Digital Commons Network^™

Single-Cell Analysis Of Chromatin And Expression Reveals Age- And Sex-Associated Alterations In The Human Heart, David F Read, Yiing Lin, Et Al.

2020-Current year OA Pubs

Sex differences and age-related changes in the human heart at the tissue, cell, and molecular level have been well-documented and many may be relevant for cardiovascular disease. However, how molecular programs within individual cell types vary across individuals by age and sex remains poorly characterized. To better understand this variation, we performed single-nucleus combinatorial indexing (sci) ATAC- and RNA-Seq in human heart samples from nine donors. We identify hundreds of differentially expressed genes by age and sex and find epigenetic signatures of variation in ATAC-Seq data in this discovery cohort. We then scale up our single-cell RNA-Seq analysis by combining …

Clinical Features And Disease Progression In Older Individuals With Rett Syndrome, Jeffrey L Neul, Timothy A Benke, Eric D Marsh, Bernhard Suter, Cary Fu, Robin C Ryther, Steven A Skinner, David N Lieberman, Timothy Feyma, Arthur Beisang, Peter Heydemann, Sarika U Peters, Amitha Ananth, Alan K Percy

2020-Current year OA Pubs

Although long-term survival in Rett syndrome (RTT) has been observed, limited information on older people with RTT exists. We hypothesized that increased longevity in RTT would be associated with genetic variants in

Mapping Neural Correlates Of Biological Motion Perception In Autistic Children Using High-Density Diffuse Optical Tomography, Dalin Yang, Alexandra M Svoboda, Tessa G George, Patricia K Mansfield, Muriah D Wheelock, Mariel L Schroeder, Sean M Rafferty, Arefeh Sherafati, Kalyan Tripathy, Tracy Burns-Yocum, Elizabeth Forsen, John R Pruett, Natasha M Marrus, Joseph P Culver, John N Constantino, Adam T Eggebrecht

2020-Current year OA Pubs

BACKGROUND: Autism spectrum disorder (ASD), a neurodevelopmental disorder defined by social communication deficits plus repetitive behaviors and restricted interests, currently affects 1/36 children in the general population. Recent advances in functional brain imaging show promise to provide useful biomarkers of ASD diagnostic likelihood, behavioral trait severity, and even response to therapeutic intervention. However, current gold-standard neuroimaging methods (e.g., functional magnetic resonance imaging, fMRI) are limited in naturalistic studies of brain function underlying ASD-associated behaviors due to the constrained imaging environment. Compared to fMRI, high-density diffuse optical tomography (HD-DOT), a non-invasive and minimally constraining optical neuroimaging modality, can overcome these limitations. …

Association Between Tumor-Infiltrating Lymphocytes And Survival In Patients With Metastatic Breast Cancer Receiving First-Line Chemotherapy: Analysis Of Calgb 40502, Daniel G Stover, Mark Watson, Et Al.

2020-Current year OA Pubs

Association of stromal tumor-infiltrating lymphocytes (sTILs) with survival outcomes among patients with metastatic breast cancer (MBC) remains unclear. The primary objective was to evaluate the association of sTILs with progression-free survival in randomized phase III trial CALGB 40502. sTILs were associated with progression-free and overall survival in chemotherapy-treated MBC when controlling for treatment arm; however, this effect did not remain significant after additional adjustment for hormone receptor status. CALGB is now part of the Alliance for Clinical Trials in Oncology. Trial Registration: ClinicalTrials.gov: NCT00785291.

A Brief Alcohol Intervention (Bai) To Reduce Alcohol Use And Improve Prep Outcomes Among Men Who Have Sex With Men In Vietnam: Study Protocol For A Randomized Controlled Trial, Hao T M Bui, Byron J Powell, Et Al.

2020-Current year OA Pubs

BACKGROUND: In Vietnam and other global settings, men who have sex with men (MSM) have become the population at greatest risk of HIV infection. Although HIV pre-exposure prophylaxis (PrEP) has been implemented as a prevention strategy, PrEP outcomes may be affected by low persistence and adherence among MSM with unhealthy alcohol use. MSM have a high prevalence of unhealthy alcohol use in Vietnam, which may affect PrEP outcomes.

