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The UCSC Genome Browser (https://genome.ucsc.edu) is a widely utilized web-based tool for visualization and analysis of genomic data, encompassing over 4000 assemblies from diverse organisms. Since its release in 2001, it has become an essential resource for genomics and bioinformatics research. Annotation data available on Genome Browser includes both internally created and maintained tracks as well as custom tracks and track hubs provided by the research community. This last year's updates include over 25 new annotation tracks such as the gnomAD 4.1 track on the human GRCh38/hg38 assembly, the addition of three new public hubs, and significant expansions to the Genome Archive[GenArk) system for interacting with the enormous variety of assemblies. We have also made improvements to our interface, including updates to the browser graphic page, such as a new popup dialog feature that now displays item details without requiring navigation away from the main Genome Browser page. GenePred tracks have been upgraded with right-click options for zooming and precise navigation, along with enhanced mouseOver functions. Additional improvements include a new grouping feature for track hubs and hub description info links. A new tutorial focusing on Clinical Genetics has also been added to the UCSC Genome Browser.

The UCSC Genome Browser (https://genome.ucsc.edu) is a web-based genomic visualization and analysis tool that serves data to over 7,000 distinct users per day worldwide. It provides annotation data on thousands of genome assemblies, ranging from human to SARS-CoV2. This year, we have introduced new data from the Human Pangenome Reference Consortium and on viral genomes including SARS-CoV2. We have added 1,200 new genomes to our GenArk genome system, increasing the overall diversity of our genomic representation. We have added support for nine new user-contributed track hubs to our public hub system. Additionally, we have released 29 new tracks on the human genome and 11 new tracks on the mouse genome. Collectively, these new features expand both the breadth and depth of the genomic knowledge that we share publicly with users worldwide.

Interactive graphical genome browsers are essential tools in genomics, but they do not contain all the recent genome assemblies. We create Genome Archive (GenArk) collection of UCSC Genome Browsers from NCBI assemblies. Built on our established track hub system, this enables fast visualization of annotations. Assemblies come with gene models, repeat masks, BLAT, and in silico PCR. Users can add annotations via track hubs and custom tracks. We can bulk-import third-party resources, demonstrated with TOGA and Ensembl gene models for hundreds of assemblies.Three thousand two hundred sixty-nine GenArk assemblies are listed at https://hgdownload.soe.ucsc.edu/hubs/ and can be searched for on the Genome Browser gateway page.

Inova Schar Heart and Vascular has an unwavering commitment to delivering excellent cardiovascular care and has integrated principles of a learning health care system to develop our system of continuous process improvement and innovation. A learning health system integrates its internal experiences with external research to enhance patient outcomes, support the discovery of new treatments and care pathways, and deliver safer, more efficient, and more personalized care. Leveraging learning across health systems maximizes the impact, allowing cardiovascular teams to gain insights into the effectiveness of different treatment strategies. In this Frontiers in Cardiovascular Medicine compendium of articles, the team at Inova describe the spectrum of research and educational activities that have contributed to our progress as a learning cardiovascular health system and support our journey to deliver excellent cardiovascular care.

The UCSC Genome Browser (https://genome.ucsc.edu) is an omics data consolidator, graphical viewer, and general bioinformatics resource that continues to serve the community as it enters its 23rd year. This year has seen an emphasis in clinical data, with new tracks and an expanded Recommended Track Sets feature on hg38 as well as the addition of a single cell track group. SARS-CoV-2 continues to remain a focus, with regular annotation updates to the browser and continued curation of our phylogenetic sequence placing tool, hgPhyloPlace, whose tree has now reached over 12M sequences. Our GenArk resource has also grown, offering over 2500 hubs and a system for users to request any absent assemblies. We have expanded our bigBarChart display type and created new ways to visualize data via bigRmsk and dynseq display. Displaying custom annotations is now easier due to our chromAlias system which eliminates the requirement for renaming sequence names to the UCSC standard. Users involved in data generation may also be interested in our new tools and trackDb settings which facilitate the creation and display of their custom annotations.

