Medicine and Health Sciences Commons^™

Social Media For Research Discourse, Dissemination, And Collaboration In Rheumatology, Ariella Coler-Reilly, Elizabeth R. Graef, Alfred H J Kim, Jean W. Liew, Michael S. Putman, Sebastian E. Sattui, Kristen J. Young, Jeffrey A. Sparks

2020-Current year OA Pubs

Social media has become an important venue for rheumatologists, patients, organizations, and other stakeholders to discuss recent research advances in diagnosis and management of rheumatic disorders. In this article, we describe the current state of how social media may enhance dissemination, discourse, and collaboration in rheumatology research. Social media may refer to social platforms like Twitter and Instagram or digital media like podcasts and other websites that are operated for providing as free, open-access medical education (FOAM). Twitter has been one of the most active social media venues and continues to host a vibrant rheumatology community. Examples of research discussions …

A Randomized Phase 2 Study Of Neoadjuvant Carboplatin And Paclitaxel With Or Without Atezolizumab In Triple Negative Breast Cancer (Tnbc) - Nci 10013, Foluso O Ademuyiwa, Feng Gao, Cherease R Street, Ina Chen, John M Herndon, Madelyn Carmody, Sherri R Davies, Sarah Larson, Zheng Liu, Ian S Hagemann, William E Gillanders, Et Al.

2020-Current year OA Pubs

Atezolizumab with chemotherapy has shown improved progression-free and overall survival in patients with metastatic PD-L1 positive triple negative breast cancer (TNBC). Atezolizumab with anthracycline- and taxane-based neoadjuvant chemotherapy has also shown increased pathological complete response (pCR) rates in early TNBC. This trial evaluated neoadjuvant carboplatin and paclitaxel with or without atezolizumab in patients with clinical stages II-III TNBC. The co-primary objectives were to evaluate if chemotherapy and atezolizumab increase pCR rate and tumor infiltrating lymphocyte (TIL) percentage compared to chemotherapy alone in the mITT population. Sixty-seven patients (ages 25-78 years; median, 52 years) were randomly assigned - 22 patients to …

Bioimpedance-Derived Membrane Capacitance: Clinically Relevant Sources Of Variability, Precision, And Reliability, Valene Garr Barry, Jasmine L Chiang, Kaylan G Bowman, Kristina D Johnson, Barbara A Gower

2020-Current year OA Pubs

Membrane capacitance (C

Studies Of Parenchymal Texture Added To Mammographic Breast Density And Risk Of Breast Cancer: A Systematic Review Of The Methods Used In The Literature, Akila Anandarajah, Yongzhen Chen, Graham A Colditz, Angela Hardi, Carolyn Stoll, Shu Jiang

2020-Current year OA Pubs

This systematic review aimed to assess the methods used to classify mammographic breast parenchymal features in relation to the prediction of future breast cancer. The databases including Medline (Ovid) 1946-, Embase.com 1947-, CINAHL Plus 1937-, Scopus 1823-, Cochrane Library (including CENTRAL), and Clinicaltrials.gov were searched through October 2021 to extract published articles in English describing the relationship of parenchymal texture features with the risk of breast cancer. Twenty-eight articles published since 2016 were included in the final review. The identification of parenchymal texture features varied from using a predefined list to machine-driven identification. A reduction in the number of features …

Clonally Related, Notch-Differentiated Spinal Neurons Integrate Into Distinct Circuits, Saul Bello-Rojas, Martha W Bagnall

2020-Current year OA Pubs

Shared lineage has diverse effects on patterns of neuronal connectivity. In mammalian cortex, excitatory sister neurons assemble into shared microcircuits. In

Socioecological Predictors Of Breastfeeding Practices In Rural Eastern Ethiopia, Marina Magalhães, Amanda Ojeda, Karah Mechlowitz, Kaitlin Brittain, Jenna Daniel, Kedir Teji Roba, Jemal Yousuf Hassen, Mark J Manary, Wondwossen A Gebreyes, Arie H Havelaar, Sarah L Mckune

2020-Current year OA Pubs

BACKGROUND: Estimates by the World Health Organization indicate that over 800,000 global neonatal deaths each year are attributed to deviations from recommended best practices in infant feeding. Identifying factors promoting ideal breastfeeding practices may facilitate efforts to decrease neonatal and infant death rates and progress towards achieving the Sustainable Development Goals set for 2030. Though numerous studies have identified the benefits of breastfeeding in reducing the risk of childhood undernutrition, infection and illness, and mortality in low- and middle-income countries, no studies have explored predictors of breastfeeding practices in rural eastern Ethiopia, where undernutrition is widespread. The aim of this …