METHODS: Design: We will conduct a two-arm hybrid type 1 effectiveness-implementation randomized controlled trial of a brief alcohol intervention (BAI) compared to the standard of care (SOC) at the Sexual Health Promotion …

Using Deepsignalingflow To Mine Signaling Flows Interpreting Mechanism Of Synergy Of Cocktails, Heming Zhang, Yixin Chen, Philip Payne, Fuhai Li

2020-Current year OA Pubs

Complex signaling pathways are believed to be responsible for drug resistance. Drug combinations perturbing multiple signaling targets have the potential to reduce drug resistance. The large-scale multi-omic datasets and experimental drug combination synergistic score data are valuable resources to study mechanisms of synergy (MoS) to guide the development of precision drug combinations. However, signaling patterns of MoS are complex and remain unclear, and thus it is challenging to identify synergistic drug combinations in clinical. Herein, we proposed a novel integrative and interpretable graph AI model, DeepSignalingFlow, to uncover the MoS by integrating and mining multi-omic data. The major innovation is …

Mice Lacking Astn2 Have Asd-Like Behaviors And Altered Cerebellar Circuit Properties, Michalina Hanzel, Kayla Fernando, Susan E Maloney, Zachi Horn, Shiaoching Gong, Kärt Mätlik, Jiajia Zhao, H Amalia Pasolli, Søren Heissel, Joseph D Dougherty, Court Hull, Mary E Hatten

2020-Current year OA Pubs

Astrotactin 2 (ASTN2) is a transmembrane neuronal protein highly expressed in the cerebellum that functions in receptor trafficking and modulates cerebellar Purkinje cell (PC) synaptic activity. Individuals with

Parent Attitudes Towards Predictive Testing For Autism In The First Year Of Life, Aurora M Washington, Amanda H Mercer, Catherine A Burrows, Stephen R Dager, Jed T Elison, Annette M Estes, Rebecca Grzadzinski, Chimei Lee, Joseph Piven, John R Pruett Jr, Mark D Shen, Benjamin Wilfond, Jason Wolff, Lonnie Zwaigenbaum, Katherine E Macduffie

2020-Current year OA Pubs

BACKGROUND: Emerging biomarker technologies (e.g., MRI, EEG, digital phenotyping, eye-tracking) have potential to move the identification of autism into the first year of life. We investigated the perspectives of parents about the anticipated utility and impact of predicting later autism diagnosis from a biomarker-based test in infancy.

METHODS: Parents of infants were interviewed to ascertain receptiveness and perspectives on early (6-12 months) prediction of autism using emerging biomarker technologies. One group had experience parenting an older autistic child (n=30), and the other had no prior autism parenting experience (n=25). Parent responses were analyzed using inductive qualitative coding methods.

RESULTS: Almost …

The Role Of Brown Adipose Tissue In Branched-Chain Amino Acid Clearance In People, Yasser G Abdelhafez, Guobao Wang, Siqi Li, Vanessa Pellegrinelli, Abhijit J Chaudhari, Anthony Ramirez, Fatma Sen, Antonio Vidal-Puig, Labros S Sidossis, Samuel Klein, Ramsey D Badawi, Maria Chondronikola

2020-Current year OA Pubs

Brown adipose tissue (BAT) in rodents appears to be an important tissue for the clearance of plasma branched-chain amino acids (BCAAs) contributing to improved metabolic health. However, the role of human BAT in plasma BCAA clearance is poorly understood. Here, we evaluate patients with prostate cancer who underwent positron emission tomography-computed tomography imaging after an injection of

Harnessing The Power Of Longitudinal Medical Imaging For Eye Disease Prognosis Using Transformer-Based Sequence Modeling, Gregory Holste, Mingquan Lin, Ruiwen Zhou, Fei Wang, Lei Liu, Qi Yan, Sarah H Van Tassel, Kyle Kovacs, Emily Y Chew, Zhiyong Lu, Zhangyang Wang, Yifan Peng