The portfolio effect plays a critical role in population productivity and stability. Age structure of spawning salmon represents an example of portfolio effects such that the risks of experiencing unfavorable conditions are spread across time. However, the distribution ofmaturation ages for Pacific salmon (Oncorhynchus spp.) is increasingly concentrated into fewer and younger ages, whichmay impact population resilience to climate change.We explored the population dynamics of Sacramento River fall-run Chinook salmon (O. tshawytscha) under different age structure scenarios using a life-cycle model and compared twomechanisms that can underlie these changes--mortality and maturation. In addition, we tested whether age structure promotes resilience to drought.We found that high age structure diversity increased the stability of population size and harvest compared with low diversity. However, mean population size responded differently depending on the underlying mechanism. Reduced mortality of adult fish ages 4-5 increased escapement, whereas delayed maturation decreased escapement. Overall, high age structure diversity was able to buffer against the adverse effects of droughts by reducing the variability of population size and harvest compared with low diversity. Our results suggest that age structure promotes stability of salmon in an increasingly variable climate.

The UCSC Genome Browser, https://genome.ucsc.edu, is a graphical viewer for exploring genome annotations. The website provides integrated tools for visualizing, comparing, analyzing, and sharing both publicly available and user-generated genomic datasets. Data highlights this year include a collection of easily accessible public hub assemblies on new organisms, now featuring BLAT alignment and PCR capabilities, and new and updated clinical tracks (gnomAD, DECIPHER, CADD, REVEL). We introduced a new Track Sets feature and enhanced variant displays to aid in the interpretation of clinical data. We also added a tool to rapidly place new SARS-CoV-2 genomes in a global phylogenetic tree enabling researchers to view the context of emerging mutations in our SARS-CoV-2 Genome Browser. Other new software focuses on usability features, including more informative mouseover displays and new fonts.

SummaryAs the use of single-cell technologies has grown, so has the need for tools to explore these large, complicated datasets. The UCSC Cell Browser is a tool that allows scientists to visualize gene expression and metadata annotation distribution throughout a single-cell dataset or multiple datasets.Availability and implementationWe provide the UCSC Cell Browser as a free website where scientists can explore a growing collection of single-cell datasets and a freely available python package for scientists to create stable, self-contained visualizations for their own single-cell datasets. Learn more at https://cells.ucsc.edu.Supplementary informationSupplementary data are available at Bioinformatics online.

Microglia are resident macrophages in the brain that emerge in early development and respond to the local environment by altering their molecular and phenotypic states. Fundamental questions about microglia diversity and function during development remain unanswered because we lack experimental strategies to interrogate their interactions with other cell types and responses to perturbations ex vivo. We compared human microglia states across culture models, including cultured primary and pluripotent stem cell-derived microglia. We developed a "report card" of gene expression signatures across these distinct models to facilitate characterization of their responses across experimental models, perturbations, and disease conditions. Xenotransplantation of human microglia into cerebral organoids allowed us to characterize key transcriptional programs of developing microglia in vitro and reveal that microglia induce transcriptional changes in neural stem cells and decrease interferon signaling response genes. Microglia additionally accelerate the emergence of synchronized oscillatory network activity in brain organoids by modulating synaptic density.

Abstract Interactive graphical genome browsers are essential tools in genomics, but they do not contain all the recent genome assemblies. We create Genome Archive (GenArk) collection of UCSC Genome Browsers from NCBI assemblies. Built on our established track hub system, this enables fast visualization of annotations. Assemblies come with gene models, repeat masks, BLAT, and in silico PCR. Users can add annotations via track hubs and custom tracks. We can bulk-import third-party resources, demonstrated with TOGA and Ensembl gene models for hundreds of assemblies. Three thousand two hundred sixty-nine GenArk assemblies are listed at https://hgdownload.soe.ucsc.edu/hubs/ and can be searched for on the Genome Browser gateway page.

