, they are best guided by theory or frameworks, but the frequent focus on intervention acceptability reflects a lack of imagination on moderators and mediators that influence outcomes. Intervention fidelity is relevant in all process evaluations. Meaningful synthesis of process evaluation studies requires a homogeneous outcome, such as …


Exposure To Agent Orange And Association With Myelodysplastic Syndromes, Mikkael A Sekeres, Matthew J Walter, Et Al. May 2026

Exposure To Agent Orange And Association With Myelodysplastic Syndromes, Mikkael A Sekeres, Matthew J Walter, Et Al.

2020-Current year OA Pubs

No abstract provided.


Feasibility Of Decentralized Real-World Monitoring Of Sars-Cov-2 Booster Vaccines And Covid-19 Outcomes In Myeloma, William A Wood, Mark A Schroeder, Ravi Vij, Et Al. May 2026

Feasibility Of Decentralized Real-World Monitoring Of Sars-Cov-2 Booster Vaccines And Covid-19 Outcomes In Myeloma, William A Wood, Mark A Schroeder, Ravi Vij, Et Al.

2020-Current year OA Pubs

Patients with multiple myeloma have an elevated risk of severe complications from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2; COVID-19) infection. To demonstrate proof of concept for a pandemic preparedness and response network, the American Society of Hematology Research Collaborative Multiple Myeloma Program developed a prospective, decentralized study within a site-based provider network. In the COVID-19 outcomes in myeloma and the impact of vaccines (COSMIC) study, patients provided consent, permitted electronic health record data collection, completed patient-reported outcomes at baseline, day 30, and day 180 through an electronic study portal, and were compensated for participation. Clinicians at participating sites facilitated …


Developmental Origins Of Exceptional Health And Survival: A Four-Generation Family Cohort Study, Matthew Thomas Keys, Søren Netra, Dorthe Almind Pedersen, Pernille Stemann Larsen, Alexander Kulminski, Mary F Feitosa, Mary Wojczynski, Michael Province, Kaare Christensen May 2026

Developmental Origins Of Exceptional Health And Survival: A Four-Generation Family Cohort Study, Matthew Thomas Keys, Søren Netra, Dorthe Almind Pedersen, Pernille Stemann Larsen, Alexander Kulminski, Mary F Feitosa, Mary Wojczynski, Michael Province, Kaare Christensen

2020-Current year OA Pubs

Descendants of longevity-enriched sibships demonstrate a broad health and survival advantage throughout the life course. However, little is known about manifestations during very early life. Here we show a pattern of lower risk of adverse early-life outcomes in third-generation grandchildren (N = 5637) of Danish longevity-enriched sibships compared to the general population, including infant mortality (Hazard Ratio = 0.53, 95% CI [0.36, 0.77]) and a range of neonatal health indicators. These associations in fourth-generation great-grandchildren (N = 14,908) were attenuated and less consistent (e.g., infant mortality, Hazard Ratio = 0.90, [0.70, 1.17]). Dilatory patterns across successive generations were independent of …


Tunable Tripcides Suppress Virulence Factor Secretion During Staphylococcus Aureus Infection And Kill Dormant Cells, Hasan Tükenmez, Taylor M Nye, Suzanne Hickerson, Chloe L P Obernuefemann, Jerome S Pinkner, Karen W Dodson, Michael G Caparon, Scott J Hultgren, Et Al. May 2026

Tunable Tripcides Suppress Virulence Factor Secretion During Staphylococcus Aureus Infection And Kill Dormant Cells, Hasan Tükenmez, Taylor M Nye, Suzanne Hickerson, Chloe L P Obernuefemann, Jerome S Pinkner, Karen W Dodson, Michael G Caparon, Scott J Hultgren, Et Al.

