The human body at cellular resolution: the NIH Human Biomolecular Atlas Program

Abstract: Transformative technologies are enabling the construction of three-dimensional maps of tissues with unprecedented spatial and molecular resolution. Over the next seven years, the NIH Common Fund Human Biomolecular Atlas Program (HuBMAP) intends to develop a widely accessible framework for comprehensively mapping the human body at single-cell resolution by supporting technology development, data acquisition, and detailed spatial mapping. HuBMAP will integrate its efforts with other funding agencies, programs, consortia, and the biomedical research community at large towards the shared vision of a comprehensive, accessible three-dimensional molecular and cellular atlas of the human body, in health and under various disease conditions

hms-dbmi/higlass-website v0.6.36

HiGlass Project Websit

common-workflow-language/cwltool: 3.1.20231020113452

<h2>What's Changed</h2> <ul> <li>temporarily downgrade galaxy-tool-util to workaround issue with newer conda by @mr-c in https://github.com/common-workflow-language /cwltool/pull/1930</li> </ul> <h3>Deps</h3> <ul> <li>Bump mypy from 1.6.0 to 1.6.1 by @dependabot in https://github.com/common-workflow-language/cwltool/pull/1927</li> <li>Update black requirement from ~=23.9 to ~=23.10 by @dependabot in https://github.com/common-workflow-language/cwltool/pull/1926</li> </ul> <p><strong>Full Changelog</strong>: https://github.com/common-workflow-language/cwltool/compare/3.1.20231016170136...3.1.20231020113452</p&gt

common-workflow-language/cwltool: 3.1.20231114134824

<h2>What's Changed</h2> <ul> <li>gh-actions: need newer setuptools to run setuptools_scm by @mr-c in https://github.com/common-workflow-language/cwltool/pull/1932</li> <li>Update ruamel-yaml requirement from <0.18,>=0.16.0 to >=0.16.0,<0.19 by @dependabot in https://github.com/common-workflow-language/cwltool/pull/1934</li> <li>software dependencies: allow newer versions of galaxy-tool-util by @mr-c in https://github.com/common-workflow-language/cwltool/pull/1936</li> <li>skip cwl-utils 0.30 by @mr-c in https://github.com/common-workflow-language/cwltool/pull/1941</li> <li>Update black requirement from ~=23.10 to ~=23.11 by @dependabot in https://github.com/common-workflow-language/cwltool/pull/1939</li> </ul> <p><strong>Full Changelog</strong>: https://github.com/common-workflow-language/cwltool/compare/3.1.20231020140205...3.1.20231114134824</p&gt

common-workflow-language/cwltool: 3.1.20231020140205

<h2>What's Changed</h2> <ul> <li>fix the pickling error for IO objects by @ndonyapour in https://github.com/common-workflow-language/cwltool/pull/1929</li> <li>gh-actions: record version before building container to publish to quay.io by @mr-c in https://github.com/common-workflow-language/cwltool/pull/1931</li> </ul> <p><strong>Full Changelog</strong>: https://github.com/common-workflow-language/cwltool/compare/3.1.20231020113452...3.1.20231020140205</p&gt

HiGlass: web-based visual exploration and analysis of genome interaction maps

We present HiGlass, an open source visualization tool built on web technologies that provides a rich interface for rapid, multiplex, and multiscale navigation of 2D genomic maps alongside 1D genomic tracks, allowing users to combine various data types, synchronize multiple visualization modalities, and share fully customizable views with others. We demonstrate its utility in exploring different experimental conditions, comparing the results of analyses, and creating interactive snapshots to share with collaborators and the broader public. HiGlass is accessible online at http://higlass.io and is also available as a containerized application that can be run on any platform.National Institutes of Health (U.S.) (U01 CA200059)National Institutes of Health (U.S.) (R00 HG007583)National Institutes of Health (U.S.) (U54 HG007963

Liraglutide and Renal Outcomes in Type 2 Diabetes.

BACKGROUND: In a randomized, controlled trial that compared liraglutide, a glucagon-like peptide 1 analogue, with placebo in patients with type 2 diabetes and high cardiovascular risk who were receiving usual care, we found that liraglutide resulted in lower risks of the primary end point (nonfatal myocardial infarction, nonfatal stroke, or death from cardiovascular causes) and death. However, the long-term effects of liraglutide on renal outcomes in patients with type 2 diabetes are unknown. METHODS: We report the prespecified secondary renal outcomes of that randomized, controlled trial in which patients were assigned to receive liraglutide or placebo. The secondary renal outcome was a composite of new-onset persistent macroalbuminuria, persistent doubling of the serum creatinine level, end-stage renal disease, or death due to renal disease. The risk of renal outcomes was determined with the use of time-to-event analyses with an intention-to-treat approach. Changes in the estimated glomerular filtration rate and albuminuria were also analyzed. RESULTS: A total of 9340 patients underwent randomization, and the median follow-up of the patients was 3.84 years. The renal outcome occurred in fewer participants in the liraglutide group than in the placebo group (268 of 4668 patients vs. 337 of 4672; hazard ratio, 0.78; 95% confidence interval [CI], 0.67 to 0.92; P=0.003). This result was driven primarily by the new onset of persistent macroalbuminuria, which occurred in fewer participants in the liraglutide group than in the placebo group (161 vs. 215 patients; hazard ratio, 0.74; 95% CI, 0.60 to 0.91; P=0.004). The rates of renal adverse events were similar in the liraglutide group and the placebo group (15.1 events and 16.5 events per 1000 patient-years), including the rate of acute kidney injury (7.1 and 6.2 events per 1000 patient-years, respectively). CONCLUSIONS: This prespecified secondary analysis shows that, when added to usual care, liraglutide resulted in lower rates of the development and progression of diabetic kidney disease than placebo. (Funded by Novo Nordisk and the National Institutes of Health; LEADER ClinicalTrials.gov number, NCT01179048 .)