Interventions To Treat And Prevent Postpartum Depression: A Protocol For Systematic Review Of The Literature And Parallel Network Meta-Analyses, David Thomas Monks, Basavaraj Ankalagi, Preet Mohinder Singh, Ebony Carter, Michelle Doering, Meg Guard, Shannon Lenze

2020-Current year OA Pubs

INTRODUCTION: Postpartum depression has costly consequences for the mother, baby, and society. Numerous pharmacological and non-pharmacological interventions are available for the prevention and treatment of postpartum depression. To date, no attempt has been made to synthesize the evidence from comparisons of interventions both within and across these categories.

METHODS: We will perform a systematic review of the literature and perform network meta-analysis of interventions to (a) prevent and (b) treat postpartum depression. This review will include studies of primiparous or multiparous women during pregnancy or within 12 months of delivery of their baby that assess either interventions initiated during pregnancy …

An Rna Interference (Rnai) Toolkit And Its Utility For Functional Genetic Analysis Of Leishmania (Viannia), Lon-Fye Lye, Katherine L Owens, Soojin Jang, Joseph E Marcus, Erin A Brettmann, Stephen M Beverley

2020-Current year OA Pubs

RNA interference (RNAi) is a powerful tool whose efficacy against a broad range of targets enables functional genetic tests individually or systematically. However, the RNAi pathway has been lost in evolution by a variety of eukaryotes including most Leishmania sp. RNAi was retained in species of the

The Performance Of Plasma Amyloid Beta Measurements In Identifying Amyloid Plaques In Alzheimer's Disease: A Literature Review, Abby L Brand, Paige E Lawler, James G Bollinger, Yan Li, Suzanne E Schindler, Melody Li, Samir Lopez, Vitaliy Ovod, Akinori Nakamura, Leslie M Shaw, Henrik Zetterberg, Oskar Hansson, Randall J Bateman

2020-Current year OA Pubs

The extracellular buildup of amyloid beta (Aβ) plaques in the brain is a hallmark of Alzheimer's disease (AD). Detection of Aβ pathology is essential for AD diagnosis and for identifying and recruiting research participants for clinical trials evaluating disease-modifying therapies. Currently, AD diagnoses are usually made by clinical assessments, although detection of AD pathology with positron emission tomography (PET) scans or cerebrospinal fluid (CSF) analysis can be used by specialty clinics. These measures of Aβ aggregation, e.g. plaques, protofibrils, and oligomers, are medically invasive and often only available at specialized medical centers or not covered by medical insurance, and PET …

Diverse Monogenic Subforms Of Human Spermatogenic Failure, Liina Nagirnaja, Wu-Lin Charng, Christina A Gurnett, Kenan R Omurtag, Et Al.

2020-Current year OA Pubs

Non-obstructive azoospermia (NOA) is the most severe form of male infertility and typically incurable. Defining the genetic basis of NOA has proven challenging, and the most advanced classification of NOA subforms is not based on genetics, but simple description of testis histology. In this study, we exome-sequenced over 1000 clinically diagnosed NOA cases and identified a plausible recessive Mendelian cause in 20%. We find further support for 21 genes in a 2-stage burden test with 2072 cases and 11,587 fertile controls. The disrupted genes are primarily on the autosomes, enriched for undescribed human "knockouts", and, for the most part, have …

Epigenetic Clock Explains White Matter Hyperintensity Burden Irrespective Of Chronological Age, Joan Jiménez-Balado, Carolina Soriano-Tárraga, Et Al.

2020-Current year OA Pubs

In this manuscript we studied the relationship between WMH and biological age (B-age) in patients with acute stroke. We included in this study 247 patients with acute stroke recruited at Hospital del Mar having both epigenetic (DNA methylation) and magnetic resonance imaging data. WMH were measured using a semi-automated method. B-age was calculated using two widely used methods: the Hannum and Horvath formulas. We used multiple linear regression models to interrogate the role of B-age on WMH volume after adjusting for chronological age (C-age) and other covariables. Average C-age of the sample was 68.4 (±11.8) and we observed a relatively …

The Role Of Er Stress In Diabetes: Exploring Pathological Mechanisms Using Wolfram Syndrome, Shuntaro Morikawa, Fumihiko Urano

