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Robust Statistical Methods For Microbiome Abundance Data, Yiming Shi Dec 2026

Robust Statistical Methods For Microbiome Abundance Data, Yiming Shi

WUSM Theses and Dissertations – All Programs

Differential abundance analysis in microbiome studies aims to identify taxa whose abundance differs across biological or clinical conditions. The observed data are typically taxon-specific sequencing read counts, representing reads assigned to different taxa within each sample. These counts are indirect measurements of the underlying microbial abundance profile and are constrained by sample-specific library sizes. Microbiome count data are also typically sparse, overdispersed, and heteroscedastic. Together, these characteristics create substantial challenges for differential abundance analysis and make the results highly sensitive to normalization procedures, model specification, and the statistical methods used for inference.

Normalization defines the scale on which samples are …


Investigating The Ability Of Presequences To Influence Mitochondrial Protein Import, Youmian Yan Dec 2026

Investigating The Ability Of Presequences To Influence Mitochondrial Protein Import, Youmian Yan

WUSM Theses and Dissertations – All Programs

Mitochondria are essential organelles housing over 1000 proteins, 99% of which are nuclear-encoded and synthesized in the cytosol. Most mitochondrial proteins are targeted by a positively charged sequence called the presequence, which lacks a common sequence motif and is poorly conserved across evolution. Accumulating evidence suggests that presequences encode meaningful information that influences mitochondrial protein uptake. For instance, multiple stress response models propose that stress sensing proteins contain “weak” presequences which allows them to monitor mitochondrial health. However, there is a lack of systematic examination about how presequences influence import kinetics and what constitutes presequence strength. These gaps in knowledge …


Complementary Vertebrate Wac Models Exhibit Phenotypes Relevant To Desanto-Shinawi Syndrome, Kang-Han Lee, Marwan Shinawi, Et Al. Sep 2026

Complementary Vertebrate Wac Models Exhibit Phenotypes Relevant To Desanto-Shinawi Syndrome, Kang-Han Lee, Marwan Shinawi, Et Al.

2020-Current year OA Pubs

Monogenic syndromes are associated with neurodevelopmental changes that result in cognitive impairments and neurobehavioral phenotypes, including autism and seizures. Limited studies and resources are available to make meaningful headway into the underlying molecular mechanisms that result in these symptoms. One such example is DeSanto-Shinawi Syndrome (DESSH), a rare disorder caused by pathogenic variants in the


Current State And Needs Of Clinical Laboratories In Selected Countries In Africa, Merih Tesfazghi, Anne E Tebo, Roa Harb, Anthony O Okorodudu, Lee Schroeder, Jeannette Guarner, Christine Bales, Jack Ladenson, Allison Targowski, Kerry Cosby, Olajumoke Oladipo Sep 2026

Current State And Needs Of Clinical Laboratories In Selected Countries In Africa, Merih Tesfazghi, Anne E Tebo, Roa Harb, Anthony O Okorodudu, Lee Schroeder, Jeannette Guarner, Christine Bales, Jack Ladenson, Allison Targowski, Kerry Cosby, Olajumoke Oladipo

2020-Current year OA Pubs

The Africa Working Group, under the auspices of the Global Laboratory Quality Initiative of the Association for Diagnostics & Laboratory Medicine (ADLM), conducted several educational workshops in Africa to promote laboratory quality in the region. The challenges faced in maintaining quality in clinical laboratories in low-resource countries may differ from region to region and country to country. To better understand current gaps and inform our engagement with partners in Africa, a needs assessment survey was distributed to 1427 ADLM members in Africa and further disseminated through local partners, resulting in 121 responses from participants across 8 countries in the region. …


Parent-Child Neural Dynamics During A Stressful Task: Probing Associations With Temperament And Anxiety, Joscelin Rocha-Hidalgo, Harmony Nguyen, Dakota Reis, Denny Schaedig, Kahlil I Thompson, Susan B Perlman, Koraly E Pérez-Edgar Sep 2026

Parent-Child Neural Dynamics During A Stressful Task: Probing Associations With Temperament And Anxiety, Joscelin Rocha-Hidalgo, Harmony Nguyen, Dakota Reis, Denny Schaedig, Kahlil I Thompson, Susan B Perlman, Koraly E Pérez-Edgar

2020-Current year OA Pubs

Dynamic social interactions between parents and children can contribute to anxiety risk, amplifying shared genetic risk. Research has focused on observed behaviors to explain intergenerational transmission. Neural synchrony may contribute as a biological conduit for behavioral transmission of risk. We examined 109 parent-child dyads (


Spinal Cord Imaging For Multiple Sclerosis: Advances, Priorities, And Opportunities, Cornelia Laule, Matthew R Brier, Et Al. Sep 2026

Spinal Cord Imaging For Multiple Sclerosis: Advances, Priorities, And Opportunities, Cornelia Laule, Matthew R Brier, Et Al.