2020-Current year OA Pubs

Deep learning has enabled breakthroughs in automated diagnosis from medical imaging, with many successful applications in ophthalmology. However, standard medical image classification approaches only assess disease presence at the time of acquisition, neglecting the common clinical setting of longitudinal imaging. For slow, progressive eye diseases like age-related macular degeneration (AMD) and primary open-angle glaucoma (POAG), patients undergo repeated imaging over time to track disease progression and forecasting the future risk of developing a disease is critical to properly plan treatment. Our proposed Longitudinal Transformer for Survival Analysis (LTSA) enables dynamic disease prognosis from longitudinal medical imaging, modeling the time to …

Newborn Screening For Spinal Muscular Atrophy: Variations In Practice And Early Management Of Infants With Spinal Muscular Atrophy In The United States, Craig M Zaidman, Cameron D Crockett, Ethan Wedge, Grace Tabatabai, Natalie Goedeker

2020-Current year OA Pubs

In the United States (U.S.), newborn screening (NBS) for spinal muscular atrophy (SMA) is implemented by individual states. There is likely variation in the practice patterns of state NBS programs and among the providers caring for newborns with SMA. This is a prospective, descriptive, observational study that seeks to quantify and describe practice patterns and heterogeneities in state NBS programs and provider practices in the U.S. We surveyed U.S. state NBS programs and care providers of newborns with SMA. Thirty states and 41 practitioners responded. NBS program practices vary by state. Most (74%) state programs provide results to both primary …

Femoral Geometry And Activity Type: Factors That Influence Loading In The Dysplastic Hip, Molly C. Shepherd

WUSM Theses and Dissertations – All Programs

Developmental dysplasia of the hip (DDH) is a bony condition characterized by a shallow hip socket that reduces coverage of the femoral head and leads to instability, resulting in altered joint loading and an increased risk for early onset osteoarthritis (OA). Understanding the factors that influence loading in the dysplastic hip is necessary for developing effective treatment strategies and improving patient outcomes. The purpose of this dissertation was to examine multiple factors that could impact joint loading in DDH: 1) sport specific activities, 2) femoral version (FV) deformities, and 3) derotational femoral osteotomy (DFO) correction for FV deformities. Analyzing how …

Single-Cell Analysis Of Innate Spinal Cord Regeneration Identifies Intersecting Modes Of Neuronal Repair, Vishnu Muraleedharan Saraswathy, Lili Zhou, Mayssa H Mokalled

2020-Current year OA Pubs

Adult zebrafish have an innate ability to recover from severe spinal cord injury. Here, we report a comprehensive single nuclear RNA sequencing atlas that spans 6 weeks of regeneration. We identify cooperative roles for adult neurogenesis and neuronal plasticity during spinal cord repair. Neurogenesis of glutamatergic and GABAergic neurons restores the excitatory/inhibitory balance after injury. In addition, a transient population of injury-responsive neurons (iNeurons) show elevated plasticity 1 week post-injury. We found iNeurons are injury-surviving neurons that acquire a neuroblast-like gene expression signature after injury. CRISPR/Cas9 mutagenesis showed iNeurons are required for functional recovery and employ vesicular trafficking as an …

An Accurate And Rapidly Calibrating Speech Neuroprosthesis, Nicholas S Card, Matthew F Glasser, Et Al.

2020-Current year OA Pubs

BACKGROUND: Brain-computer interfaces can enable communication for people with paralysis by transforming cortical activity associated with attempted speech into text on a computer screen. Communication with brain-computer interfaces has been restricted by extensive training requirements and limited accuracy.