2020-Current year OA Pubs

Antimicrobial resistance (AMR) in common bacterial pathogens, including methicillin-resistant


Inflammatory Markers In The Emergency Department And Ptsd Symptoms In The Aurora Study: A Longitudinal Cohort Study, Kristen Nishimi, Stacey L House, Et Al. May 2026

Inflammatory Markers In The Emergency Department And Ptsd Symptoms In The Aurora Study: A Longitudinal Cohort Study, Kristen Nishimi, Stacey L House, Et Al.

2020-Current year OA Pubs

BACKGROUND: Systemic inflammation is hypothesized to contribute to post-traumatic stress disorder (PTSD) vulnerability. Few studies have examined inflammation shortly after trauma as a predictor of later PTSD symptoms. We examined whether inflammation from the emergency department (ED) post-trauma is associated with PTSD symptom severity over the following 6 months.

METHODS: Our sample included 742 AURORA participants, a longitudinal cohort of patients in 29 EDs across the United States after a traumatic stressor, followed up to 6 months. Plasma cytokines were assessed from a study blood draw in the ED: an inflammatory index (standardized sum of generally pro-inflammatory markers interleukin [IL]-6, …


Nivolumab Plus Ipilimumab For Chemotherapy-Refractory Metastatic Castration-Resistant Prostate Cancer: Results From The Randomized Portion Of The Phase 2 Checkmate 650 Trial, Padmanee Sharma, Russell K Pachynski, Et Al. May 2026

Nivolumab Plus Ipilimumab For Chemotherapy-Refractory Metastatic Castration-Resistant Prostate Cancer: Results From The Randomized Portion Of The Phase 2 Checkmate 650 Trial, Padmanee Sharma, Russell K Pachynski, Et Al.

2020-Current year OA Pubs

We report on the randomized portion of the phase 2, open-label CheckMate 650 trial (NCT02985957), in which docetaxel-experienced, biologically male patients with chemotherapy-refractory metastatic castration-resistant prostate cancer were randomized 2:2:1:2 to nivolumab 3 mg /kg plus ipilimumab 1 mg /kg (n = 73), nivolumab 1 mg /kg plus ipilimumab 3 mg /kg (n = 74), ipilimumab 3 mg /kg (n = 38), or cabazitaxel (n = 74). Primary endpoints were objective response rate and radiographic progression-free survival; key secondary endpoints included overall survival, prostate-specific antigen response rate, and safety. This portion of CheckMate 650 was not designed to statistically compare …


Cellular And Molecular Basis Of Pfcoronin Function In Artemisinin Resistance In Plasmodium Falciparum, Imran Ullah, Eva S Istvan, Et Al. May 2026

Cellular And Molecular Basis Of Pfcoronin Function In Artemisinin Resistance In Plasmodium Falciparum, Imran Ullah, Eva S Istvan, Et Al.

2020-Current year OA Pubs

Artemisinin combination therapies are central to malaria control, but their efficacy is threatened by the emergence of resistant Plasmodium falciparum strains. While the role of Pfkelch13 mutations is well established, mutations in Pfcoronin have also been implicated in treatment failure, revealing layers of resistance complexity. Here, we define the cellular mechanism of Pfcoronin‑mediated artemisinin resistance. PfCoronin interacts with PfActin and localizes to the parasite plasma membrane, the digestive vacuole membrane, and small vesicles containing host cell material. Mutations in PfCoronin disrupt its localization and perturb PfActin homeostasis, altering the distribution of ring‑stage morphologies, including a reduced proportion of parasites adopting …


Gut Microbiota Modulation Of Regulatory Dna Elements Revealed By Massively Parallel Functional Characterization, Chadmirah Zaratiana, Adheet Ganesh, Yang E Li, Et Al. May 2026

Gut Microbiota Modulation Of Regulatory Dna Elements Revealed By Massively Parallel Functional Characterization, Chadmirah Zaratiana, Adheet Ganesh, Yang E Li, Et Al.