2020-Current year OA Pubs

The spinal cord plays a central role in the pathophysiology and clinical manifestations of multiple sclerosis (MS), yet remains under-studied compared with the brain. This review summarizes key insights from the 2025 North American Imaging in MS Spinal Cord Imaging Workshop, highlighting recent advances, ongoing challenges, and future opportunities in MS spinal cord imaging. We review pathological studies and outline the clinical relevance of spinal cord lesions and atrophy for diagnosis, prognosis, and disease monitoring, highlighting emerging biomarkers of progression independent of relapse activity. Correlations between magnetic resonance imaging, histopathology, and clinical outcomes support the validation and translational potential of …


Heritable Transgenic Schistosomes As A Living Platform For Sars-Cov-2 Neutralizing Antibody Secretion, Wannaporn Ittiprasert, Bruce A Rosa, Sergej Djuranovic, Makedonka Mitreva, Et Al. Aug 2026

Heritable Transgenic Schistosomes As A Living Platform For Sars-Cov-2 Neutralizing Antibody Secretion, Wannaporn Ittiprasert, Bruce A Rosa, Sergej Djuranovic, Makedonka Mitreva, Et Al.

2020-Current year OA Pubs

We report the generation and propagation of not only the first heritable transgenic schistosome line but also a line that secretes a functional therapeutic protein in vivo. Using multiplexed CRISPR/Cas-mediated homology-directed knock-in targeted to a predicted genomic safe-harbor, we inserted a VHH-IgG1 Fc (termed C5-Fc) transgene into Schistosoma mansoni eggs. Single-miracidium infections of Biomphalaria glabrata yielded parental P0 lines; serial passage through snail and mouse hosts produced an F2 cohort in which all parasites carried the C5-Fc transgene and secreted C5-Fc into the murine venous circulation. Molecular assays confirmed chromosomal insertion, germline transmission and systemic secretion. Sera from mice harboring …


Altered Postnatal Chromatin Development In The Nucleus Accumbens Primes Enduring Stress Sensitivity, Rebekah L Rashford, Lisa Z Fang, Michael Deberardine, Hye Ji J Kim, Laura W Hirschfield, Ella Cervi, Mason R Barrett, Jeremy M Thompson, Meaghan C Creed, Catherine Jensen Peña Aug 2026

Altered Postnatal Chromatin Development In The Nucleus Accumbens Primes Enduring Stress Sensitivity, Rebekah L Rashford, Lisa Z Fang, Michael Deberardine, Hye Ji J Kim, Laura W Hirschfield, Ella Cervi, Mason R Barrett, Jeremy M Thompson, Meaghan C Creed, Catherine Jensen Peña

2020-Current year OA Pubs

Early life stress (ELS) sensitizes individuals to subsequent stressors to increase lifetime risk for psychiatric disorders. Within the nucleus accumbens (NAc)-a key limbic and reward-associated brain region-ELS sensitizes both cellular and transcriptional response to later stress, which are programmed by enduring epigenetic changes. Among the histone modifications persistently enriched by ELS in NAc is H3K4me1, which is associated with open chromatin and epigenetic priming of genomic enhancers. Here, we sought to determine whether H3K4me1 enrichment in NAc was sufficient to prime cellular and behavioral responses to adult stress. Viral-mediated overexpression of the histone H3 monomethyltransferase


Host-Pathogen Dynamics Underpinning Staphylococcus Aureus Growth During Intracellular Osteoclast Infection, Luke D. O'Connor Aug 2026

Host-Pathogen Dynamics Underpinning Staphylococcus Aureus Growth During Intracellular Osteoclast Infection, Luke D. O'Connor