METHODS: A 45-year-old man with amyotrophic lateral sclerosis (ALS) with tetraparesis and severe dysarthria underwent surgical implantation of four microelectrode arrays into his left ventral precentral gyrus 5 years after the onset of the illness; these arrays recorded neural activity from 256 intracortical electrodes. We report the results of decoding his cortical neural activity as he attempted to speak in both prompted …

Complexity Organization Of Resting-State Functional-Mri Networks, Gabriel Trevino, John J Lee, Joshua S Shimony, Patrick H Luckett, Eric C Leuthardt

2020-Current year OA Pubs

Entropy measures are increasingly being used to analyze the structure of neural activity observed by functional magnetic resonance imaging (fMRI), with resting-state networks (RSNs) being of interest for their reproducible descriptions of the brain's functional architecture. Temporal correlations have shown a dichotomy among these networks: those that engage with the environment, known as extrinsic, which include the visual and sensorimotor networks; and those associated with executive control and self-referencing, known as intrinsic, which include the default mode network and the frontoparietal control network. While these inter-voxel temporal correlations enable the assessment of synchrony among the components of individual networks, entropic …

5Β-Dihydrosteroids: Formation And Properties, Trevor M Penning, Douglas F Covey

2020-Current year OA Pubs

5β-Dihydrosteroids are produced by the reduction of Δ

Immunological Correlates Of Protection Mediated By A Whole Organism,Cryptococcus Neoformans, Vaccine Deficient In Chitosan, Charles A Specht, Ruiying Wang, Lorena V N Oliveira, Maureen M Hester, Christina Gomez, Zhongming Mou, Diana Carlson, Chrono K Lee, Camaron R Hole, Woei C Lam, Rajendra Upadhya, Jennifer K Lodge, Stuart M Levitz

2020-Current year OA Pubs

UNLABELLED: The global burden of infections due to the pathogenic fungus

IMPORTANCE: The fungus

Development Of Vla4 And Cxcr4 Antagonists For The Mobilization Of Hematopoietic Stem And Progenitor Cells, Peter G Ruminski, Michael P Rettig, John F Dipersio

2020-Current year OA Pubs

The treatment of patients diagnosed with hematologic malignancies typically includes hematopoietic stem cell transplantation (HSCT) as part of a therapeutic standard of care. The primary graft source of hematopoietic stem and progenitor cells (HSPCs) for HSCT is mobilized from the bone marrow into the peripheral blood of allogeneic donors or patients. More recently, these mobilized HSPCs have also been the source for gene editing strategies to treat diseases such as sickle-cell anemia. For a HSCT to be successful, it requires the infusion of a sufficient number of HSPCs that are capable of adequate homing to the bone marrow niche and …

Neuronal Activity In The Gustatory Cortex During Economic Choice, Ahmad Jezzini, Camillo Padoa-Schioppa

2020-Current year OA Pubs

An economic choice entails computing and comparing the values of individual offers. Offer values are represented in the orbitofrontal cortex (OFC)-an area that participates in value comparison-but it is unknown where offer values are computed in the first place. One possibility is that this computation takes place in OFC. Alternatively, offer values might be computed upstream of OFC. For choices between edible goods, a primary candidate is the gustatory region of the anterior insula (gustatory cortex, GC). Here we recorded from the GC of male rhesus monkeys choosing between different juice types. As a population, neurons in GC represented the …

Sac1 Links Phosphoinositide Turnover To Cryptococcal Virulence, Elizabeth A Gaylord, Hau Lam Choy, Guohua Chen, Sydney L Briner, Tamara L Doering

2020-Current year OA Pubs

No abstract provided.

Dominance Analysis To Assess Solute Contributions To Multicomponent Phase Equilibria, Daoyuan Qian, Hannes Ausserwoger, Tomas Sneideris, Mina Farag, Rohit V Pappu, Tuomas P J Knowles

2020-Current year OA Pubs

Phase separation in aqueous solutions of macromolecules underlies the generation of biomolecular condensates in cells. Condensates are membraneless bodies, representing dense, macromolecule-rich phases that coexist with the dilute, macromolecule-deficient phases. In cells, condensates comprise hundreds of different macromolecular and small molecule solutes. How do different solutes contribute to the driving forces for phase separation? To answer this question, we introduce a formalism we term energy dominance analysis. This approach rests on analysis of shapes of the dilute phase boundaries, slopes of tie lines, and changes to dilute phase concentrations in response to perturbations of concentrations of different solutes. The framework …

Dual Role Of Neuroplastin In Pancreatic Β Cells: Regulating Insulin Secretion And Promoting Islet Inflammation, Rie Asada Kitamura, Devynn Hummel, Alessandro Ustione, David W. Piston, Fumihiko Urano

2020-Current year OA Pubs

No abstract provided.