Online supplemental material is available for this article. See also the editorial by Grant in this issue.

Haploinsufficiency of transcriptional regulators causes human congenital heart disease (CHD); however, the underlying CHD gene regulatory network (GRN) imbalances are unknown. Here, we define transcriptional consequences of reduced dosage of the CHD transcription factor, TBX5, in individual cells during cardiomyocyte differentiation from human induced pluripotent stem cells (iPSCs). We discovered highly sensitive dysregulation of TBX5-dependent pathways-including lineage decisions and genes associated with heart development, cardiomyocyte function, and CHD genetics-in discrete subpopulations of cardiomyocytes. Spatial transcriptomic mapping revealed chamber-restricted expression for many TBX5-sensitive transcripts. GRN analysis indicated that cardiac network stability, including vulnerable CHD-linked nodes, is sensitive to TBX5 dosage. A GRN-predicted genetic interaction between Tbx5 and Mef2c, manifesting as ventricular septation defects, was validated in mice. These results demonstrate exquisite and diverse sensitivity to TBX5 dosage in heterogeneous subsets of iPSC-derived cardiomyocytes and predicts candidate GRNs for human CHDs, with implications for quantitative transcriptional regulation in disease.

For more than two decades, the UCSC Genome Browser database (https://genome.ucsc.edu) has provided high-quality genomics data visualization and genome annotations to the research community. As the field of genomics grows and more data become available, new modes of display are required to accommodate new technologies. New features released this past year include a Hi-C heatmap display, a phased family trio display for VCF files, and various track visualization improvements. Striving to keep data up-to-date, new updates to gene annotations include GENCODE Genes, NCBI RefSeq Genes, and Ensembl Genes. New data tracks added for human and mouse genomes include the ENCODE registry of candidate cis-regulatory elements, promoters from the Eukaryotic Promoter Database, and NCBI RefSeq Select and Matched Annotation from NCBI and EMBL-EBI (MANE). Within weeks of learning about the outbreak of coronavirus, UCSC released a genome browser, with detailed annotation tracks, for the SARS-CoV-2 RNA reference assembly.

For more than two decades, the UCSC Genome Browser database (https://genome.ucsc.edu) has provided high-quality genomics data visualization and genome annotations to the research community. As the field of genomics grows and more data become available, new modes of display are required to accommodate new technologies. New features released this past year include a Hi-C heatmap display, a phased family trio display for VCF files, and various track visualization improvements. Striving to keep data up-to-date, new updates to gene annotations include GENCODE Genes, NCBI RefSeq Genes, and Ensembl Genes. New data tracks added for human and mouse genomes include the ENCODE registry of candidate cis-regulatory elements, promoters from the Eukaryotic Promoter Database, and NCBI RefSeq Select and Matched Annotation from NCBI and EMBL-EBI (MANE). Within weeks of learning about the outbreak of coronavirus, UCSC released a genome browser, with detailed annotation tracks, for the SARS-CoV-2 RNA reference assembly.

Objectives: The 2018 change in the heart transplant allocation system resulted in greater use of temporary mechanical circulatory support. We hypothesized that the allocation change has increased hospital resource utilization, including length of stay and cost. Methods: All heart transplant patients within a regional Society of Thoracic Surgeons database were included (2012-2020). Patients were stratified before and after the transplant allocation changes into early (January 2012-September 2018) and late eras (November 2018-June 2020). Costs were adjusted for inflation and presented in 2020 dollars. Results: Of 535 heart transplants, there were 410 early and 125 late era patients. Baseline characteristics were similar, except for greater lung and valvular disease in the late era. Fewer patients in the late era were bridged with durable left ventricular assist devices (69% vs 31%; P