2020-Current year OA Pubs

Cis-regulatory elements (CREs) are central to dynamic gene regulation in hepatocytes, yet most functional annotations derive from in vitro models that poorly capture physiological regulation. We systematically profiled 109,386 human liver-derived CREs using massively parallel reporter assays in hepatocytes under matched in vitro and in vivo conditions. In vivo-active functional CREs (fCREs) were enriched for H3K27ac and chromatin accessibility and were regulated by diverse transcription factors in the human liver. We further demonstrate that gut microbiota-derived signals modulate fCRE activity and target gene expression in vivo, in part via the KEAP1/NFE2L2 antioxidant pathway. Specific microbial metabolites directly altered the activity …


+Cd49a+Cd103+ Cytotoxic Tissue-Resident Natural Killer Cells Infiltrate And Control Solid Epithelial Tumor Growth In Mice, Nina B Horowitz, Jennifer A Foltz, Et Al. May 2026

+Cd49a+Cd103+ Cytotoxic Tissue-Resident Natural Killer Cells Infiltrate And Control Solid Epithelial Tumor Growth In Mice, Nina B Horowitz, Jennifer A Foltz, Et Al.

2020-Current year OA Pubs

Human tissue-resident natural killer (NK) cells (trNK cells), broadly defined by markers of tissue residency, such as CD49a [


Early-Life Wnt4 Expressing Colon Stromal Cells Orchestrate Lifelong Mucosal Homeostasis Via Bmp-Driven Inkt Cell Imprinting, Xi Lin, Chloe Hyun-Jung Lee, Ting Zhang, Agne Antanaviciute, Thomas Hanley, Jonathan N Glickman, Nikhila S Bharadwaj, Vicki Rosen, Jenny E Gumperz, Matthew K Waldor, Alison Simmons, Thomas Gensollen, Richard S Blumberg May 2026

Early-Life Wnt4 Expressing Colon Stromal Cells Orchestrate Lifelong Mucosal Homeostasis Via Bmp-Driven Inkt Cell Imprinting, Xi Lin, Chloe Hyun-Jung Lee, Ting Zhang, Agne Antanaviciute, Thomas Hanley, Jonathan N Glickman, Nikhila S Bharadwaj, Vicki Rosen, Jenny E Gumperz, Matthew K Waldor, Alison Simmons, Thomas Gensollen, Richard S Blumberg

2020-Current year OA Pubs

The early-life intestinal microenvironment plays a pivotal role in shaping immune cell development. Here, we identify a colonic Wnt4-expressing stromal cell, enriched during early-life, that promotes iNKT cell proliferation via BMP-MAPK signaling. These stromal cells are spatially associated with iNKT cells and macrophages and exhibit high Bmp2 expression during the neonatal period. Depletion of BMP2 in Wnt4


Genealogy-Based Trait Association With Locater Boosts Power At Loci With Allelic Heterogeneity, Xinxin Wang, Ryan Christ, Erica Young, Chul Joo Kang, Indraniel Das, Edward A Belter, Markku Laakso, Louis J M Aslett, David Steinsaltz, Nathan O Stitziel, Ira M Hall May 2026

Genealogy-Based Trait Association With Locater Boosts Power At Loci With Allelic Heterogeneity, Xinxin Wang, Ryan Christ, Erica Young, Chul Joo Kang, Indraniel Das, Edward A Belter, Markku Laakso, Louis J M Aslett, David Steinsaltz, Nathan O Stitziel, Ira M Hall

2020-Current year OA Pubs

A key methodological challenge for genome-wide association studies is how to leverage haplotype diversity and allelic heterogeneity to improve trait association power, especially in noncoding regions where it is difficult to predict variant impacts and define functional units for variant aggregation. Genealogy-based association methods have the potential to bridge this gap by testing combinations of common and rare haplotypes based purely on their ancestral relationships. In parallel work, we have developed an efficient local ancestry inference engine and a novel statistical method (LOCATER) for combining signals present on different branches of a locus-specific haplotype tree. Here, we develop a genome-wide …


Large-Scale Genetic Characterization Of Parkinson's Disease In The African And African Admixed Populations, Fulya Akçimen, Scott A Norris, Erin R Foster, Et Al. May 2026

Large-Scale Genetic Characterization Of Parkinson's Disease In The African And African Admixed Populations, Fulya Akçimen, Scott A Norris, Erin R Foster, Et Al.

