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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 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.

Research suggests that health locus of control (HLOC) is related to important health and neurocognitive outcomes in people living with HIV (PLWH). However, the role of ethnicity in these relationships remains poorly understood. This study explored the role of HLOC on neurocognition in a diverse sample of 134 PLWH (Latinx: n = 96; non-Latinx White [NLW]: n = 38) who completed comprehensive neurocognitive evaluations and the Multidimensional Health Locus of Control Scale-Form C (MHLS-C). Results indicate no ethnocultural differences in HLOC beliefs (p’s > .05). External HLOC (i.e., chance and powerful others) related to worse neurocognition in the Latinx group and contributed to significant variance in global neurocognition and learning, memory, and verbal fluency, underscoring the role of external HLOC beliefs on neurocognition, particularly for Latinx individuals. Additional research is needed to better characterize the mechanistic relationship between HLOC beliefs and neurocognitive function and to further explore this relationship among other underrepresented populations also disproportionately impacted by HIV.

Cada vez sabemos más sobre este enemigo mortal de la familia de los Betacoronavirus, llamado inicialmente 19-nCoV, causante de la COVID-19 (Coronavirus infectous disease por su sigla en inglés), hoy clasificado SARS-CoV-2, porque es responsable de producir el SARS (síndrome respiratorio agudo severo, por sus siglas en inglés) y que comparte una fuerte homología de secuencia con el SARS-CoV, su primo hermano causante de la epidemia en 2003 del SARS, ambos capaces de diseminarse rápidamente, en particular este, y causar un gran caos mundial como ha sucedido con esta pandemia. Con base en estudios previos de focalización en el SARS-CoV, y también en el virus causante del MERS (síndrome respiratorio del Oriente Medio, por sus siglas en inglés), y con el conocimiento que se tiene actualmente sobre el SARS-CoV-2, se exploran en este articulo algunas opciones terapéuticas para el manejo de la infección por este virus complejo y con capacidad letal, mencionando algunos aspectos de relevancia patogénica.Se enfatizó en las posibles alternativas de manejo desde la fisiopatología y patogénesis hasta la evidencia actualmente disponible. Exploraremos el uso probable de ECA2 recombinante, algunas moléculas experimentales, revisaremos los antimaláricos (cloroquina e hidroxicloroquina), esteroides, azitromicina, antivirales específicos como remdesivir, lopinavir/ritonavir, biológicos como tocilizumab, anticuerpos monoclonales antivirales, y haremos énfasis en la trasfusión de plasma de convalecientes desde el principio de inmuni- zación pasiva, de gran utilidad

The UCSC Genome Browser has been an important tool for genomics and clinical genetics since the sequence of the human genome was first released in 2000. As it has grown in scope to display more types of data it has also grown more complicated. The data, which are dispersed at many locations worldwide, are collected into one view on the Browser, where the graphical interface presents the data in one location. This supports the expertise of the researcher to interpret variants in the genome. Because the analysis of Single Nucleotide Variants (SNVs) and Copy Number Variants (CNVs) require interpretation of data at very different genomic scales, different data resources are required. We present here several Recommended Track Sets designed to facilitate the interpretation of variants in the clinic, offering quick access to datasets relevant to the appropriate scale.

La celulitis orbitaria es una infrecuente y potencialmente fatal condición, asociada a trauma ocular o infecciones del tracto respiratorio superior, especialmente sinusitis. Dentro de las complicaciones asociadas se describe el compromiso de sistema nervioso central incluyendo meningitis, trombosis del seno cavernoso y formación de absceso, los cuales se dan con mayor frecuencia en niños y adolescentes. Presentamos el caso de un joven de 20 años quien presentó como complicación un empiema cerebral, denotando la importancia de la tomografía computarizada y el valor del manejo antibiótico y quirúrgico precoz, ya que los resultados fueron satisfactorios ante la ausencia de secuelas

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.

