Detection by Single-Cell RNA Sequencing of Virally Mediated Skin Diseases.

Viruses are well-documented agents of specific skin diseases. However, their role and precise mechanism of action in other skin diseases remain unknown. We describe a single-cell RNA-sequencing-based strategy to interrogate human skin biopsies for viral transcripts, permitting detection of viral infection within a sample, single-cell resolution of virally infected cells and identification of subsequent transcriptomic perturbations.

Association of Integrated Proteomic and Metabolomic Modules with Risk of Kidney Disease Progression.

Key Points: Integrated analysis of proteome and metabolome identifies modules associated with CKD progression and kidney failure. Ephrin transmembrane proteins and podocyte-expressed CRIM1 and NPNT emerged as central components and warrant experimental and clinical investigation.

Background: Proteins and metabolites play crucial roles in various biological functions and are frequently interconnected through enzymatic or transport processes.

Spatially coordinated heterochromatinization of long synaptic genes in fragile X syndrome.

Short tandem repeat (STR) instability causes transcriptional silencing in several repeat expansion disorders. In fragile X syndrome (FXS), mutation-length expansion of a CGG STR represses FMR1 via local DNA methylation. Here, we find megabase-scale H3K9me3 domains on autosomes and encompassing FMR1 on the X chromosome in FXS patient-derived iPSCs, iPSC-derived neural progenitors, EBV-transformed lymphoblasts, and brain tissue with mutation-length CGG expansion.

Proteomics analysis of plasma from middle-aged adults identifies protein markers of dementia risk in later life.

A diverse set of biological processes have been implicated in the pathophysiology of Alzheimer's disease (AD) and related dementias. However, there is limited understanding of the peripheral biological mechanisms relevant in the earliest phases of the disease. Here, we used a large-scale proteomics platform to examine the association of 4877 plasma proteins with 25-year dementia risk in 10,981 middle-aged adults.

A qualitative study of Canadian resident experiences with Competency-Based Medical Education.

Background: Competency-based medical education (CBME) is an outcomes-based curricular paradigm focused on ensuring that graduates are competent to meet the needs of patients. Although resident engagement is key to CBME's success, few studies have explored how trainees have experienced CBME implementation. We explored the experiences of residents in Canadian training programs that had implemented CBME.

Alterations in the Circulating Proteome Associated with Albuminuria.

Significance Statement: We describe circulating proteins associated with albuminuria in a population of African American Study of Kidney Disease and Hypertension with CKD (AASK) using the largest proteomic platform to date: nearly 7000 circulating proteins, representing approximately 2000 new targets. Findings were replicated in a subset of a general population cohort with kidney disease (ARIC) and a population with CKD Chronic Renal Insufficiency Cohort (CRIC). In cross-sectional analysis, 104 proteins were significantly associated with albuminuria in the Black group, of which 67 of 77 available proteins were replicated in ARIC and 68 of 71 available proteins in CRIC.

A Novel Creatinine Muscle Index Based on Creatinine Filtration: Associations with Frailty and Mortality.

Significance Statement: Low muscle mass is related to frailty and increased mortality in older adults. However, muscle mass is not easily assessed in routine clinical practice. This paper describes a novel creatinine muscle index (CMI) on the basis of serum creatinine and cystatin C.

Objective estimation of fusional reserves using infrared eye tracking: the digital fusion-range test.

Clinical Relevance: Horizontal fusional reserves are used in the diagnosis and monitoring of common vergence disorders, such as convergence insufficiency, which can cause asthenopia and impact near work. Infrared eyetracking technology shows promise for obtaining automated and objective measurements of fusional reserves, expanding options for screening, clinical testing, and at-home monitoring/vision training.

Background: Current clinical tests for fusional reserves rely on subjective judgements made by patients (for diplopia) and clinicians (for eye movements).

Integrated proteomic and metabolomic modules identified as biomarkers of mortality in the Atherosclerosis Risk in Communities study and the African American Study of Kidney Disease and Hypertension.

Background: Proteins and metabolites are essential for many biological functions and often linked through enzymatic or transport reactions. Individual molecules have been associated with all-cause mortality. Many of these are correlated and might jointly represent pathways or endophenotypes involved in diseases.

