The UCSC Genome Browser database: 2024 update.

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.

On one of the smallest Amazonian scorpions: a new species of Microtityus (Scorpiones, Buthidae) from Brazil, with amended diagnosis and potential distribution analysis for the genus

A new scorpion species, Microtityus adriki n. sp., is described based on adult specimens collected in Cantá, state of Roraima (RR), northern Brazil. Microtityus adriki n. sp. is the second species of Microtityus Kjellesvig-Waering, 1966 known from Brazil and is one of the smallest scorpion species (12.39-19.47 mm) in the Amazonian region. In this study, we propose an amended generic diagnosis and a specific diagnosis, describe the male hemispermatophore of Microtityus, give the sequence of COI barcode, and present a potential distribution analysis for the genus. The morphology of the male hemispermatophore of Microtityus differs from that of other Neotropical buthid genera, except for the number of lobes (three lobes), which is a character state shared with several genera. The potential distribution model generated by MaxEnt suggests high environmental suitability for the genus in the Antilles and northern South America, with scattered high suitability in several regions of Central America. However, the model did not indicate high suitability in areas where Brazilian species occur (i.e., Microtityus adriki n. sp. and Microtityus vanzolinii Lourenço & Eickstedt, 1983), and this could be explained by a sampling bias. Therefore, future studies, including extensive sampling, are required to better understand the biogeographic processes behind the distribution of this genus.

GenArk: towards a million UCSC genome browsers.

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.

Suicide risk and associated factors in healthcare workers seeking psychological support during COVID-19: a cross-sectional study.

Healthcare workers have been one of the groups most severely affected by the COVID-19 pandemic, leaving them with serious psychological effects. Some of these effects have not been treated promptly, leading to further psychological symptoms. The objective of this study was to evaluate suicide risk in healthcare workers seeking psychological help during the COVID-19 pandemic, and factors associated with this risk on participants that were searching for treatment during the COVID-19 pandemic. This is a cross-sectional study analyzing data from 626 Mexican healthcare workers seeking psychological help due to the COVID-19 pandemic through the www.personalcovid.com platform. Before they entered treatment, the Plutchik Suicide Risk Scale, the Depression Scale of the Center for Epidemiologic Studies, the Pittsburgh Sleep Quality Index, and the Professional Quality of Life Measure, were administered. Results: 49.4% (n = 308) presented suicide risk. The most severely affected groups were nurses (62%, n = 98) and physicians (52.7%, n = 96). Predictors of suicide risk in healthcare workers were secondary traumatic stress, high depressive affect, low positive affect, emotional insecurity and interpersonal problems, and medication use. Conclusions: The suicidal risk detected was high, found mostly in nurses and doctors. This study suggests the presence of psychological effects on healthcare workers, despite the time that has elapsed since the onset of the pandemic.

GenArk: Towards a million UCSC Genome Browsers.

Interactive graphical genome browsers are essential tools for biologists working with DNA sequences. Although tens of thousands of new genome assemblies have become available over the last decade, accessibility is limited by the work involved in manually creating browsers and curating annotations. The results can push the limits of data storage infrastructure. To facilitate managing this increasing number of genome assemblies, we created the Genome Archive (GenArk) collection of UCSC Genome Browsers from assemblies hosted at NCBI(1). Built on our established assembly hub system, this collection enables fast, on-demand visualization of chromosome regions without requiring a database server. Available annotations include gene models, some mapped through whole-genome alignments, repeat masks, GC content, and others. We also modified our popular BLAT(2) aligner and in-silico PCR to support a large number of genomes using limited RAM. Users can upload additional annotations themselves via track hubs(3) and custom tracks. We can import more annotations in bulk from third-party resources, demonstrated here with TOGA(4) gene models. 2,430 GenArk assemblies are listed at https://hgdownload.soe.ucsc.edu/hubs/ and can be found by searching on the main UCSC gateway page. We will continue to add human high-quality assemblies and for other organisms, we are looking forward to receiving requests from the research community for ever more browsers and whole-genome alignments via http://genome.ucsc.edu/assemblyRequest.html.

On the noxious black Amazonian scorpion, Tityus obscurus (Scorpiones, Buthidae): Taxonomic notes, biology, medical importance and envenoming treatment.