WUSM Theses and Dissertations – All Programs

Bone infection is most commonly caused by the gram-positive bacterium Staphylococcus aureus. It has myriad ways in which it can circumvent or subvert killing by the host or antibiotics. Intracellular infection is one such niche that is protective from immune and antibiotic attack. In 2019, Krauss and colleagues discovered that infected osteoclasts (OCs) allow S. aureus to replicate intracellularly. There they found that the ability of S. aureus to grow inside the cell was tied to OC differentiation. The magnitude of overnight bacterial expansion positively correlated with OC maturity and duration cultured with the osteoclastogenic factor RANK ligand (RANKL). Bacterial …


“Something Else To Focus On”: Perinatal Havening And Stress Coping In Pregnant Black Women, Brittany L. Ferrell Young Aug 2026

“Something Else To Focus On”: Perinatal Havening And Stress Coping In Pregnant Black Women, Brittany L. Ferrell Young

WUSM Theses and Dissertations – All Programs

Black women in the United States experience maternal mortality at more than three times the rate of white women, a disparity driven by chronic stress rooted in structural racism rather than individual behavior or biology. Accessible, culturally responsive tools for managing stress during pregnancy remain scarce. This mixed-methods pilot feasibility study examined Perinatal Havening, a self-administered psychosensory technique, as a stress management intervention for pregnant Black women. Guided by Lazarus and Folkman's Transactional Theory of Stress and Coping, the study addressed three questions: how Black women experience acute and chronic stress during pregnancy, the acceptability and preliminary influence of Perinatal …


Premarket Clinical Evidence Strength And Recalls Of High-Risk Therapeutic Medical Devices, Maryam Mooghali, Faaizah Arshad, Vinay K Rathi, Kushal T Kadakia, Alexander O Everhart, Joseph S Ross, Sanket S Dhruva Aug 2026

Premarket Clinical Evidence Strength And Recalls Of High-Risk Therapeutic Medical Devices, Maryam Mooghali, Faaizah Arshad, Vinay K Rathi, Kushal T Kadakia, Alexander O Everhart, Joseph S Ross, Sanket S Dhruva

2020-Current year OA Pubs

IMPORTANCE: High-risk medical devices approved through the US Food and Drug Administration (FDA) premarket approval (PMA) pathway may be supported by limited premarket clinical evidence, leaving uncertainties about safety. Whether device, premarket clinical evidence, or regulatory characteristics are associated with subsequent device recalls is unknown.

OBJECTIVE: To examine the association between device, premarket clinical evidence, and regulatory characteristics and serious recalls among high-risk therapeutic devices.

DESIGN AND SETTING: This cross-sectional study reviewed 193 high-risk therapeutic medical devices approved through the FDA's PMA pathway between January 1, 2014, and December 31, 2023. Data were analyzed between August 2025 and December 2025. …


Sex-Aware Causal Inference Assessment Of The Immune System In Complex Neurodegenerative Diseases, Frida Lona-Durazo, Ross P Byrne, Marc-Olivier Pilon, Michael D Greicius, Marie-Pierre Dubé, Michael E Belloy, Russell L Mclaughlin, Sarah A Gagliano Taliun Aug 2026

Sex-Aware Causal Inference Assessment Of The Immune System In Complex Neurodegenerative Diseases, Frida Lona-Durazo, Ross P Byrne, Marc-Olivier Pilon, Michael D Greicius, Marie-Pierre Dubé, Michael E Belloy, Russell L Mclaughlin, Sarah A Gagliano Taliun

2020-Current year OA Pubs

Sex differences, in terms of prevalence, symptoms and disease progression, are established in the aetiology of complex neurodegenerative diseases, including amyotrophic lateral sclerosis, Parkinson's disease and Alzheimer's disease, but the underlying biology driving these differences remains poorly understood. There is emerging evidence from genetic and functional analyses affirming the role of the immune system in such diseases, but a thorough assessment of sex differences in the link between the immune system and neurodegenerative diseases remains lacking. Here, we applied a robust causal inference approach, two-sample Mendelian randomization, to evaluate the causal effect of immune-related protein levels on three neurodegenerative diseases …


Acute Opioid Responses Are Modulated By Dynamic Interactions Of Oprm1 And Fgf12, Paige M Lemen, Alexander S Hatoum, Arpana Agrawal, Et Al. Jul 2026

Acute Opioid Responses Are Modulated By Dynamic Interactions Of Oprm1 And Fgf12, Paige M Lemen, Alexander S Hatoum, Arpana Agrawal, Et Al.