2020-Current year OA Pubs

The endoplasmic reticulum (ER) is a cytosolic organelle that plays an essential role in the folding and processing of new secretory proteins, including insulin. The pathogenesis of diabetes, a group of metabolic disorders caused by dysfunctional insulin secretion (Type 1 diabetes, T1DM) or insulin sensitivity (Type 2 diabetes, T2DM), is known to involve the excess accumulation of "poorly folded proteins", namely, the induction of pathogenic ER stress in pancreatic β-cells. ER stress is known to contribute to the dysfunction of the insulin-producing pancreatic β-cells. T1DM and T2DM are multifactorial diseases, especially T2DM; both environmental and genetic factors are involved in …

Associations Between Mental Health And Hiv Status Among Sexual Minority And Heterosexual Adolescents In Nigeria, Morenike Oluwatoyin Folayan, Olakunle Oginni, Olanrewaju Ibikunle Ibigbami, Uma Philip, Nserd Ntonoba Mfam, Chinedu Mbam, Amos Ganyam, Agada A Salem, Christopher Osuji, Cory Bradley, Joanne Lusher, Nadia Adjoa Sam-Agudu

2020-Current year OA Pubs

BACKGROUND: We aimed to determine associations between the mental health status of adolescents by self-reported sexual identity; and to determine associations between the mental health status of sexual minority adolescents living with and without HIV.

METHODS: This cross-sectional study collected data from Nigerians aged 13-19 years old using an online survey. We collected information on dependent (sexual identity) and independent (presence of depressive symptoms, generalised anxiety disorder, suicidal attempt/ideation, HIV status) study variables. A multivariate regression model determined associations between the dependent and independent variables. A second multivariate regression model was developed to establish associations between HIV status among sexual …

In Silico Activity And Admet Profiling Of Phytochemicals From Ethiopian Indigenous Aloes Using Pharmacophore Models, Lemessa Etana Bultum, Gemechu Bekele Tolossa, Gwangmin Kim, Ohhyeon Kwon, Doheon Lee

2020-Current year OA Pubs

In silico profiling is used in identification of active compounds and guide rational use of traditional medicines. Previous studies on Ethiopian indigenous aloes focused on documentation of phytochemical compositions and traditional uses. In this study, ADMET and drug-likeness properties of phytochemicals from Ethiopian indigenous aloes were evaluated, and pharmacophore-based profiling was done using Discovery Studio to predict therapeutic targets. The targets were examined using KEGG pathway, gene ontology and network analysis. Using random-walk with restart algorithm, network propagation was performed in CODA network to find diseases associated with the targets. As a result, 82 human targets were predicted and found …

Trem2 Dependent And Independent Functions Of Microglia In Alzheimer's Disease, Jinchao Hou, Yun Chen, Gary Grajales-Reyes, Marco Colonna

2020-Current year OA Pubs

Microglia are central players in brain innate immunity and have been the subject of extensive research in Alzheimer's disease (AD). In this review, we aim to summarize the genetic and functional discoveries that have advanced our understanding of microglia reactivity to AD pathology. Given the heightened AD risk posed by rare variants of the microglial triggering receptor expressed on myeloid cells 2 (TREM2), we will focus on the studies addressing the impact of this receptor on microglia responses to amyloid plaques, tauopathy and demyelination pathologies in mouse and human. Finally, we will discuss the implications of recent discoveries on microglia …

Myocardial Contractility Pattern Characterization In Radiation-Induced Cardiotoxicity Using Magnetic Resonance Imaging: A Pilot Study With Contractix, El-Sayed H Ibrahim, Antonio Sosa, Sherry-Ann Brown, Dayeong An, Slade Klawikowski, John Baker, Carmen Bergom

2020-Current year OA Pubs

Radiation therapy (RT) plays an integral role in treating thoracic cancers, despite the risk of radiation-induced cardiotoxicity. We hypothesize that our newly developed magnetic resonance imaging (MRI)-based contractility index (ContractiX) is a sensitive marker for early detection of RT-induced cardiotoxicity in a preclinical rat model of thoracic cancer RT. Adult salt-sensitive rats received image-guided heart RT and were imaged with MRI at 8 weeks and 10 weeks post-RT or sham. The MRI exam included cine and tagging sequences to measure left-ventricular ejection fraction (LVEF), mass, myocardial strain, and ContractiX. Furthermore, ventricular torsion, diastolic strain rate, and mechanical dyssynchrony were measured. …