Tityus obscurus has caused mild, moderate and severe accidents of medical relevance in the eastern Brazilian Amazon and French Guiana. Tityus obscurus has sexual dimorphism although males and females have uniform black coloration. In the Amazon, one of the habitats of this scorpion is seasonally flooded forests (igapós and várzeas). However, most stings occur in terra firme forest areas (non-flooded region), where most rural communities are located. Adults and children stung by T. obscurus may experience an "electric shock" sensation for more than 30 h after the sting. Our data shows that people inhabiting remote forest areas, including rubber tappers, fishermen and indigenous people, with no access to anti-scorpion serum, use parts of native plants, such as seeds and leaves, against pain and vomiting caused by scorpion stings. Although there is a technical effort to produce and distribute antivenoms in the Amazon, many cases of scorpion stings are geographically unpredictable in this region, due to the lack of detailed knowledge of the natural distribution of these animals. In this manuscript, we compile information on the natural history of T. obscurus and the impact of its envenoming on human health. We identify the natural sites that host this scorpion in the Amazon, in order to warn about the risk of human envenoming. The use of specific antivenom serum is the recommended treatment for accidents involving venomous animals. However, atypical symptoms not neutralized by the available commercial antivenom are reported in the Amazon region. Facing this scenario, we present some challenges to the study of venomous animals in the Amazon rainforest and possible experimental bottlenecks and perspectives for establishing a method aimed at producing an efficient antivenom.

Neuronal accumulation of hyperphosphorylated tau protein predicts stable memory impairment in people living with HIV.

OBJECTIVES: As lifespans increase in people with HIV (PWH), there is concern that age-related neurodegenerative disorders may contribute to cognitive decline. We asked whether brain accumulation of Alzheimer's disease (AD)-associated proteins amyloid-beta (Aß) and hyperphosphorylated tau (p-tau) predicted cognitive performance in middle-aged PWH. METHODS: In a prospectively followed, cognitively-characterized autopsy sample of 135 PWH, we used immunohistochemistry to assess Aß plaques and neuronal p-tau in medial temporal and lateral frontal lobes. These pathologies were tested for associations with cognitive performance in seven domains: motor, speed of information processing, working memory, memory encoding, memory retrieval, verbal fluency, and abstraction/executive function. Univariate and multivariate analyses accounting for HIV-associated variables, reading level, and comorbidities were conducted. Longitudinal trajectories of memory functions were evaluated in 60 individuals with a median follow-up of 6.0 years. RESULTS: In this population with mean age 51.4 ± 0.9 years, 58% displayed neuronal p-tau and 29% Aß plaques. Neuronal p-tau, but not Aß, predicted worse memory encoding and retrieval, but not other cognitive functions. With an ordinal hierarchy of neuronal p-tau locations (entorhinal, hippocampal, neocortical), decreased memory performance correlated with neocortical distribution. Memory function trajectories could not be distinguished between individuals with and without neuronal p-tau, and over 80% of the sample showed no change over time. CONCLUSION: In this middle-aged sample, neuronal p-tau accumulation contributes to memory deficits, but is not associated with accelerated decline in function over time. In the absence of AD-like deterioration, other etiologies for neuronal p-tau in cognitively impaired PWH must be considered.

The UCSC Genome Browser database: 2023 update.

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.

On the noxious black amazonian scorpion, Tityus obscurus (Scorpiones, Buthidae): taxonomic notes, biology, medical importance and envenoming treatment

Tityus obscurus has caused mild, moderate and severe accidents of medical relevance in the eastern Brazilian Amazon and French Guiana. Tityus obscurus has sexual dimorphism although males and females have uniform black coloration. In the Amazon, one of the habitats of this scorpion is seasonally flooded forests (igapós and várzeas). However, most stings occur in terra firme forest areas (non-flooded region), where most rural communities are located. Adults and children stung by T. obscurus may experience an “electric shock” sensation for more than 30 h after the sting. Our data shows that people inhabiting remote forest areas, including rubber tappers, fishermen and indigenous people, with no access to anti-scorpion serum, use parts of native plants, such as seeds and leaves, against pain and vomiting caused by scorpion stings. Although there is a technical effort to produce and distribute antivenoms in the Amazon, many cases of scorpion stings are geographically unpredictable in this region, due to the lack of detailed knowledge of the natural distribution of these animals. In this manuscript, we compile information on the natural history of T. obscurus and the impact of its envenoming on human health. We identify the natural sites that host this scorpion in the Amazon, in order to warn about the risk of human envenoming. The use of specific antivenom serum is the recommended treatment for accidents involving venomous animals. However, atypical symptoms not neutralized by the available commercial antivenom are reported in the Amazon region. Facing this scenario, we present some challenges to the study of venomous animals in the Amazon rainforest and possible experimental bottlenecks and perspectives for establishing a method aimed at producing an efficient antivenom.