2020-Current year OA Pubs

We generated time-series data for 105 morphine- and naloxone-related traits across ~700 BXD mice (64 diverse strains for both sexes) for 3 hr after a single morphine injection. Variations in responses were mapped using genome sequencing-based genotypes. The locomotor responses to morphine mapped to the µ opioid receptor gene (


Recent Advances In Alzheimer's Disease: From Molecular Mechanisms To Therapeutic Strategies, Michelle D Rudman, Jason D Ulrich, David M Holtzman Jul 2026

Recent Advances In Alzheimer's Disease: From Molecular Mechanisms To Therapeutic Strategies, Michelle D Rudman, Jason D Ulrich, David M Holtzman

2020-Current year OA Pubs

Alzheimer's disease (AD) remains the leading cause of dementia worldwide and an escalating global health crisis. The hallmark amyloid plaques and neurofibrillary tangles (NFT) are now known to be accompanied by a complex array of pathologies that culminate in neurodegeneration and cognitive decline. New disease-modifying therapies for AD can now slow cognitive decline through the removal of amyloid plaques from the brain, but treatments to stop or prevent cognitive impairment remain elusive. In this review, we summarize the most recent updates in AD research on pathologic disease mechanisms and therapeutic strategies, highlighting advancements in apolipoprotein E (APOE) biology, neuroimmunology, biomarker …


Tgf-Β Drives The Conversion Of Conventional Nk Cells Into Uterine Tissue-Resident Nk Cells To Support Murine Pregnancy, Josselyn D Barahona, Liping Yang, D Michael Nelson, Wayne M Yokoyama Jul 2026

Tgf-Β Drives The Conversion Of Conventional Nk Cells Into Uterine Tissue-Resident Nk Cells To Support Murine Pregnancy, Josselyn D Barahona, Liping Yang, D Michael Nelson, Wayne M Yokoyama

2020-Current year OA Pubs

Tissue microenvironments shape lymphocyte differentiation to align immune function with local physiological demands. Uterine natural killer (NK) cells are critical for reproductive success, yet the molecular cues in the uterus that instruct their specialized identities remain incompletely understood. Here, we identify a TGF-β-dependent differentiation pathway by which circulating conventional NK cells convert into uterine tissue-resident NK cells during murine pregnancy. Loss of TGF-β receptor II expression in


Subunit Composition Of The Katp Channels That Modulate Contractility Of Skeletal Muscle During Fatigue, Rosa Scala, Yuezhou Chen, Berk Mizrak, Gretchen A Meyer, Colin G Nichols Jul 2026

Subunit Composition Of The Katp Channels That Modulate Contractility Of Skeletal Muscle During Fatigue, Rosa Scala, Yuezhou Chen, Berk Mizrak, Gretchen A Meyer, Colin G Nichols

2020-Current year OA Pubs

ATP-sensitive potassium (KATP) channels are among the most expressed ion channels in skeletal muscle sarcolemma. While all KATP subunits can be detected in skeletal muscles, transcripts are enriched for KCNJ11 and ABCC9, suggesting that noncanonical Kir6.2/SUR2A assembly may constitute the majority of sarcolemmal KATP channels, but there has been no systematic dissection of KATP makeup in skeletal muscles. Here, we used a unique collection of murine lines selectively lacking specific channel-forming subunits (knockout, KO), and combined a genetic and pharmacological approach to determine which subunits of KATP channels are functionally relevant for skeletal muscle contraction. Under fatiguing conditions, isometric tetanic …


Long-Term Inactivation Mediated By Different Fgf-A Homologues On Heterologously Expressed Nav1.2 Currents, Yenisleidy Lorenzo-Ceballos, Pedro L Martinez-Espinosa, Xiao-Ming Xia, Christopher J Lingle Jul 2026

Long-Term Inactivation Mediated By Different Fgf-A Homologues On Heterologously Expressed Nav1.2 Currents, Yenisleidy Lorenzo-Ceballos, Pedro L Martinez-Espinosa, Xiao-Ming Xia, Christopher J Lingle

2020-Current year OA Pubs

A-isoforms of cytosolic growth factor homologous factors (FGF11-14) mediate long-term inactivation (LTI) of voltage-dependent sodium (NaV) channels. LTI is a rapid onset process that is competitive with the fast inactivation (IF) intrinsic to NaV channels, with little or no interconversion between inactivated states. Since recovery from LTI is orders of magnitude slower than recovery from IF, repetitive depolarizations lead to use-dependent accumulation of NaV channels in slow recovery states, thereby limiting NaV availability during trains of action potentials. Of the two or more N-terminal splice variants of the various FGF homologues, LTI specifically arises only from the A-isoform of each …


