Middle and High School LGBTQ Students Report What Makes School LGBTQ-Affirming Across Race/Ethnicity and Gender Identity, a Topic Modeling Method.

BACKGROUND: Affirming spaces have been associated with improved mental health outcomes for lesbian, gay, bisexual, transgender, queer, and questioning (LGBTQ) adolescents. METHODS: With data from adolescents currently enrolled in middle or high school across the United States, this study used topic modeling methods to examine students' reports of what they were looking for in LGBTQ-affirming schools and, separately, the association of LGBTQ-affirming schools with suicide risk reduction. RESULTS: Topic models demonstrated consistent themes in how students determined that their school was affirming, such as LGBTQ clubs, teachers requesting pronouns, pride flags, and accepting peers. Students of color uniquely looked for actionable responses in addressing LGBTQ issues. Transgender and nonbinary students required explicit mention of support for transgender issues. Quantitatively, LGBTQ students who reported that their school was LGBTQ-affirming had 20% lower odds of attempting suicide in the past year (adjusted odds ratio = 0.80). CONCLUSIONS: These findings suggest that schools must be safe for all youth and implementing policies that make LGBTQ students feel seen and supported in their identities is a protective factor for mental health. IMPLICATIONS: School policies must ensure that youth have access to supportive people, symbols of support, and LGBTQ clubs and that they are also salient to LGBTQ students of color and transgender and nonbinary students.

"I Get Treated Poorly in Regular School-Why Add To It?": Transgender Girls' Experiences Choosing to Play or Not Play Sports.

Purpose: Transgender girls' right to participate in high school sports has been attacked by legislation banning them from doing so. This study uses open-ended survey responses among transgender high school girls to examine reasons that they choose to participate or not participate in sports. Methods: Data come from 294 transgender girls currently in high school who answered one of two open-ended questions about sports participation as part of a larger survey on lesbian, gay, bisexual, transgender, queer, or questioning (LGBTQ) youth mental health. An inductive approach with exploratory and descriptive codes was used, resulting in a codebook with 14 codes about high school girls' choices to participate or not participate in sports. Results: Among respondents' answers about why they participate in sports, six codes were identified: physical health benefits, mental health benefits, fun, social connections, family expectations, and gender affirmation. Among respondents' answers about why they do not participate in sports, eight codes were identified: not interested in sports, gendered teams or spaces, not athletic, physical or mental health limitations, social discomfort around peer athletes, worsened gender dysphoria, bullying or harassment, and lack of resources or access. These codes were not mutually exclusive and many responses were tagged with multiple codes. Conclusion: This study highlights the need for inclusive sports environments for transgender athletes. Providing LGBTQ cultural competence training for coaches, administrators, and parents may decrease barriers and increase comfort for transgender athletes, allowing them to benefit from the skills and education that sports provide.

Losing a Close Friend or Family Member Due to COVID-19 and Mental Health among LGBTQ Youth.

This study examines the association between having lost a close friend or family member to COVID-19 and mental health outcomes among lesbian, gay, bisexual, transgender, or queer (LGBTQ) youth. Data come from 33,993 respondents in the United States, ages 13 to 24, who completed an online survey of LGBTQ youth mental health. Multivariate logistic regression was used to determine the adjusted odds of recent anxiety, depression, considering, or attempting suicide in the past year based on whether or not the youth reported having lost a close friend or family member to COVID-19. Among the full sample, experiences of COVID-19 loss were associated with recent anxiety (adjusted odds ratio (aOR) = 1.29, 95% confidence interval (CI) = 1.20-1.40), recent depression (aOR = 1.23, 95% CI [1.15, 1.32]), seriously considering suicide in the past year (aOR = 1.22, 95% CI (1.14, 1.30)), and attempting suicide in the past year (aOR = 1.55, 95% CI (1.41, 1.69)). These findings highlight the urgent need for investment in low-barrier, affirming mental health services for LGBTQ youth who have experienced COVID-19 loss to support their grief, overall mental health, and healthy development.

Physical Dating Violence Victimization among LGBTQ Youth: Disclosure and Association with Mental Health.