E-Health Psychological Intervention for COVID-19 Healthcare Workers: Protocol for its Implementation and Evaluation.

(1) Background: Healthcare workers have been affected by the COVID-19 pandemic. Digital interventions have been carried out that have been effective with this population; however, few have been reported in Latin America. Our aim is to describe the components and methods to evaluate the feasibility and utility of an online multi-component psychological intervention for healthcare workers in Mexico during COVID-19. (2) Methods: This study is a randomized clinical trial with two arms: (1) self-applied intervention and (2) intervention delivered online by therapists. The participants are randomly assigned to one arm, receiving the same treatment contents in both groups. The "Personal COVID" intervention consists of an internet platform containing 9 nuclear and 3 complementary modules. The objectives of the intervention are: (1) to reduce anxiety, depressive symptoms, burnout, and compassion fatigue, and (2) to increase the quality of life, sleep quality, self-care, and their skills to give bad news. The protocol has been registered on ClinicalTrials.gov (identifier: NCT04890665). (3) Discussion: This protocol is designed according to the highest scientific standards following the SPIRIT guidelines. The "Personal COVID" intervention is expected to be of high efficacy in treating the emotional distress of healthcare workers and promoting their health during the COVID-19 pandemic.

Preliminary Findings from a Telephone-Based Cognitive Screening of an Adult HIV Research Cohort during the COVID-19 Pandemic.

OBJECTIVES: Few publications have documented the utility of in-home telephone-based cognitive screeners during COVID-19. This manuscript describes the adaptation of select face-to-face (FTF) neuropsychological tests to telephonic administration in a longitudinal cohort of people with HIV (PWH). Using the cohort's pre-pandemic neuropsychological data, we explore the utility of telephonic administration in this population. METHODS: Of a longitudinal cohort of 170 adult PWH, 59 completed telephonic medical and cognitive screenings with comparable pre-pandemic FTF data. Telephone screeners and FTF evaluations were compared using repeated measures ANCOVAs to examine whether test performance differed between administration types and levels of pre-pandemic cognitive performance. Individuals with pre-pandemic test scores more than a standard deviation below the demographically-corrected mean were categorized as "below average" cognitive performance (n = 23), and the remainder as "average" (n = 36). RESULTS: Over 90% of participants gave positive feedback about the telephone encounter. The average cognitive performance group scored higher than the below average group on all measures across both administration types. Telephone and FTF test scores did not differ significantly for measures of category fluency, letter fluency, and verbal learning. However, the below average group scored higher on a verbal memory measure administered via telephone compared with FTF. CONCLUSIONS: Support for telephonic adaptation of select FTF measures in longitudinal research is mixed, with verbal fluency tasks showing the strongest equivalency. When employed carefully with a clear understanding of their limitations, telephone adaptations can provide an opportunity to continue study objectives, promote equity, and monitor participant well-being during times of duress.

Variant interpretation: UCSC Genome Browser Recommended Track Sets.

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 and copy number variants 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.

Health Locus of Control and Neurocognitive Function in Latinx and Non-Latinx White People Living With HIV: A Cross-sectional Study.

ABSTRACT: Research suggests that health locus of control (HLOC) is related to important health and neurocognitive outcomes in people living with HIV. 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 people living with HIV (Latinx: n = 96; non-Latinx White: n = 38) who completed comprehensive neurocognitive evaluations and the Multidimensional HLOC Scale-Form C. Results indicate no ethnocultural differences in HLOC beliefs (ps > .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 affected by HIV.

The UCSC Genome Browser database: 2022 update.

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.

Bringing order to a complex system: phenotypic and genotypic evidence contribute to the taxonomy of Tityus (Scorpiones, Buthidae) and support the description of a new species.