Laser Interstitial Thermal Therapy Enhances Bidirectional Blood-Brain Barrier Permeability In Glioblastoma, Ryan T Cleary, Yiwei Fu, David Giles, Jinyun Yuan, Diogo P Moniz Garcia, Danny Palmer, Rowland H Han, Timothy Woodiwiss, Alicia B Yang, Dimitrios Mathios, Hong Chen, Albert H Kim Jul 2026

Laser Interstitial Thermal Therapy Enhances Bidirectional Blood-Brain Barrier Permeability In Glioblastoma, Ryan T Cleary, Yiwei Fu, David Giles, Jinyun Yuan, Diogo P Moniz Garcia, Danny Palmer, Rowland H Han, Timothy Woodiwiss, Alicia B Yang, Dimitrios Mathios, Hong Chen, Albert H Kim

2020-Current year OA Pubs

BACKGROUND: Laser interstitial thermal therapy (LITT) is a minimally invasive treatment for glioblastoma that increases blood-brain barrier (BBB) permeability. However, the mechanisms and spatiotemporal features of this effect remain unclear. It is also unknown whether LITT promotes release of circulating tumor DNA (ctDNA).

METHODS: Using our previously developed LITT mouse model, we employed single-cell RNA-sequencing (scRNA-seq) to investigate gene expression changes in endothelial cells following LITT in the naive mouse brain. Brains were also harvested at multiple time points to assess LITT effects on tight junction (TJ) integrity and transcytosis via immunofluorescence and transmission electron microscopy. Human glioblastoma tissues were …


Modern Molecular Profiling Recontextualizes The Nrg/Rtog 0539 Trial And Reveals Hidden High-Risk And Radiotherapy-Resistant Meningiomas, Leeor S Yefet, Clifford Robinson, Et Al. Jul 2026

Modern Molecular Profiling Recontextualizes The Nrg/Rtog 0539 Trial And Reveals Hidden High-Risk And Radiotherapy-Resistant Meningiomas, Leeor S Yefet, Clifford Robinson, Et Al.

2020-Current year OA Pubs

BACKGROUND: Meningiomas exhibit clinical heterogeneity. Radiotherapy (RT) remains the only adjuvant therapy, but tumor-control is variable, and biomarkers are limited. NRG/RTOG-0539 is the first prospective phase 2 trial to stratify meningioma patients for adjuvant RT based on clinical risk. Here, we apply modern molecular tools to this cohort and identify correlates of RT response.

METHODS: Tumor tissue from 100 RTOG-0539 patients was profiled using DNA methylation arrays, RNA sequencing, and whole-exome sequencing. Recurrence scores, Molecular Groups, gene expression, and copy number alterations were compared across clinical groups and between RT responders and non-responders; non-response was defined as progression or death …


A Call To Investigate The Association Between Histoplasmosis And Fatigue, Christian Hendrix, Julio Zuniga-Moya, Andrej Spec, Patrick Mazi Jul 2026

A Call To Investigate The Association Between Histoplasmosis And Fatigue, Christian Hendrix, Julio Zuniga-Moya, Andrej Spec, Patrick Mazi

2020-Current year OA Pubs

Historically, infections are subjectively associated with fatigue, a common yet poorly delineated syndrome. The impact on patient quality of life is the ultimate justification to evaluate fatigue in patients with infections. While fungal infections are subjectively associated with fatigue, there are minimal quantifiable fungal research outcomes that evaluate histoplasmosis and fatigue.


Enhancing Validation Of Case-Control Omics Signatures Through "Minimalist" Single-Subject Analysis (N-Of-1 Trials): Proof Of Concept In Sepsis, Liam S Wilson, Nima Pouladi, Rachel F Nelson, Elizabeth A Middleton, Neal D Tolley, Mahdieh Shabanian, Colleen Kenost, Robert A Campbell, Matthew T Rondina, Yves A Lussier Jul 2026

Enhancing Validation Of Case-Control Omics Signatures Through "Minimalist" Single-Subject Analysis (N-Of-1 Trials): Proof Of Concept In Sepsis, Liam S Wilson, Nima Pouladi, Rachel F Nelson, Elizabeth A Middleton, Neal D Tolley, Mahdieh Shabanian, Colleen Kenost, Robert A Campbell, Matthew T Rondina, Yves A Lussier

2020-Current year OA Pubs

OBJECTIVE: To evaluate if a single-subject study (S3) design, utilizing paired transcriptome samples from the same patient (eg, "sepsis" vs "recovered"), can replicate transcriptomic signatures from small case-control studies, addressing challenges in patient accrual for rare or sub-stratified diseases.