Youth dating violence and youth suicide are both major public health concerns. However, little research examines the intersection of these issues among lesbian, gay, bisexual, transgender, queer, and questioning (LGBTQ) youth. The current study examined the association between physical dating violence victimization and mental health using online survey data collected from 39,126 LGBTQ youth of ages 13 to 24 in the United States. Overall, 11% of LGBTQ youth who were in a relationship in the past year experienced physical dating violence victimization, with 4% having experienced it once and 7% having experienced it multiple times. Rates of experiencing physical dating violence victimization varied based on a number of youth characteristics and environmental factors. Past-year physical dating violence victimization was associated with nearly four times the odds of attempting suicide in the past year. Given the intersection of suicide risk and dating violence among LGBTQ youth, dating violence prevention organizations must be LGBTQ-inclusive, and suicide prevention must be equipped to address dating violence victimization. The higher rates of physical dating violence victimization among multiple marginalized and socioeconomically disadvantaged LGBTQ youth suggest the need for an intersectional approach that addresses the structural factors that place LGBTQ youth at risk for physical dating violence.

The EN-TEx resource of multi-tissue personal epigenomes & variant-impact models.

Understanding how genetic variants impact molecular phenotypes is a key goal of functional genomics, currently hindered by reliance on a single haploid reference genome. Here, we present the EN-TEx resource of 1,635 open-access datasets from four donors (∼30 tissues × âˆ¼15 assays). The datasets are mapped to matched, diploid genomes with long-read phasing and structural variants, instantiating a catalog of >1 million allele-specific loci. These loci exhibit coordinated activity along haplotypes and are less conserved than corresponding, non-allele-specific ones. Surprisingly, a deep-learning transformer model can predict the allele-specific activity based only on local nucleotide-sequence context, highlighting the importance of transcription-factor-binding motifs particularly sensitive to variants. Furthermore, combining EN-TEx with existing genome annotations reveals strong associations between allele-specific and GWAS loci. It also enables models for transferring known eQTLs to difficult-to-profile tissues (e.g., from skin to heart). Overall, EN-TEx provides rich data and generalizable models for more accurate personal functional genomics.

Association of Updating Identification Documents with Suicidal Ideation and Attempts among Transgender and Nonbinary Youth.

This study examines the association of access to concordant identity documents with attempting suicide in the last year among transgender and nonbinary youth. Data came from 6581 transgender and nonbinary youth who completed an online survey of lesbian, gay, bisexual, transgender, or queer (LGBTQ) youth ages 13−24 residing in the United States. Multivariate logistic regression was used to determine the adjusted odds of attempting suicide in the past year based on whether or not youth were able to change their identification documents. Both wanting to update one's documents but not being able to (aOR = 2.04, CI = 1.412−2.95; p < 0.001) and being able to update one's documents but not having done so (aOR = 1.74, CI = 1.22−2.50; p < 0.001) were associated with greater odds of attempting suicide in the last year, compared to youth who had changed their documents. Revising the way gender is captured on legal documents may be an efficacious public health intervention to reduce suicide risk among transgender and nonbinary youth.

Association of Gender-Affirming Hormone Therapy With Depression, Thoughts of Suicide, and Attempted Suicide Among Transgender and Nonbinary Youth.

PURPOSE: There are no large-scale studies examining mental health among transgender and nonbinary youth who receive gender-affirming hormone therapy (GAHT). The purpose of this study is to examine associations among access to GAHT with depression, thoughts of suicide, and attempted suicide among a large sample of transgender and nonbinary youth. METHODS: Data were collected as part of a 2020 survey of 34,759 lesbian, gay, bisexual, transgender, queer, and questioning youth aged 13-24, including 11,914 transgender or nonbinary youth. Adjusted logistic regression assessed whether receipt of GAHT was associated with lower levels of depression, thoughts of suicide, and attempted suicide among those who wanted to receive GAHT. RESULTS: Half of transgender and nonbinary youth said they were not using GAHT but would like to, 36% were not interested in receiving GAHT, and 14% were receiving GAHT. Parent support for their child's gender identity had a strong relationship with receipt of GAHT, with nearly 80% of those who received GAHT reporting they had at least one parent who supported their gender identity. Use of GAHT was associated with lower odds of recent depression (adjusted odds ratio [aOR] = .73, p < .001) and seriously considering suicide (aOR = .74, p < .001) compared to those who wanted GAHT but did not receive it. For youth under age 18, GAHT was associated with lower odds of recent depression (aOR = .61, p < .01) and of a past-year suicide attempt (aOR = .62, p < .05). CONCLUSIONS: Findings support a relationship between access to GAHT and lower rates of depression and suicidality among transgender and nonbinary youth.

Incarcerated individuals' experiences of COVID-19 in the United States.