Background Mental health consequences of the COVID-19 pandemic have been observed. Psychiatric symptoms in people living with HIV, and their relationship to physical symptomatology and prior psychopathology, are not yet reported. Setting An HIV cohort sheltering-in-place in New York City. Methods Forty-nine participants in a longitudinal study were contacted by telephone in April 2020. A structured interview queried COVID-19-associated physical symptoms, and mental health screens were performed with the generalized anxiety disorder-2 (GAD-2) and patient health questionnaire-2 (PHQ-2). Prior medical and neuropsychiatric data were obtained from preceding study visits. Post-hoc analyses were performed. Results The mean age of respondents was 62.1 years, 39% were women, and 35% African American, 37% Latinx, and 28% Caucasian. COVID-19-indicator symptoms were present in 69%; 41% had respiratory and 61% extra-pulmonary symptoms. Mental health symptoms were endorsed in 45% with PHQ-2 and 43% with GAD-2, although threshold for major depression was met in only 4% and for GAD in 14%. Higher PHQ scores were associated with respiratory symptoms, but not prior mood or anxiety disorders. GAD-2 scores were higher with past mood disorders, but not with prior anxiety disorders or respiratory symptoms. Conclusions Physical symptoms were frequent and mild psychiatric symptoms were common, but serious anxiety and depression were not often endorsed by this group of people living with HIV at the acute height of the New York City COVID-19 pandemic. Reasons for this are unclear, as this preliminary report is descriptive in nature. Short- and long-term consequences of acute mental health symptoms require further study.

BackgroundResearchers are generating molecular data pertaining to the SARS-CoV-2 RNA genome and its proteins at an unprecedented rate during the COVID-19 pandemic. As a result, there is a critical need for rapid and continuously updated access to the latest molecular data in a format in which all data can be quickly cross-referenced and compared. We adapted our genome browser visualization tool to the viral genome for this purpose. Molecular data, curated from published studies or from database submissions, are mapped to the viral genome and grouped together into “annotation tracks” where they can be visualized along the linear map of the viral genome sequence and programmatically downloaded in standard format for analysis.ResultsThe UCSC Genome Browser for SARS-CoV-2 (https://genome.ucsc.edu/covid19.html) provides continuously updated access to the mutations in the many thousands of SARS-CoV-2 genomes deposited in GISAID and the international nucleotide sequencing databases, displayed alongside phylogenetic trees. These data are augmented with alignments of bat, pangolin, and other animal and human coronavirus genomes, including per-base evolutionary rate analysis. All available annotations are cross-referenced on the virus genome, including those from major databases (PDB, RFAM, IEDB, UniProt) as well as up-to-date individual results from preprints. Annotated data include predicted and validated immune epitopes, promising antibodies, RT-PCR and sequencing primers, CRISPR guides (from research, diagnostics, vaccines, and therapies), and points of interaction between human and viral genes. As a community resource, any user can add manual annotations which are quality checked and shared publicly on the browser the next day.ConclusionsWe invite all investigators to contribute additional data and annotations to this resource to accelerate research and development activities globally. Contact us atgenome-www@soe.ucsc.eduwith data suggestions or requests for support for adding data. Rapid sharing of data will accelerate SARS-CoV-2 research, especially when researchers take time to integrate their data with those from other labs on a widely-used community browser platform with standardized machine-readable data formats, such as the SARS-CoV-2 Genome Browser.

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.

The UCSC Genome Browser (https://genome.ucsc.edu) is a graphical viewer for exploring genome annotations. For almost two decades, the Browser has provided visualization tools for genetics and molecular biology and continues to add new data and features. This year, we added a new tool that lets users interactively arrange existing graphing tracks into new groups. Other software additions include new formats for chromosome interactions, a ChIP-Seq peak display for track hubs and improved support for HGVS. On the annotation side, we have added gnomAD, TCGA expression, RefSeq Functional elements, GTEx eQTLs, CRISPR Guides, SNPpedia and created a 30-way primate alignment on the human genome. Nine assemblies now have RefSeq-mapped gene models.

The UCSC Genome Browser (https://genome.ucsc.edu) provides a web interface for exploring annotated genome assemblies. The assemblies and annotation tracks are updated on an ongoing basis—12 assemblies and more than 28 tracks were added in the past year. Two recent additions are a display of CRISPR/Cas9 guide sequences and an interactive navigator for gene interactions. Other upgrades from the past year include a command-line version of the Variant Annotation Integrator, support for Human Genome Variation Society variant nomenclature input and output, and a revised highlighting tool that now supports multiple simultaneous regions and colors.