Testican-2 Is Associated with Reduced Risk of Incident ESKD.

Background: Testican-2 was recently identified as a podocyte-derived protein that is released into circulation by the kidneys and is positively correlated with eGFR and eGFR slope. However, whether higher testican-2 levels are associated with lower risk of ESKD is unknown.

Methods: Aptamer-based proteomics assessed blood testican-2 levels among participants in the African American Study of Kidney Disease and Hypertension (AASK, n =703), the Chronic Renal Insufficiency Cohort (CRIC) study ( n =3196), and the Atherosclerosis Risk in Communities (ARIC) study ( n =4378).

Metabolite profiling of CKD progression in the chronic renal insufficiency cohort study.

BACKGROUNDMetabolomic profiling in individuals with chronic kidney disease (CKD) has the potential to identify novel biomarkers and provide insight into disease pathogenesis.METHODSWe examined the association between blood metabolites and CKD progression, defined as the subsequent development of end-stage renal disease (ESRD) or estimated glomerular filtrate rate (eGFR) halving, in 1,773 participants of the Chronic Renal Insufficiency Cohort (CRIC) study, 962 participants of the African-American Study of Kidney Disease and Hypertension (AASK), and 5,305 participants of the Atherosclerosis Risk in Communities (ARIC) study.RESULTSIn CRIC, more than half of the measured metabolites were associated with CKD progression in minimally adjusted Cox proportional hazards models, but the number and strength of associations were markedly attenuated by serial adjustment for covariates, particularly eGFR.

Serum Metabolites and Kidney Outcomes: The Atherosclerosis Risk in Communities Study.

Rationale & Objective: Novel metabolite biomarkers of kidney failure with replacement therapy (KFRT) may help identify people at high risk for adverse kidney outcomes and implicated pathways may aid in developing targeted therapeutics.

Study Design: Prospective cohort.

Setting & Participants: The cohort included 3,799 Atherosclerosis Risk in Communities study participants with serum samples available for measurement at visit 1 (1987-1989).

Identification of 969 protein quantitative trait loci in an African American population with kidney disease attributed to hypertension.

Investigations into the causal underpinnings of disease processes can be aided by the incorporation of genetic information. Genetic studies require populations varied in both ancestry and prevalent disease in order to optimize discovery and ensure generalizability of findings to the global population. Here, we report the genetic determinants of the serum proteome in 466 African Americans with chronic kidney disease attributed to hypertension from the richly phenotyped African American Study of Kidney Disease and Hypertension (AASK) study.

Cohesin-mediated loop anchors confine the locations of human replication origins.

DNA replication occurs through an intricately regulated series of molecular events and is fundamental for genome stability. At present, it is unknown how the locations of replication origins are determined in the human genome. Here we dissect the role of topologically associating domains (TADs), subTADs and loops in the positioning of replication initiation zones (IZs).

HiCuT: An efficient and low input method to identify protein-directed chromatin interactions.

3D genome organization regulates gene expression, and disruption of these long-range (>20kB) DNA-protein interactions results in pathogenic phenotypes. Chromosome conformation methods in conjunction with chromatin immunoprecipitation were used to decipher protein-directed chromatin interactions. However, these methods required abundant starting material (>500,000 cells), sizable number of sequencing reads (>100 million reads), and elaborate data processing methods to reduce background noise, which limited their use in primary cells.

Trans-ethnic genome-wide association study of blood metabolites in the Chronic Renal Insufficiency Cohort (CRIC) study.

Metabolomics genome wide association study (GWAS) help outline the genetic contribution to human metabolism. However, studies to date have focused on relatively healthy, population-based samples of White individuals. Here, we conducted a GWAS of 537 blood metabolites measured in the Chronic Renal Insufficiency Cohort (CRIC) Study, with separate analyses in 822 White and 687 Black study participants.

Polygenic Risk Scores for Kidney Function and Their Associations with Circulating Proteome, and Incident Kidney Diseases.

Background: Genome-wide association studies (GWAS) have revealed numerous loci for kidney function (eGFR). The relationship between polygenic predictors of eGFR, risk of incident adverse kidney outcomes, and the plasma proteome is not known.