Stakeholder Perspectives On The Demand And Supply Factors Driving Substandard And Falsified Blood Pressure Lowering Medications In Nigeria: A Qualitative Study, Grace Shedul, Olutobi Adekunle Sanuade, Eugenia N Ugwuneji, Tunde M Ojo, Aishwarya Vijay, Patrick Ponzing, Inuwa Okpe, Gabriel Lamkur Shedul, Mark D Huffman, Dike Ojji, Lisa R Hirschhorn

2020-Current year OA Pubs

OBJECTIVES: Although substandard and falsified (SF) blood pressure (BP) lowering medications are a global problem, qualitative research exploring factors driving this in Nigeria has not been reported. This study provides information on factors driving demand for and supply of low-quality BP lowering medications in Nigeria and potential strategies to address these factors.

METHODS: This was a cross-sectional qualitative study. Between August 2020 and September 2020, we conducted 11 in-depth interviews and 7 focus group discussions with administrators of health facilities, major manufacturers and distributors of BP lowering medications, pharmacists, drug regulators, patients and primary care physicians purposively sampled from the …

Effectiveness Of Soluble Ctla-4-Fc In The Inhibition Of Bone Marrow T-Cell Activation In Context Of Indoleamine 2.3-Dioxygenase (Ido) And Cd4+Foxp3+ Treg Induction, Magdalena Massalska, Marzena Ciechomska, Ewa Kuca-Warnawin, Tomasz Burakowski, Anna Kornatka, Anna Radzikowska, Dariusz Pawlak, Barbara Muz, Adrianna Loniewska-Lwowska, Andrzej Palucha, Pawel Maldyk, Wlodzimierz Maslinski

2020-Current year OA Pubs

BACKGROUND: Rheumatoid arthritis (RA) is a chronic autoimmune disease with systemic inflammation finally resulting in damaged joints. One of the RA development models suggests bone marrow (BM) as a place of inflammation development further leading to disease progression. We aimed to investigate the potential of CTLA-4-Fc molecule in inducing tolerogenic milieu in BM measured as indoleamine 2,3-dioxygenase (IDO) expression, CD4

METHODS: Bone marrow mononuclear cells (BMMC) were stimulated by pro-inflammatory cytokines and CTLA-4-Fc. Next IDO expression, CD4

RESULTS: We found that CTLA-4-Fc and IFN-γ stimulation results in IDO production by BMMC. CTLA-4-Fc induced tryptophan catabolism can inhibit mitogen-induced CD4

CONCLUSION: …

Utilization Of Cardiovascular Magnetic Resonance (Cmr) Imaging For Resumption Of Athletic Activities Following Covid-19 Infection: An Expert Consensus Document On Behalf Of The American Heart Association Council On Cardiovascular Radiology And Intervention (Cvri) Leadership And Endorsed By The Society For Cardiovascular Magnetic Resonance (Scmr), Frederick L. Ruberg, Aaron L. Baggish, Allison G. Hays, Michael Jerosch-Herold, Jiwon Kim, Karen G. Ordovas, Gautham Reddy, Chetan Shenoy, Jonathan W. Weinsaft, Pamela K. Woodard

2020-Current year OA Pubs

The global pandemic of coronavirus disease 2019 (COVID-19) caused by infection with severe acute respiratory suyndrome coronavirus 2 (SARS-CoV-2) is now entering its 4th year with little evidence of abatement. As of December 2022, the World Health Organization Coronavirus (COVID-19) Dashboard reported 643 million cumulative confirmed cases of COVID-19 worldwide and 98 million in the United States alone as the country with the highest number of cases. While pneumonia with lung injury has been the manifestation of COVID-19 principally responsible for morbidity and mortality, myocardial inflammation and systolic dysfunction though uncommon are well-recognized features that also associate with adverse prognosis. …

Lecanemab In Patients With Early Alzheimer's Disease: Detailed Results On Biomarker, Cognitive, And Clinical Effects From The Randomized And Open-Label Extension Of The Phase 2 Proof-Of-Concept Study, Eric Mcdade, Jeffrey L Cummings, Shobha Dhadda, Chad J Swanson, Larisa Reyderman, Michio Kanekiyo, Akihiko Koyama, Michael Irizarry, Lynn D Kramer, Randall J Bateman

2020-Current year OA Pubs

BACKGROUND: Lecanemab, a humanized IgG1 monoclonal antibody that targets soluble aggregated Aβ species (protofibrils), has demonstrated robust brain fibrillar amyloid reduction and slowing of clinical decline in early AD. The objective of this analysis is to report results from study 201 blinded period (core), the open-label extension (OLE), and gap period (between core and OLE) supporting the effectiveness of lecanemab.