Background: Localized prostate cancer (PCa) treatment is associated with reduced health-related quality of life (HRQoL). Current literature is limited by short-term follow-up. Objective: To prospectively evaluate the 5-yr HRQoL outcomes in men undergoing radical prostatectomy (RP), external beam radiotherapy (EBRT), or active surveillance (AS). Design, setting, and participants: We prospectively evaluated HRQoL in patients with low-risk/favorable intermediate-risk PCa enrolled in the Center for Prostate Disease Research multicenter database between 2007 and 2017. Intervention: Of 1012 patients included in the study, 252 (24.9%) underwent AS, 557 (55.0%) RP, and 203 (20.0%) EBRT. Patients complete the Expanded Prostate Cancer Index Composite and the 36-item Medical Outcomes Study Short Form at baseline and thereafter each year up to 5 yr after treatment. Outcome measurements and statistical analysis: Temporal changes in HRQoL were compared between treatments and were modeled using linear regression models adjusted for baseline HRQoL, demographic, and clinical characteristics. Results and limitations: RP showed the least irritative symptoms and worse incontinence in comparison with AS (p

The University of California Santa Cruz Genome Browser website (https://genome.ucsc.edu) enters its 20th year of providing high-quality genomics data visualization and genome annotations to the research community. In the past year, we have added a new option to our web BLAT tool that allows search against all genomes, a single-cell expression viewer (https://cells.ucsc.edu), a 'lollipop' plot display mode for high-density variation data, a RESTful API for data extraction and a custom-track backup feature. New datasets include Tabula Muris single-cell expression data, GeneHancer regulatory annotations, The Cancer Genome Atlas Pan-Cancer variants, Genome Reference Consortium Patch sequences, new ENCODE transcription factor binding site peaks and clusters, the Database of Genomic Variants Gold Standard Variants, Genomenon Mastermind variants and three new multi-species alignment tracks.

Patients can present with chief complaints and symptoms that differ from the eventual diagnoses. The differences between aetiologies versus complications must be appreciated through careful evaluation and use of clinical investigations, laboratory testing, trial of hypotheses, and clinical gestalt. Herein, this article discusses the case of a 58-year old individual who presented with impaired physical functioning, malnutrition, depression, and cognitive impairment. These four symptoms are known collectively as failure to thrive, and they often portend adverse patient outcomes. The internal medicine care team initially attributed the failure to thrive to the combination of an ongoing cervicofacial infection and a pre-existing mood disorder, but its true aetiology was more complex. In the context of various physical and psychiatric health derangements, the patient displayed clear signs of a rare disorder called Cotard’s syndrome. Due to the concern of the care team and the patient’s acting medical power of attorney, the eventual working diagnosis was made, and electroconvulsive therapy and aripiprazole combination therapy initiated, resulting in significant and improved outcomes. In addition to discussing the patient’s course of care, this case report also addresses the caution inherent in prescribing medications, the evaluation of decision making capacity, and the utilisation of a medical power of attorney. The authors also present their thoughts on minimising inefficiencies in care delivery to better the patient’s health outcomes.

Climate change is expected to alter nitrogen (N) export from Arctic rivers, with potential implications for fragile coastal ecosystems and fisheries. Yet, the directionality of change is poorly understood, as increased mobilization of N in a ‘thawing’ Arctic is countered by higher rates of vegetative uptake in a ‘greening’ Arctic, particularly in the understudied region of Greenland. We use an unprecedented dataset of long-term ( n = 18 years) river chemistry, streamflow, and catchment-scale changes in snow and vegetation to document changing riverine N loss in Greenland. We documented decreasing inorganic and organic N loads, linked to decreasing snow stores, warming soils, and enhanced plant uptake. Higher variability in N export across years also points to the increasing role of high flow events in driving downstream N loss. This alteration in N cycling may significantly reduce both inorganic and organic N transport across the terrestrial-aquatic boundary during the open water season in a rapidly warming Greenland.