Objective Health locus of control (HLOC) refers to health attributions related to one’s actions, chance, doctors, or powerful others and impacts health service utilization. Locus of control (LOC) relates to better neurocognitive (NC) function in healthy adults, medication adherence, and quality of life in persons living with HIV (PLWH). No studies have examined HLOC and NC function in PLWH. This study examined how HLOC contributes to NC function in PLWH. Participants and Method This cross-sectional study included 130 PLWH (Latinx: n = 95; non-Latinx White [NLW]: n = 35) who completed an NC battery and Multidimensional Health Locus of Control Scale Form C (MHLS-C). MHLS-C has 4 subscales (internal, chance, doctors, and powerful others; 1 = Strongly Disagree – 6 = Strongly Agree). Demographically corrected NC T-scores were used for average global NC and domain T-scores. Results The Latinx group did worse than the NLW group in global NC, learning, memory, and verbal function (ps < .05). In the Latinx group, MHLS-C Chance negatively related to global NC, learning, memory, and fluency (ps < .05); Powerful Others was negatively related to global NC, learning, and memory (ps < .05). In the NLW group, MHLS-C Chance negatively related to learning and memory (ps < .05). In hierarchical regressions, our model (Step 1: ethnicity and Step 2: MHLC Chance and Powerful Others subscales) predicted global NC (R^2 = .10), learning (R^2 = .30), and memory (R^2=.27; all ps < .05), such that ethnicity was not significant (all ps > .05). Additionally, greater MHLS-C Chance predicted worse NC function (β’s = -.22 to -.40, ps < .05). Conclusions Chance HLOC is related to worse NC function in Latinx and NLW groups, but more strongly in the Latinx group. Ethnicity no longer predicted NC function once chance HLOC was considered. These findings align with prior research in the Latinx population about “fatalismo,” a belief that life events are predestined, and highlight the importance of health professionals addressing perceptions of control over one’s health to improve outcomes, including NC functioning.

Objective Barriers like poor health literacy and patient-provider communication add to health disparities in diverse populations. Perceived autonomy has been shown to improve patients’ health satisfaction and knowledge of their illness. However, no studies have examined these issues in HIV patients. This study examined the roles of health literacy and physician-patient relationship in health outcomes (e.g., mental health and emotional/physical functioning) in persons living with HIV (PLWH). Participants and Method This cross-sectional study included 91 PLWH (74% Latinx and 26% non-Latinx White; 68% Male) who completed the Test of Functional Health Literacy in Adults (TOFHLA), Physician–Patient Relationship Scale (PPRS), and Medical Outcomes Study-HIV Health Survey (MOS). The study variables included: TOFHLA total score, PPRS Part Decision- Making (PDM) and Trust subscales, and MOS Mental Health and Health Transition subscales. Results A linear regression showed that our model (ethnicity, TOFHLA, PPRS PDM and Trust) predicted MOS HT (R2 = .14, p < 0.05), such that Latinx ethnicity (β = .30) and better TOFHLA scores (β = -.22) predicted better MOS HT scores (ps < .05). Another regression showed that our model predicted MOS MH (R2 = 0.07, p = Conclusions Ethnicity and better health literacy were related to improved emotional/physical functioning over a 4-week period and greater shared decision-making was related to better overall mental health. These findings highlight the importance of identifying sociocultural factors and interpersonal processes of care to inform culturally-tailored interventions that can result in enhanced and effective treatment for PLWH patients and in improved physical and mental health outcomes.

Since its 2001 debut, the University of California, Santa Cruz (UCSC) Genome Browser (http://genome.ucsc.edu/) team has provided continuous support to the international genomics and biomedical communities through a web-based, open source platform designed for the fast, scalable display of sequence alignments and annotations landscaped against a vast collection of quality reference genome assemblies. The browser's publicly accessible databases are the backbone of a rich, integrated bioinformatics tool suite that includes a graphical interface for data queries and downloads, alignment programs, command-line utilities and more. This year's highlights include newly designed home and gateway pages; a new 'multi-region' track display configuration for exon-only, gene-only and custom regions visualization; new genome browsers for three species (brown kiwi, crab-eating macaque and Malayan flying lemur); eight updated genome assemblies; extended support for new data types such as CRAM, RNA-seq expression data and long-range chromatin interaction pairs; and the unveiling of a new supported mirror site in Japan.