METHODS: The lecanemab study 201 core was a double-blind, randomized, placebo-controlled study of 856 patients randomized to one of five dose regimens or placebo. An OLE of study 201 was initiated to allow patients to receive open-label lecanemab 10mg/kg biweekly …

Impact Of Cd4 T Cells On Intratumoral Cd8 T-Cell Exhaustion And Responsiveness To Pd-1 Blockade Therapy In Mouse Brain Tumors, Saad M. Khan, Rupen Desai, Andrew Coxon, Alexandra Livingstone, Gavin P Dunn, Allegra Petti, Tanner M Johanns

2020-Current year OA Pubs

BACKGROUND: Glioblastoma is a fatal disease despite aggressive multimodal therapy. PD-1 blockade, a therapy that reinvigorates hypofunctional exhausted CD8 T cells (T

METHODS: Single-cell RNA sequencing was performed on flow sorted tumor-infiltrating lymphocytes from female C57/BL6 mice implanted with each model, with and without PD-1 blockade therapy. CD8

RESULTS: The CD8 T-cell compartment of the models is composed of heterogenous CD8 T

CONCLUSIONS: Here, we describe that dysfunctional CD4 T cells are associated with terminal CD8 T-cell exhaustion, suggesting CD4 T cells impact PD-1 blockade efficacy by controlling the severity of exhaustion. Given that CD4 lymphopenia is frequently observed in …

Advice To Clinicians On Communication From Adolescents And Young Adults With Cancer And Parents Of Children With Cancer, Meghana Srinivas, Erica C Kaye, Lindsay J Blazin, Justin N Baker, Jennifer W Mack, James M Dubois, Bryan A Sisk

2020-Current year OA Pubs

Effective communication is integral to patient and family-centered care in pediatric and adolescent and young adult (AYA) oncology and improving healthcare delivery and outcomes. There is limited knowledge about whether AYAs and parents have similar communication preferences and needs. By eliciting and comparing communication advice from AYAs and parents, we can identify salient guidance for how clinicians can better communicate. We performed secondary analysis of semi-structured interviews from 2 qualitative communication studies. In one study, 80 parents of children with cancer during treatment, survivorship, or bereavement were interviewed. In the second study, AYAs with cancer during treatment or survivorship were …

Sodium Content And Labelling Of Packaged Foods And Beverages In Nigeria: A Cross-Sectional Study, Adedayo E Ojo, Mark D Huffman, Et Al.

2020-Current year OA Pubs

Increased consumption of unhealthy processed foods, particularly those high in sodium, is a major risk factor for cardiovascular diseases. The nutrition information on packaged foods can help guide consumers toward products with less sodium and support government actions to improve the healthiness of the food supply. The aims of this study were to estimate the proportion of packaged foods displaying nutrition information for sodium and other nutrients specified by Nigerian nutrition labelling regulations and to determine the amount of sodium in packaged foods sold in Nigeria using data from the nutritional information panel. Data were collected from November 2020 to …

Expanded Proteomic Survey Of The Human Parasite Leishmania Major Focusing On Changes In Null Mutants Of The Golgi Gdp-Mannose/Fucose/Arabinopyranose Transporter, Gloria Polanco, Nichollas E Scott, Lon F Lye, Stephen M Beverley

2020-Current year OA Pubs

The trypanosomatid protozoan parasite

A Mobile Phone Text Messaging Intervention To Manage Fatigue For People With Multiple Sclerosis, Spinal Cord Injury, And Stroke: Development And Usability Testing, Kerri A Morgan, Alex W K Wong, Kim Walker, Rachel Heeb Desai, Tina M Knepper, Pamela K Newland

2020-Current year OA Pubs

BACKGROUND: Fatigue significantly affects daily functioning in persons with disabilities. Fatigue management can be challenging, and the information provided during routine physician visits to manage fatigue can be overwhelming. One way to address fatigue is to increase knowledge, skills, and confidence for self-management (ie, patient activation). Self-management programs have shown promising effects in targeting fatigue in persons with disabilities. However, satisfaction with self-management programs is low for persons with disabilities, and tailoring interventions to personalized needs has been recommended. SMS text messaging is increasingly being used to implement health behavior change interventions in a person's natural environment. Little has been …

Antibodies Targeting The Neuraminidase Active Site Inhibit Influenza H3n2 Viruses With An S245n Glycosylation Site, Daniel Stadlbauer, Ali H Ellebedy, Et Al.