METHODS: We generated a sepsis gene signature (SGS) comprising 300 differentially expressed genes (DEGs; FDR <  5%) from a human sepsis case-control cohort using general linear models (GLMs). Reproducibility of SGS was assessed through three approaches applied to sub-sampled independent datasets: single-subject analyses (N-of-1-MixEnrich), anticipated to perform better; conventional paired-sample GLM analyses; and a traditional case-control GLM analysis.

RESULTS: SGS reproducibility in GLM analyses was inconsistent at smaller cohort sizes (∼80% reproducibility; n = 5) but stabilized at cohort sizes >6. Remarkably, the single-subject-study approach consistently reproduced SGS in each of the 18 subjects individually (100% reproducibility; n = 1).

DISCUSSION: Conventional GLMs are …


Patterns Of Brain-Wide Associations Reflect Socioeconomics, Scott Marek, Meghan Rose Donohue, Nicole R Karcher, Caroline P Hoyniak, Roselyne J Chauvin, Ashley C Meyer, John Miller, Andrew N Van, Anxu Wang, Noah J Baden, Vahdeta Suljic, Kristen M Scheidter, Julia Monk, Forrest I Whiting, Nadeshka J Ramirez-Perez, Samuel R Krimmel, Athanasia Metoki, Rebecca F Schwarzlose, Steven E Petersen, Joan Luby, Benjamin P Kay, Evan M Gordon, Timothy O Laumann, Deanna M Barch, Nico U F Dosenbach, Et Al. Jun 2026

Patterns Of Brain-Wide Associations Reflect Socioeconomics, Scott Marek, Meghan Rose Donohue, Nicole R Karcher, Caroline P Hoyniak, Roselyne J Chauvin, Ashley C Meyer, John Miller, Andrew N Van, Anxu Wang, Noah J Baden, Vahdeta Suljic, Kristen M Scheidter, Julia Monk, Forrest I Whiting, Nadeshka J Ramirez-Perez, Samuel R Krimmel, Athanasia Metoki, Rebecca F Schwarzlose, Steven E Petersen, Joan Luby, Benjamin P Kay, Evan M Gordon, Timothy O Laumann, Deanna M Barch, Nico U F Dosenbach, Et Al.

2020-Current year OA Pubs

Previous brain-wide association studies (BWAS) have linked specific environmental and behavioral variables to brain variability. In this work, we mapped 649 variables to children's brains and compared the resultant BWAS maps with each other and with neurobiological reference patterns. Socioeconomic status (SES) showed the strongest brain-wide associations. The SES associations were strongest in motor and sensory but not cognitive regions, a pattern shared across many BWAS maps, including intelligence quotient (IQ). A single, common BWAS brain pattern existed across variables that was most reflective of a child's socioeconomics. Adjusting for SES weakened brain-IQ associations, eliminating the BWAS motor and sensory …


Growth In Early Infancy Drives Optimal Brain Functional Connectivity Which Predicts Cognitive Flexibility In Later Childhood, Chiara Bulgarelli, Anna Blasi, Samantha Mccann, Bosiljka Milosavljevic, Giulia Ghillia, Ebrima Mbye, Ebou Touray, Tijan Fadera, Lena Acolatse, Sophie E Moore, Sarah Lloyd-Fox, Clare E Elwell, Adam T Eggebrecht, Bright Study Team Jun 2026

Growth In Early Infancy Drives Optimal Brain Functional Connectivity Which Predicts Cognitive Flexibility In Later Childhood, Chiara Bulgarelli, Anna Blasi, Samantha Mccann, Bosiljka Milosavljevic, Giulia Ghillia, Ebrima Mbye, Ebou Touray, Tijan Fadera, Lena Acolatse, Sophie E Moore, Sarah Lloyd-Fox, Clare E Elwell, Adam T Eggebrecht, Bright Study Team