Methods: We developed a genome-wide polygenic risk score (PRS) for eGFR by applying the LDpred algorithm to summary statistics generated from a multiethnic meta-analysis of CKDGen Consortium GWAS ( n =765,348) and UK Biobank GWAS (90% of the cohort; n =451,508), followed by best-parameter selection using the remaining 10% of UK Biobank data ( n =45,158).

Proteins Associated with Risk of Kidney Function Decline in the General Population.

Background: Proteomic profiling may allow identification of plasma proteins that associate with subsequent changesin kidney function, elucidating biologic processes underlying the development and progression of CKD.

Methods: We quantified the association between 4877 plasma proteins and a composite outcome of ESKD or decline in eGFR by ≥50% among 9406 participants in the Atherosclerosis Risk in Communities (ARIC) Study (visit 3; mean age, 60 years) who were followed for a median of 14.4 years.

Serum albumin and risks of hospitalization and death: Findings from the Atherosclerosis Risk in Communities study.

Objectives: To determine whether lower serum albumin in community-dwelling, older adults is associated with increased risk of hospitalization and death independent of pre-existing disease.

Design: Prospective cohort study of participants in the fifth visit of the Atherosclerosis Risk in Communities (ARIC) study. Baseline data were collected from 2011 to 2013.

Large-scale plasma proteomic analysis identifies proteins and pathways associated with dementia risk.

The plasma proteomic changes that precede the onset of dementia could yield insights into disease biology and highlight new biomarkers and avenues for intervention. We quantified 4,877 plasma proteins in nondemented older adults in the Atherosclerosis Risk in Communities cohort and performed a proteome-wide association study of dementia risk over five years (n = 4,110; 428 incident cases). Thirty-eight proteins were associated with incident dementia after Bonferroni correction.

Combined Use of PGPRs and Reduced Rates of Azoxystrobin to Improve Management of Sheath Blight of Rice.

Farmers rely heavily on the use of strobilurin fungicides to manage sheath blight (ShB) caused by AG1-IA, the most important disease in rice in the southern United States. Greenhouse and field studies were conducted to evaluate the potential use of plant growth-promoting rhizobacteria (PGPRs) in combination with a reduced rate of azoxystrobin application as a strategy to improve the current fungicide-reliant management. Of the nine antagonistic PGPR strains screened in the greenhouse, strain MBI600 provided the most significant and consistent suppression of ShB.

Consequences of PCA graphs, SNP codings, and PCA variants for elucidating population structure.

SNP datasets are high-dimensional, often with thousands to millions of SNPs and hundreds to thousands of samples or individuals. Accordingly, PCA graphs are frequently used to provide a low-dimensional visualization in order to display and discover patterns in SNP data from humans, animals, plants, and microbes-especially to elucidate population structure. PCA is not a single method that is always done the same way, but rather requires three choices which we explore as a three-way factorial: two kinds of PCA graphs by three SNP codings by six PCA variants.

Research environment of clinician-scientists in China in health policy/health services research.

Objectives: The aim of the study was to describe the research environment of scientists in health services and policy research in China.

Study Design: Study was conducted during the 2016 Westlake Youth Forum with grantees of China Medical Board and key informants. Mixed methods used anonymous, survey of grantees, semistructured open-ended interviews with randomly selected awardees, convenience samples of extramural reviewers, and senior scientists with research experience in China.

Disease-Associated Short Tandem Repeats Co-localize with Chromatin Domain Boundaries.

More than 25 inherited human disorders are caused by the unstable expansion of repetitive DNA sequences termed short tandem repeats (STRs). A fundamental unresolved question is why some STRs are susceptible to pathologic expansion, whereas thousands of repeat tracts across the human genome are relatively stable. Here, we discover that nearly all disease-associated STRs (daSTRs) are located at boundaries demarcating 3D chromatin domains.

Efficacy and Safety of Apremilast Monotherapy for Moderate to Severe Psoriasis: Retrospective Study.

Background: Apremilast is a new oral drug for the treatment of moderate to severe plaque psoriasis that reduces inflammation by inhibiting phosphodiesterase 4. Its efficacy and safety data are limited; hence, real-world outcomes are important for elucidating the full spectrum of its adverse events (AEs) and expanding generalizability of clinical trial findings.

Objective: Assess the efficacy and safety of apremilast monotherapy in real-world practice.