2020-Current year OA Pubs

Elucidating the genetic contributions to Parkinson's disease aetiology across diverse ancestries is a critical priority for the development of targeted therapies in a global context. We conducted the largest sequencing characterization of potentially disease-causing, protein-altering and splicing mutations in 710 cases and 11 827 controls from genetically predicted African or African admixed ancestries. We explored copy number variants (CNVs) and runs of homozygosity in prioritized early onset and familial cases. Our study identified rare GBA1 coding variants to be the most frequent mutations among patients with Parkinson's disease, with a frequency of 4% in our case cohort. Of the 18 …


Logistic Regression For Estimating Functional Effects With Spatial Transcriptomics, Michael Barkasi, Cody Nhan Pham, Demetrios Neophytou, Hysell V Oviedo May 2026

Logistic Regression For Estimating Functional Effects With Spatial Transcriptomics, Michael Barkasi, Cody Nhan Pham, Demetrios Neophytou, Hysell V Oviedo

2020-Current year OA Pubs

Spatial transcriptomics (ST) unlocks potential for studying gene functions in processes that depend on orchestration of transcription across space. However, analysis tools for ST remain aimed at data exploration, with few resources for hypothesis testing. What's missing is a way to test whether a factor of interest affects functionally relevant parameters of a gene's spatial distribution. We present a tool to fill this gap, which we call a warped sigmoidal Poisson-process mixed-effects (WSP, pronounced "wisp") model. WSP models are the first ST tool allowing researchers to test critical questions without bespoke preprocessing pipelines for identifying key spatial parameters. By aligning …


Mitochondrial Etf Insufficiency Drives Neoplastic Growth By Selectively Optimizing Cancer Bioenergetics, David Papadopoli, Sergej Djuranovic, Et Al. May 2026

Mitochondrial Etf Insufficiency Drives Neoplastic Growth By Selectively Optimizing Cancer Bioenergetics, David Papadopoli, Sergej Djuranovic, Et Al.

2020-Current year OA Pubs

Mitochondrial electron transport flavoprotein (ETF) insufficiency causes metabolic diseases known as a multiple acyl-CoA dehydrogenase deficiency (MADD). In contrast to muscle, ETFDH is a non-essential gene in acute lymphoblastic leukemia NALM6 cells, and its expression is reduced across human cancers. In various human cancer cell lines and mouse models, ETF insufficiency caused by decreased ETFDH expression limits flexibility of OXPHOS fuel utilisation but paradoxically increases bioenergetics and accelerates neoplastic growth via activation of the mTORC1/BCL-6/4E-BP1 axis. Collectively, these findings reveal that while ETF insufficiency is rare and has detrimental effects in non-malignant tissues, it is common in neoplasia, where ETFDH …


Transcriptome Predictors Of Second Breast Events In Ductal Carcinoma In Situ: A Case‒Control Study Including Black And White Women, Aditi Hazra, Emma Berdan, Thomas Walsh, Sarah Humble, Jen Tappenden, Katherine Deschryver, Deborah Veis, Kiran Vij, Shannan Ho Sui, Graham A Colditz May 2026

Transcriptome Predictors Of Second Breast Events In Ductal Carcinoma In Situ: A Case‒Control Study Including Black And White Women, Aditi Hazra, Emma Berdan, Thomas Walsh, Sarah Humble, Jen Tappenden, Katherine Deschryver, Deborah Veis, Kiran Vij, Shannan Ho Sui, Graham A Colditz

2020-Current year OA Pubs

BACKGROUND: Black women diagnosed with ductal carcinoma in situ (DCIS) experience disproportionately higher risk of second breast cancer events (SBEs), including both ipsilateral and contralateral recurrences, yet remain underrepresented in molecular biomarker studies compared to non-Hispanic White women.