2020-Current year OA Pubs

Functional brain network organisation, measured by functional connectivity (FC), reflects key neurodevelopmental processes for healthy development. Early exposure to adversity, for example undernutrition, affects neurodevelopment, observable via disrupted FC, and leads to poorer outcomes from preschool age onwards. We assessed longitudinally the impact of early growth trajectories on developmental FC in a rural Gambian population from age 5-24 months. To investigate how these early trajectories relate to later childhood outcomes, we assessed cognitive flexibility at 3-5 years. We observed that early physical growth before the fifth month of life drove optimal developmental trajectories of FC that in turn predicted cognitive …


Autoregulation Of Three Yeast Ribosomal Protein Genes By Splicing Inhibition, David Granas, Anirudh Kesanapally, Michael A White, Gary D Stormo Jun 2026

Autoregulation Of Three Yeast Ribosomal Protein Genes By Splicing Inhibition, David Granas, Anirudh Kesanapally, Michael A White, Gary D Stormo

2020-Current year OA Pubs

Yeast ribosomal protein genes RPL18B, RPL28, and RPS22B are autoregulated by inhibition of splicing. This is demonstrated by inserting their introns into a chromosomal copy of GFP and observing repression upon induction of the cognate protein. In RPL18B and RPS22B, a predicted conserved secondary structure within the intron is required for regulation, while in RPL28, it is not.


Spatial Transcriptomic Profiling Of Decalcified Murine Musculoskeletal Samples Via Xenium Prime 5k, Lindsey Lammlin, Huong X Tran, Aanya Mohan, Michael D Newton, Scarlet C Howser, Stephen J Redding, Christina A Capobianco, Kurt D Hankenson, Alexander J Knights, Tristan Maerz Jun 2026

Spatial Transcriptomic Profiling Of Decalcified Murine Musculoskeletal Samples Via Xenium Prime 5k, Lindsey Lammlin, Huong X Tran, Aanya Mohan, Michael D Newton, Scarlet C Howser, Stephen J Redding, Christina A Capobianco, Kurt D Hankenson, Alexander J Knights, Tristan Maerz

2020-Current year OA Pubs

Successful generation of high-quality spatial transcriptomics data from murine musculoskeletal tissues has been impeded by the challenge of preserving RNA integrity through the harsh tissue processing steps required for histological sectioning. In particular, the need to thoroughly fix and decalcify mineralized tissues has proven problematic. We detail a comprehensive sample processing pipeline for 3 common murine musculoskeletal tissue samples, enabling high-quality transcript detection via imaging-based spatial transcriptomics using the Xenium Prime 5K platform from 10x Genomics. Our protocol outlines methodological details for transcardiac perfusion, fixation, decalcification, paraffin processing, and a sample co-embedding strategy facilitating anatomically consistent and simultaneous sectioning of …


Human Stem Cell-Based Embryo Models: Innovation, Ethics, And Policy, Alfonso Martinez Arias, Thorold Theunissen, Et Al. Jun 2026

Human Stem Cell-Based Embryo Models: Innovation, Ethics, And Policy, Alfonso Martinez Arias, Thorold Theunissen, Et Al.

2020-Current year OA Pubs

The aim of this White Paper is to establish a foundational framework for research, technological development, and regulation in the emerging field of stem cell-based embryo models (SCBEMs). These models, generated from Pluripotent Stem Cells, are designed to recapitulate essential events in early stages of human development. They have the potential to illuminate the early stages of embryo development and implantation and hold promise as an avenue to address global health challenges, including infertility and pregnancy loss, congenital, neonatal and adult conditions, and the need for organ transplants. While SCBEMs are not a substitute for human embryos, their tractability for …


Wayfindr: Investigating Feedback In Biological Pathways, Polina Bombina, Reginald L Mcgee Ii, Jake Reed, Zachary B Abrams, Lynne V Abruzzo, Kevin R Coombes Jun 2026

Wayfindr: Investigating Feedback In Biological Pathways, Polina Bombina, Reginald L Mcgee Ii, Jake Reed, Zachary B Abrams, Lynne V Abruzzo, Kevin R Coombes

2020-Current year OA Pubs

Understanding biological pathways requires more than static diagrams. We present WayFindR, an R package that converts pathway data from WikiPathways and KEGG into graph structures using igraph, enabling computational analysis of regulatory features such as negative feedback loops. Rooted in control theory, negative feedback is essential for system stability, yet it is often underrepresented in curated pathway data. In this study, we systematically analyzed pathway information from both databases across multiple species and found that feedback loops-particularly negative ones-are rarely captured. This gap likely reflects both biological and technical challenges. Biologically, feedback mechanisms are inherently complex and often remain uncharted …