PURPOSE: This study aims to examine steps taken by correctional staff to prevent COVID-19 from spreading through correctional facilities and explores strategies used by incarcerated individuals to reduce their own risk of contracting COVID-19 during confinement. DESIGN/METHODOLOGY/APPROACH: Data were drawn from interviews with 327 individuals incarcerated after March 16, 2020, in Midwest1, Midwest2 and Southeast state using a questionnaire developed for this purpose. All study participants were actively involved in a randomized controlled trial of a behavioral health reentry intervention and the human subjects board approved the supplement of this study on COVID-19; interviews were conducted from April 15 to November 19, 2020. FINDINGS: Overall, 9.89% of participants contracted COVID-19. Most (68.50%) individuals learned about COVID-19 from television compared to official correctional facility announcements (32.42%). Participants wore face masks (85.02%), washed hands (84.40%) and practiced physical distancing when possible (66.36%). Participants reported that facilities suspended visitation (89.60%) and volunteers (82.57%), provided face masks (83.18%), sanitized (68.20%), conducted temperature checks (55.35%) and released individuals early (7.34%). SOCIAL IMPLICATIONS: Longitudinal observational study on the implementation and effectiveness of public health guidelines in prisons and jails may identify best practices for containing the infectious disease. Maximizing transparent communications, as well as COVID-19 prevention and mitigation efforts, are critical to achieving universal best practices for virus containment and amplifying public health. ORIGINALITY/VALUE: Data presented indicate the early adoption of many Centers for Disease Control guidelines by individuals and correctional facilities, although broad variation existed. Data support the identification of containment strategies for feasible implementation in a range of correctional spaces.

A limited set of transcriptional programs define major cell types.

We have produced RNA sequencing data for 53 primary cells from different locations in the human body. The clustering of these primary cells reveals that most cells in the human body share a few broad transcriptional programs, which define five major cell types: epithelial, endothelial, mesenchymal, neural, and blood cells. These act as basic components of many tissues and organs. Based on gene expression, these cell types redefine the basic histological types by which tissues have been traditionally classified. We identified genes whose expression is specific to these cell types, and from these genes, we estimated the contribution of the major cell types to the composition of human tissues. We found this cellular composition to be a characteristic signature of tissues and to reflect tissue morphological heterogeneity and histology. We identified changes in cellular composition in different tissues associated with age and sex, and found that departures from the normal cellular composition correlate with histological phenotypes associated with disease.

Expanded encyclopaedias of DNA elements in the human and mouse genomes.

The human and mouse genomes contain instructions that specify RNAs and proteins and govern the timing, magnitude, and cellular context of their production. To better delineate these elements, phase III of the Encyclopedia of DNA Elements (ENCODE) Project has expanded analysis of the cell and tissue repertoires of RNA transcription, chromatin structure and modification, DNA methylation, chromatin looping, and occupancy by transcription factors and RNA-binding proteins. Here we summarize these efforts, which have produced 5,992 new experimental datasets, including systematic determinations across mouse fetal development. All data are available through the ENCODE data portal (https://www.encodeproject.org), including phase II ENCODE1 and Roadmap Epigenomics2 data. We have developed a registry of 926,535 human and 339,815 mouse candidate cis-regulatory elements, covering 7.9 and 3.4% of their respective genomes, by integrating selected datatypes associated with gene regulation, and constructed a web-based server (SCREEN; http://screen.encodeproject.org) to provide flexible, user-defined access to this resource. Collectively, the ENCODE data and registry provide an expansive resource for the scientific community to build a better understanding of the organization and function of the human and mouse genomes.

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. Comparative analysis of conserved miRNAs in mouse and human revealed stronger clustering of expression patterns by organ type rather than by species. An analysis of messenger RNA expression clusters compared with miRNA expression clusters identifies the potential role of specific miRNA expression clusters in suppressing the expression of mRNAs specific to other developmental programs in the organ in which these miRNAs are expressed during embryonic development. Our results provide the most comprehensive time-course of miRNA expression as part of an integrated ENCODE reference data set for mouse embryonic development.

Prevention of data duplication for high throughput sequencing repositories.

Database URL: https://www.encodeproject.org/.

The interaction of serious mental disorder and race on time to reincarceration.

