The ENCODE mouse postnatal developmental time course identifies regulatory programs of cell types and cell states.

Postnatal genomic regulation significantly influences tissue and organ maturation but is under-studied relative to existing genomic catalogs of adult tissues or prenatal development in mouse. The ENCODE4 consortium generated the first comprehensive single-nucleus resource of postnatal regulatory events across a diverse set of mouse tissues. The collection spans seven postnatal time points, mirroring human development from childhood to adulthood, and encompasses five core tissues.

Nonpharmacological pain management approaches among U.S. construction workers: A cross-sectional pilot study.

Background: U.S. construction workers experience high rates of injury that can lead to chronic pain.

Identification of robust cellular programs using reproducible LDA that impact sex-specific disease progression in different genotypes of a mouse model of AD.

The gene expression profiles of distinct cell types reflect complex genomic interactions among multiple simultaneous biological processes within each cell that can be altered by disease progression as well as genetic background. The identification of these active cellular programs is an open challenge in the analysis of single-cell RNA-seq data. Latent Dirichlet Allocation (LDA) is a generative method used to identify recurring patterns in counts data, commonly referred to as topics that can be used to interpret the state of each cell.

The ENCODE Uniform Analysis Pipelines.

The Encyclopedia of DNA elements (ENCODE) project is a collaborative effort to create a comprehensive catalog of functional elements in the human genome. The current database comprises more than 19000 functional genomics experiments across more than 1000 cell lines and tissues using a wide array of experimental techniques to study the chromatin structure, regulatory and transcriptional landscape of the and genomes. All experimental data, metadata, and associated computational analyses created by the ENCODE consortium are submitted to the Data Coordination Center (DCC) for validation, tracking, storage, and distribution to community resources and the scientific community.

The ENCODE4 long-read RNA-seq collection reveals distinct classes of transcript structure diversity.

The majority of mammalian genes encode multiple transcript isoforms that result from differential promoter use, changes in exonic splicing, and alternative 3' end choice. Detecting and quantifying transcript isoforms across tissues, cell types, and species has been extremely challenging because transcripts are much longer than the short reads normally used for RNA-seq. By contrast, long-read RNA-seq (LR-RNA-seq) gives the complete structure of most transcripts.

The ENCODE Uniform Analysis Pipelines.

The Encyclopedia of DNA elements (ENCODE) project is a collaborative effort to create a comprehensive catalog of functional elements in the human genome. The current database comprises more than 19000 functional genomics experiments across more than 1000 cell lines and tissues using a wide array of experimental techniques to study the chromatin structure, regulatory and transcriptional landscape of the and genomes. All experimental data, metadata, and associated computational analyses created by the ENCODE consortium are submitted to the Data Coordination Center (DCC) for validation, tracking, storage, and distribution to community resources and the scientific community.

A Cluster of Health Symptoms After a Law Enforcement Operation: A Case Study.

Law enforcement officers (LEOs) often encounter rapidly changing and uncontrolled situations that expose them to various hazards. A law enforcement agency requested an evaluation by the National Institute for Occupational Safety and Health (NIOSH) when multiple LEOs reported illness after executing a search warrant and taking a suspect into custody. NIOSH investigators interviewed LEOs and reviewed medical records, forensic laboratory results for collected evidence, and environmental testing results of samples taken after the operation.

Mapping and modeling the genomic basis of differential RNA isoform expression at single-cell resolution with LR-Split-seq.

The rise in throughput and quality of long-read sequencing should allow unambiguous identification of full-length transcript isoforms. However, its application to single-cell RNA-seq has been limited by throughput and expense. Here we develop and characterize long-read Split-seq (LR-Split-seq), which uses combinatorial barcoding to sequence single cells with long reads.

Correction: A quality improvement initiative for COPD patients: A cost analysis.

[This corrects the article DOI: 10.1371/journal.pone.

The changing mouse embryo transcriptome at whole tissue and single-cell resolution.

During mammalian embryogenesis, differential gene expression gradually builds the identity and complexity of each tissue and organ system. Here we systematically quantified mouse polyA-RNA from day 10.5 of embryonic development to birth, sampling 17 tissues and organs.

Spatiotemporal DNA methylome dynamics of the developing mouse fetus.