METHODS: We performed RNA sequencing on 200 archival DCIS samples from the Resource of Archival Breast Tissue cohort, including 33% self-reported Black women. We correlated transcriptomic and clinical data to identify predictors of SBEs. Cases (n = 100) who developed SBEs between 1999 and 2019 were matched 1:1 to controls (n = 100) on age, race, and margin status, who remained event-free …


Recommendations Made And Accepted By A Telehealth-Enabled Antimicrobial Stewardship Program Implemented At Rural Veterans Affairs Medical Centers, Taissa A Bej, Jason P Burnham, Joshua D. Nordman, Et Al. May 2026

Recommendations Made And Accepted By A Telehealth-Enabled Antimicrobial Stewardship Program Implemented At Rural Veterans Affairs Medical Centers, Taissa A Bej, Jason P Burnham, Joshua D. Nordman, Et Al.

2020-Current year OA Pubs

BACKGROUND: To support Antimicrobial Stewardship programs (ASPs) as well as the clinical care of patients with infections, we disseminated and implemented a Videoconference Antimicrobial Stewardship Team (VAST) to connect multidisciplinary teams from rural Veterans Affairs (VA) medical centers with geographically distant ID experts. Here, we describe the clinical syndromes discussed and the response to recommendations made during VAST sessions.

METHODS: Between September 2021 to February 2024, eight ID consultants established VASTs with ten rural VAMCs, holding regularly scheduled videoconference sessions to discuss clinical cases and provide recommendations. Data were collected on patient demographics, clinical syndromes, and recommendations. Acceptance of recommendations …


Securepose: Automated Face Blurring And Human Movement Kinematics Extraction From Videos Recorded In Clinical Settings, Rishabh Bajpai, Bhooma Aravamuthan May 2026

Securepose: Automated Face Blurring And Human Movement Kinematics Extraction From Videos Recorded In Clinical Settings, Rishabh Bajpai, Bhooma Aravamuthan

2020-Current year OA Pubs

Movement disorder diagnosis often relies on expert evaluation of patient videos, but sharing these videos poses privacy risks. Current methods for de-identifying videos, such as blurring faces, are often manual, inconsistent, or inaccurate. Furthermore, these methods can compromise automated kinematics extraction-a valuable aid to movement analysis. To address these challenges, we developed SecurePose, open-source software that provides both reliable de-identification and automated body kinematic extraction from videos recorded in clinic settings using smartphones/tablets. We validated SecurePose on gait videos recorded in outpatient clinic visits of 116 children with cerebral palsy, assessing both the accuracy of its de-identification compared to the …


Spleen Volume Reduction And Transfusion Independence With Momelotinib Versus Ruxolitinib And Associated Overall Survival With Momelotinib In Jak Inhibitor-Naive Patients With Myelofibrosis And Anemia: Subgroup Analyses Of Simplify-1, Francesca Palandri, Stephen T Oh, Et Al. May 2026

Spleen Volume Reduction And Transfusion Independence With Momelotinib Versus Ruxolitinib And Associated Overall Survival With Momelotinib In Jak Inhibitor-Naive Patients With Myelofibrosis And Anemia: Subgroup Analyses Of Simplify-1, Francesca Palandri, Stephen T Oh, Et Al.

2020-Current year OA Pubs

INTRODUCTION: Improvements in splenomegaly, anemia, and overall survival (OS) are key considerations in the management of patients with myelofibrosis. In the phase III SIMPLIFY-1 trial (NCT01969838), momelotinib was noninferior to ruxolitinib for spleen volume reduction ≥ 35% (SVR35) and nominally superior for transfusion independence (TI) at week 24 in Janus kinase (JAK) inhibitor-naive patients. However, the relative impact of these endpoints on OS in anemic patients has not been described.

MATERIALS AND METHODS: The present post hoc analysis evaluated week 24 SVR35, TI, and dual responses (SVR35 + TI) in patients with baseline hemoglobin < 10 g/dL.

RESULTS: SVR35 rates were similar overall …