Individuals with a serious mental disorder (SMD) are disproportionately incarcerated in state prisons, and research has shown that individuals with SMD are more likely to recidivate upon release. Persons of color are also disproportionately incarcerated and at risk for repeat incarcerations. However, minimal research has yet to examine whether the relationship between SMD and recidivism is conditioned on race. This study used proportional hazards Cox regression modeling to investigate the effect of SMD on criminal recidivism over an 8-year period among 22,376 former prisoners in North Carolina. The interaction between race and SMD is explored to test for cross-racial variation in time-to-reincarceration. A significant interaction effect of non-Black minority by SMD was found. Non-Black minority former prisoners with SMD returned to prison significantly quicker than non-Black minorities without SMD. No interaction effect was found for either Black or White former prisoners. Hazard to return to prison was also significantly increased for former prisoners that were younger in age, male, Black, not employed at arrest, and indicated for substance abuse. Those factors contributing to the effect of SMD on criminal recidivism within non-Black minority former prisoners is unclear. Additional research is needed on the interactive effects of racial group and SMD on postprison experiences. (PsycINFO Database Record

The Encyclopedia of DNA elements (ENCODE): data portal update.

The Encyclopedia of DNA Elements (ENCODE) Data Coordinating Center has developed the ENCODE Portal database and website as the source for the data and metadata generated by the ENCODE Consortium. Two principles have motivated the design. First, experimental protocols, analytical procedures and the data themselves should be made publicly accessible through a coherent, web-based search and download interface. Second, the same interface should serve carefully curated metadata that record the provenance of the data and justify its interpretation in biological terms. Since its initial release in 2013 and in response to recommendations from consortium members and the wider community of scientists who use the Portal to access ENCODE data, the Portal has been regularly updated to better reflect these design principles. Here we report on these updates, including results from new experiments, uniformly-processed data from other projects, new visualization tools and more comprehensive metadata to describe experiments and analyses. Additionally, the Portal is now home to meta(data) from related projects including Genomics of Gene Regulation, Roadmap Epigenome Project, Model organism ENCODE (modENCODE) and modERN. The Portal now makes available over 13000 datasets and their accompanying metadata and can be accessed at: https://www.encodeproject.org/.

Incarcerated Women's Experiences and Perceptions of Participating in Research.

The research process within prisons has largely considered researchers' perspectives. Only one known study explicitly examined incarcerated persons' perceptions and no known studies have explored incarcerated persons' experiences with research on sensitive topics. This study examines incarcerated women's experiences with participating in research on victimization. A thematic analysis was conducted on responses to open-ended questions about participating in a research study from 227 women in two prisons who participated in a study about victimization. Women prisoners were overwhelmingly positive about participating in the research study with the vast majority willing to participate in a future study. Participants believed participating in the study provided opportunities for them to share their story, heal, reflect, grow, and help others. Some women mentioned that discussing certain topics created uncomfortable emotions and memories. Participants perceived benefits of participating in research. Implications for research in prisons are presented.

High-throughput annotation of full-length long noncoding RNAs with capture long-read sequencing.

Accurate annotation of genes and their transcripts is a foundation of genomics, but currently no annotation technique combines throughput and accuracy. As a result, reference gene collections remain incomplete-many gene models are fragmentary, and thousands more remain uncataloged, particularly for long noncoding RNAs (lncRNAs). To accelerate lncRNA annotation, the GENCODE consortium has developed RNA Capture Long Seq (CLS), which combines targeted RNA capture with third-generation long-read sequencing. Here we present an experimental reannotation of the GENCODE intergenic lncRNA populations in matched human and mouse tissues that resulted in novel transcript models for 3,574 and 561 gene loci, respectively. CLS approximately doubled the annotated complexity of targeted loci, outperforming existing short-read techniques. Full-length transcript models produced by CLS enabled us to definitively characterize the genomic features of lncRNAs, including promoter and gene structure, and protein-coding potential. Thus, CLS removes a long-standing bottleneck in transcriptome annotation and generates manual-quality full-length transcript models at high-throughput scales.

FANTOM5 CAGE profiles of human and mouse samples.

In the FANTOM5 project, transcription initiation events across the human and mouse genomes were mapped at a single base-pair resolution and their frequencies were monitored by CAGE (Cap Analysis of Gene Expression) coupled with single-molecule sequencing. Approximately three thousands of samples, consisting of a variety of primary cells, tissues, cell lines, and time series samples during cell activation and development, were subjected to a uniform pipeline of CAGE data production. The analysis pipeline started by measuring RNA extracts to assess their quality, and continued to CAGE library production by using a robotic or a manual workflow, single molecule sequencing, and computational processing to generate frequencies of transcription initiation. Resulting data represents the consequence of transcriptional regulation in each analyzed state of mammalian cells. Non-overlapping peaks over the CAGE profiles, approximately 200,000 and 150,000 peaks for the human and mouse genomes, were identified and annotated to provide precise location of known promoters as well as novel ones, and to quantify their activities.