Cytosine DNA methylation is essential for mammalian development but understanding of its spatiotemporal distribution in the developing embryo remains limited. Here, as part of the mouse Encyclopedia of DNA Elements (ENCODE) project, we profiled 168 methylomes from 12 mouse tissues or organs at 9 developmental stages from embryogenesis to adulthood. We identified 1,808,810 genomic regions that showed variations in CG methylation by comparing the methylomes of different tissues or organs from different developmental stages.

An atlas of dynamic chromatin landscapes in mouse fetal development.

The Encyclopedia of DNA Elements (ENCODE) project has established a genomic resource for mammalian development, profiling a diverse panel of mouse tissues at 8 developmental stages from 10.5 days after conception until birth, including transcriptomes, methylomes and chromatin states. Here we systematically examined the state and accessibility of chromatin in the developing mouse fetus.

A quality improvement initiative for COPD patients: A cost analysis.

The objective of this analysis was to evaluate and report on the economic impact of implementing an integrated, quality, and operational improvement program on chronic obstructive pulmonary disease (COPD) care from acute through post-acute care settings. This initiative was established in a cohort of 12 hospitals in Alabama and sought to address COPD readmission through improved workflows pertaining to early diagnosis, efficient care transitions, and patient visibility across the entire care episode. Implementation of the initiative was influenced by lean principles, particularly cross-functional agreement of workflows to improve COPD care delivery and outcomes.

Effectiveness of a paraverterbral nerve block versus local portal blocks for laparoscopic closure of the nephrosplenic space: A pilot study.

Objective: To compare the effectiveness of a paravertebral nerve block vs local portal blocks for laparoscopic closure of the nephrosplenic space in standing sedated research horses.

Study Design: Randomized clinical trial.

Animals: Twelve horses were randomly allocated to two groups (n = 6 per group), paravertebral block of nerves T , L , and L or local blocks of the three laparoscopic portals.

Dynamics of microRNA expression during mouse prenatal development.

MicroRNAs (miRNAs) play a critical role as posttranscriptional regulators of gene expression. The ENCODE Project profiled the expression of miRNAs in an extensive set of organs during a time-course of mouse embryonic development and captured the expression dynamics of 785 miRNAs. We found distinct organ-specific and developmental stage-specific miRNA expression clusters, with an overall pattern of increasing organ-specific expression as embryonic development proceeds.

Hospital-Based Research Internship for Nurses: The Value of Academic Librarians as Cofaculty.

With so few nurse scientists, it is important to increase the research activities of nurses. A nurse scientist and a librarian investigated if increasing library skills in a hospital-based research internship increases nurses' scholarship. Library-related content was added throughout the internship; interns were surveyed to measure specific skills.

Normograde nasolacrimal placement of an ocular-lavage system for treatment of equine eye diseases.

The standard placement of a subpalpebral lavage system may not be feasible in some horses with eyelid disease. We describe placement of a commercially available, indwelling nasolacrimal lavage system that circumvents eyelid perforation. This novel approach provided for effective delivery of drugs to 1 horse with periocular and corneal disease.

Health effects from unintentional occupational exposure to opioids among law enforcement officers: Two case investigations.

Recent increases in the rate of drug overdose-related deaths, the emergence of potent opioids such as carfentanil, and media reports of incidents have raised concerns about the potential for work-related exposure to a variety of illicit drugs among law enforcement officers (LEOs), other emergency responders, and other workers in the United States. To characterize the risk associated with unintentional occupational exposure to drugs, we retrospectively investigated two incidents that occurred in 2017 and 2018 where LEOs were exposed to opioid and stimulant drugs and experienced health effects. We interviewed five affected LEOs and others.

Development of a Diabetes Mellitus Knowledge Resource for Clinical Decision Support Assisting Primary Care Physicians With Work-Related Issues.

Objective: The aim of this study was to describe the process by which a group of subject matter experts (SMEs) in the area of occupational health and primary care developed a clinical decision support (CDS) tool addressing work-related issues, which are important in the care of patients with diabetes mellitus (DM). The CDS is intended for primary care clinicians caring for employed adults with DM.

Methods: The SME's selected guidelines for the management of DM in working adults, reviewed pertinent literature, and developed specific recommendations for action in the clinical setting.