2020-Current year OA Pubs

Contemporary influenza A H3N2 viruses circulating since 2016 have acquired a glycosylation site in the neuraminidase in close proximity to the enzymatic active site. Here, we investigate if this S245N glycosylation site, as a result of antigenic evolution, can impact binding and function of human monoclonal antibodies that target the conserved active site. While we find that a reduction in the inhibitory ability of neuraminidase active site binders is measurable, this class of broadly reactive monoclonal antibodies maintains protective efficacy in vivo.

Utilization Of Cardiovascular Magnetic Resonance (Cmr) Imaging For Resumption Of Athletic Activities Following Covid-19 Infection: An Expert Consensus Document On Behalf Of The American Heart Association Council On Cardiovascular Radiology And Intervention (Cvri) Leadership And Endorsed By The Society For Cardiovascular Magnetic Resonance (Scmr), Frederick L Ruberg, Aaron L Baggish, Allison G Hays, Michael Jerosch-Herold, Jiwon Kim, Karen G Ordovas, Gautham Reddy, Chetan Shenoy, Jonathan W Weinsaft, Pamela K Woodard

2020-Current year OA Pubs

The global pandemic of coronavirus disease 2019 (COVID-19) caused by infection with severe acute respiratory suyndrome coronavirus 2 (SARS-CoV-2) is now entering its 4th year with little evidence of abatement. As of December 2022, the World Health Organization Coronavirus (COVID-19) Dashboard reported 643 million cumulative confirmed cases of COVID-19 worldwide and 98 million in the United States alone as the country with the highest number of cases. While pneumonia with lung injury has been the manifestation of COVID-19 principally responsible for morbidity and mortality, myocardial inflammation and systolic dysfunction though uncommon are well-recognized features that also associate with adverse prognosis. …

A Genome-Wide Association Study Of 2304 Extreme Longevity Cases Identifies Novel Longevity Variants, Harold Bae, Ping An, Mary Feitosa, Et Al.

2020-Current year OA Pubs

We performed a genome-wide association study (GWAS) of human extreme longevity (EL), defined as surviving past the 99th survival percentile, by aggregating data from four centenarian studies. The combined data included 2304 EL cases and 5879 controls. The analysis identified a locus in CDKN2B-AS1 (rs6475609,

Caregiver Perceptions Of Change In Pediatric Asthma Control During The Covid-19 Pandemic, Gabrielle Pogge, Erika A Waters, Gregory D Webster, Sreekala Prabhakaran, Jean M Hunleth, David A Fedele, James A Shepperd

2020-Current year OA Pubs

PURPOSE: Although several indicators suggest that pediatric asthma control in the United States improved early in the pandemic, other indicators suggest not. Missing are reports from caregivers of the experiences of their children with asthma early in the pandemic.

METHODS: Using the PP-ACT and other measures that we specifically constructed for our research, we conducted a cross-sectional national survey of US caregivers of children with asthma (N=595) to examine perceived change in their child's asthma control and changes in reports of ED visits and use of emergency relief medicine and controller medicine pre-pandemic (January to March 2020) versus early-pandemic (June …

Quality Assessment And Refinement Of Chromatin Accessibility Data Using A Sequence-Based Predictive Model, Seong Kyu Han, Yoshiharu Muto, Parker C Wilson, Benjamin D Humphreys, Matthew G Sampson, Aravinda Chakravarti, Dongwon Lee

2020-Current year OA Pubs

Chromatin accessibility assays are central to the genome-wide identification of gene regulatory elements associated with transcriptional regulation. However, the data have highly variable quality arising from several biological and technical factors. To surmount this problem, we developed a sequence-based machine learning method to evaluate and refine chromatin accessibility data. Our framework, gapped k-mer SVM quality check (gkmQC), provides the quality metrics for a sample based on the prediction accuracy of the trained models. We tested 886 DNase-seq samples from the ENCODE/Roadmap projects to demonstrate that gkmQC can effectively identify "high-quality" (HQ) samples with low conventional quality scores owing to marginal …