Biomedgraphica: An All-In-One Platform For Joint Textual Biomedical Prior Knowledge And Numeric Graph Generation, Heming Zhang, Shunning Liang, Tim Xu, Wenyu Li, Di Huang, Yuhan Dong, Philip Miller, Peter Goedegebuure, Marco Sardiello, Jonathan Cooper, William Buchser, Patricia Dickson, Ryan C Fields, Carlos Cruchaga, Yixin Chen, Michael Province, Philip Payne, Fuhai Li, Et Al. Jun 2026

Biomedgraphica: An All-In-One Platform For Joint Textual Biomedical Prior Knowledge And Numeric Graph Generation, Heming Zhang, Shunning Liang, Tim Xu, Wenyu Li, Di Huang, Yuhan Dong, Philip Miller, Peter Goedegebuure, Marco Sardiello, Jonathan Cooper, William Buchser, Patricia Dickson, Ryan C Fields, Carlos Cruchaga, Yixin Chen, Michael Province, Philip Payne, Fuhai Li, Et Al.

2020-Current year OA Pubs

MOTIVATION: Multiomics data analysis is essential for scientific discovery in precision medicine. However, translating analysis results of omics data analysis into novel scientific hypotheses remains a significant challenge. Human experts must manually review analysis results and generate new hypotheses based on extensive and interconnected biomedical prior knowledge, which is subjective and not scalable. While large language models can accelerate the discovery, their reasoning improves when grounded in structured, auditable, and comprehensive biomedical prior knowledge. However, biomedical knowledge is scattered across heterogeneous databases that use diverse and inconsistent nomenclature systems, making it difficult to integrate resources into a unified format for …


Role Of Households With Children In Community Spread Of Multidrug-Resistant Enterobacterales, St. Louis, Missouri, Usa, Barrett Breeze, Ahmed Babiker, Sreenivas Konda, Alaina L Robinson, Stefan J Green, Catherine C Babbs, Federico Cunha, Katherine Y Shen, India Shepherd Hammond, Stephanie A Fritz, Latania K Logan Jun 2026

Role Of Households With Children In Community Spread Of Multidrug-Resistant Enterobacterales, St. Louis, Missouri, Usa, Barrett Breeze, Ahmed Babiker, Sreenivas Konda, Alaina L Robinson, Stefan J Green, Catherine C Babbs, Federico Cunha, Katherine Y Shen, India Shepherd Hammond, Stephanie A Fritz, Latania K Logan

2020-Current year OA Pubs

Community-acquired multidrug-resistant (MDR) Enterobacterales bacteria are an increasing public health concern, yet whether households play a role in community spread remains unclear. We investigated 150 households with children in St. Louis, Missouri, USA, for MDR Enterobacterales. We cultured swab specimens from household members and environmental surfaces for identification and antimicrobial susceptibility testing. We also performed whole-genome sequencing in the 53 (35%) households where >1 MDR Enterobacterales species were recovered. Enterobacter hormaechei predominated, followed by Klebsiella pneumoniae and Pantoea species. Whole-genome sequencing revealed closely related strains shared between persons and environmental surfaces, suggesting potential intra-household transmission. We identified >1 horizontal gene …


Viscoelastic And Morphologic Changes In The Lumbar Intervertebral Discs Of The 5xfad Mouse Model Of Alzheimer's Disease, C E Gonzalez, C A Schurman, K A Wilson, B Schilling, L M Ellerby, S Y Tang Jun 2026

Viscoelastic And Morphologic Changes In The Lumbar Intervertebral Discs Of The 5xfad Mouse Model Of Alzheimer's Disease, C E Gonzalez, C A Schurman, K A Wilson, B Schilling, L M Ellerby, S Y Tang

2020-Current year OA Pubs

BACKGROUND: Chronic low back pain, commonly associated with intervertebral disc (IVD) degeneration, is highly prevalent in patients with Alzheimer's disease (AD), and the severity of the pain is correlated with the severity of the dementia. While incidences of both afflictions increase dramatically in the elderly population, it is unknown whether AD exacerbates the health of the IVD.

AIMS: The aim of this study is to examine how AD-related mutations affect the structure and mechanics of the IVD.

MATERIALS AND METHODS: Utilizing one-year-old male and female 5xFAD mice that constitutively express human APP and PSEN1 transgenes with five AD-linked mutations, we …