Multimodal Mechanisms Of Pathogenic Variants In The Signal Peptide Of Fix Leading To Hemophilia B, Meng Gao, Long Chen, Jinlong Yang, Shixia Dong, Qing Cao, Zihan Cui, Yanyan Dong, Hongli Liu, Yan Shen, Haiping Yang, Zhenyu Hao, Lei Zhang, Weikai Li, Jian-Ke Tie, Guomin Shen

2020-Current year OA Pubs

Signal peptide (SP) is essential for protein secretion, and pathogenic variants in the SP of factor IX (FIX) have been identified in hemophilia B (HB). However, the underlying mechanism for the genotype-phenotype correlation of these variants has not been well studied. Here, we systematically examined the effects of 13 pathogenic point variants in the SP of FIX using different approaches. Our results showed that these point variants lead to HB by missense variants and/or aberrant premessenger RNA (pre-mRNA) splicing. The missense variants in a hydrophobic core (h-region) mainly affected the cotranslational translocation function of the SP, and those in C-terminal …

Infection Prevention And Control In 2030: A First Qualitative Survey By The Crystal Ball Initiative, Hugo Sax, Jonas Marschall, Crystal Ball Initiative

2020-Current year OA Pubs

BACKGROUND: Healthcare delivery is undergoing radical changes that influence effective infection prevention and control (IPC). Futures research (short: Futures), the science of deliberating on multiple potential future states, is increasingly employed in many core societal fields. Futures might also be helpful in IPC to facilitate current education and organisational decisions. Hence, we conducted an initial survey as part of the IPC Crystal Ball Initiative.

METHODS: In 2019, international IPC experts were invited to answer a 10-item online questionnaire, including demographics, housekeeping, and open-ended core questions (Q) on the "status of IPC in 2030" (Q1), "people in charge of IPC" (Q2), …

An Integrated Structural Model Of The Dna Damage-Responsive H3k4me3 Binding Wdr76:Spin1 Complex With The Nucleosome, Xingyu Liu, Yixuan Xie, Benjamin A Garcia, Et Al.

2020-Current year OA Pubs

Serial capture affinity purification (SCAP) is a powerful method to isolate a specific protein complex. When combined with cross-linking mass spectrometry and computational approaches, one can build an integrated structural model of the isolated complex. Here, we applied SCAP to dissect a subpopulation of WDR76 in complex with SPIN1, a histone reader that recognizes trimethylated histone H3 lysine4 (H3K4me3). In contrast to a previous SCAP analysis of the SPIN1:SPINDOC complex, histones and the H3K4me3 mark were enriched with the WDR76:SPIN1 complex. Next, interaction network analysis of copurifying proteins and microscopy analysis revealed a potential role of the WDR76:SPIN1 complex in …

A Simplified G-Csf-Free Procedure Allows For In Vivo Hsc Gene Therapy Of Sickle Cell Disease In A Mouse Model, Chang Li, Anna K Anderson, Peter Ruminski, Michael Rettig, Darja Karpova, Hans-Peter Kiem, John F Dipersio, André Lieber

2020-Current year OA Pubs

We have reported the direct repair of the sickle cell mutation in vivo in a disease model using vectorized prime editors after hematopoietic stem cell (HSC) mobilization with granulocyte colony-stimulating factor (G-CSF)/AMD3100. The use of G-CSF for HSC mobilization is a hurdle for the clinical translation of this approach. Here, we tested a G-CSF-free mobilization regimen using WU-106, an inhibitor of integrin α4β1, plus AMD3100 for in vivo HSC prime editing in sickle cell disease (SCD) mice. Mobilization with WU-106 + AMD3100 in SCD mice was rapid and efficient. In contrast to the G-CSF/AMD3100 approach, mobilization of activated granulocytes and …