We present a molecular phylogenetic analysis including a survey for overlooked phenotypic characters. Based on both analysis and characters a new cave-dwelling species is described: Tityus (Tityus) spelaeussp. nov. from the Russão II cave, Posse, state of Goiás, Central Brazil. Characters such as the glandular regions of the female pectinal basal piece and basal middle lamellae of pectines, and the distribution of the ventral setae of telotarsi I-IV proved to be useful to constructing the taxonomy of species and species groups of Tityus. The new species is a member of the Tityustrivittatus species-group of Tityus (Tityus) and can be readily recognized by the immaculate coloration pattern and the more developed glandular region on the female pectinal basal piece. In addition, we provide a discussion of the phylogenetic relationships observed within Tityus, on the relevance of the new phenotypic characters to the modern taxonomy of the genus Tityus, and to the records of Brazilian cave scorpions.

The UCSC Genome Browser database: 2021 update.

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.

Physical and Mental Health Screening in a New York City HIV Cohort During the COVID-19 Pandemic: A Preliminary Report.

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.

Patrones de interacción profesor- estudiante en colegios colombianos de alto y bajo desempeño en ciencias / Patterns of teacher-student interaction in Colombian schools of high and low performance in sciences

Resumen El objetivo de este estudio fue comparar los patrones de interacción profesorestudiante en colegios colombianos de alto y bajo rendimiento en el área de ciencias. Para esto se observaron las interacciones de 12 profesores y 118 estudiantes en clases de física, química y biología de secundaria. Se utilizó la pauta de observación Classroom Assessment Scoring System (CLASS-Upper Elementary) para describir las interacciones en los dominios de apoyo pedagógico, apoyo emocionaly organización de la clase durante tres sesiones de una misma unidad temática. Las puntuaciones en estos dominios fueron comparadas entre los colegios de alto y bajo desempeño en pruebas estandarizadas en ciencias. En general no se encontraron diferencias significativas en los patrones de interacción entre profesor y estudiantes pertenecientes a colegios de alto y bajo desempeño en ciencias. Sin embargo, dentro del dominio de apoyo pedagógico se encontraron diferencias en relación con las dimensiones de comprensión del contenido y dialogo instruccional; en estas dimensiones, los patrones de interacción de los profesores-estudiantes pertenecientes a colegios con alto desempeño en ciencias mostraron mejores desempeños que los de bajo desempeño. Se discuten las implicaciones educativas de los hallazgosy se realizan sugerencias para trabajos observacionales similares.

Abstract This study aimed to compare the student teacher interaction patterns in high and low performance Colombian schools in science. We observed the interactions of 12 teachers and 118 high school students in physics, chemistry and biology courses. We used the Classroom Assessment Scoring System (CLASS) to describe the interactions in the domains of instructional support, emotional support and class organization during three class sessions. We compared the scores in these domains between the high and low performance schools in standardized science tests. In general, we didn´t find any significant difference except in the domain of instructional support in the dimensions of content understanding and instructional dialogue. We discuss the educational implications of the findings and make suggestions for similar observational work.

COVID-19. Opciones terapéuticas desde la viro-patogénesis a la evidencia clínica / COVID-19. Therapeutics options from the viro-pathogenesis to the clinical evidence

Resumen 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 artículo 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 inmunización pasiva, de gran utilidad.

Abstract We know more and more about this deadly enemy of the Betacoronavirus family, initially called 19- nCoV that causes COVID-19 (Coronavirus infectous disease), today classified SARS-CoV-2, because it is responsible for producing SARS (severe acute respiratory syndrome), It shares a strong sequence homology with SARS-CoV, its cousin that caused the 2003 SARS epidemic, both capable of spreading rapidly, particularly this one and causing great global chaos as has happened with this pandemic. Based on previous studies targeting SARS-CoV, and also on the virus that causes MERS (Middle East Respiratory Syndrome); and with the current knowledge about SARS-CoV-2, we will explore some therapeutic options for the management of infection by this complex and lethal virus, mentioning some aspects of pathogenic relevance. Possible management alternatives from the pathophysiology and pathogenesis to the evidence currently available were emphasized. We will explore the probable use of ECA2 recombinate, some experimental molecules, we will review some of the antimalarials (chloroquine and hydroxychloroquine), steroids, azithromycin, specific antivirals such as remdesivir, lopinavir / ritonavir, biologics such as tocilizumab, monoclonal antiviral antibodies, and we will emphasize transfusion of convalescent plasma from the passive immunization principle, very useful.