Neoantigen Landscape Supports Feasibility Of Personalized Cancer Vaccine For Follicular Lymphoma, Cody A Ramirez, Michelle Becker-Hapak, Kartik Singhal, David A Russler-Germain, Erica K Barnell, Ethan D Mcclain, Sweta Desai, Timothy Schappe, Onyinyechi C Onyeador, Susanna Kiwala, Jasreet Hundal, Zachary L Skidmore, Marcus P Watkins, Thomas B Mooney, Jason R Walker, Kilannin Krysiak, Felicia Gomez, Catrina C Fronick, Robert S Fulton, Robert D Schreiber, Neha Mehta-Shah, Amanda F Cashen, Brad S Kahl, Nancy L Bartlett, Malachi Griffith, Obi L Griffith, Todd A Fehniger, Et Al.

2020-Current year OA Pubs

Personalized cancer vaccines designed to target neoantigens represent a promising new treatment paradigm in oncology. In contrast to classical idiotype vaccines, we hypothesized that "polyvalent" vaccines could be engineered for the personalized treatment of follicular lymphoma (FL) using neoantigen discovery by combined whole-exome sequencing (WES) and RNA sequencing (RNA-seq). Fifty-eight tumor samples from 57 patients with FL underwent WES and RNA-seq. Somatic and B-cell clonotype neoantigens were predicted and filtered to identify high-quality neoantigens. B-cell clonality was determined by the alignment of B-cell receptor (BCR) CDR3 regions from RNA-seq data, grouping at the protein level, and comparison with the BCR …

Signaling By A Bacterial Phytochrome Histidine Kinase Involves A Conformational Cascade Reorganizing The Dimeric Photoreceptor, E Sethe Burgie, Katherine Basore, Michael J Rau, Brock Summers, Alayna J Mickles, Vadim Grigura, James A J Fitzpatrick, Richard D Vierstra

2020-Current year OA Pubs

Phytochromes (Phys) are a divergent cohort of bili-proteins that detect light through reversible interconversion between dark-adapted Pr and photoactivated Pfr states. While our understandings of downstream events are emerging, it remains unclear how Phys translate light into an interpretable conformational signal. Here, we present models of both states for a dimeric Phy with histidine kinase (HK) activity from the proteobacterium Pseudomonas syringae, which were built from high-resolution cryo-EM maps (2.8-3.4-Å) of the photosensory module (PSM) and its following signaling (S) helix together with lower resolution maps for the downstream output region augmented by RoseTTAFold and AlphaFold structural predictions. The head-to-head …

Kat2a And Kat2b Prevent Double-Stranded Rna Accumulation And Interferon Signaling To Maintain Intestinal Stem Cell Renewal, Mai-Uyen Nguyen, Angela Halstead, José B Sáenz, Et Al.

2020-Current year OA Pubs

Histone acetyltransferases

Untargeted Lipidomics Reveals Racial Differences In Lipid Species Among Women, Ghazaleh Pourali, Liang Li, Kayla R Getz, Myung Sik Jeon, Jingqin Luo, Chongliang Luo, Adetunji T Toriola

2020-Current year OA Pubs

Understanding the biological mechanisms underlying racial differences in diseases is crucial to developing targeted prevention and treatment. There is, however, limited knowledge of the impact of race on lipids. To address this, we performed comprehensive lipidomics analyses to evaluate racial differences in lipid species among 506 non-Hispanic White (NHW) and 163 non-Hispanic Black (NHB) women. Plasma lipidomic profiling quantified 982 lipid species. We used multivariable linear regression models, adjusted for confounders, to identify racial differences in lipid species and corrected for multiple testing using a Bonferroni-adjusted p-value <  10