Genome-scale chromatin binding dynamics of RNA Polymerase II general transcription machinery components.

A great deal of work has revealed, in structural detail, the components of the preinitiation complex (PIC) machinery required for initiation of mRNA gene transcription by RNA polymerase II (Pol II). However, less-well understood are the in vivo PIC assembly pathways and their kinetics, an understanding of which is vital for determining how rates of in vivo RNA synthesis are established. We used competition ChIP in budding yeast to obtain genome-scale estimates of the residence times for five general transcription factors (GTFs): TBP, TFIIA, TFIIB, TFIIE and TFIIF. While many GTF-chromatin interactions were short-lived ( < 1 min), there were numerous interactions with residence times in the range of several minutes. Sets of genes with a shared function also shared similar patterns of GTF kinetic behavior. TFIIE, a GTF that enters the PIC late in the assembly process, had residence times correlated with RNA synthesis rates. The datasets and results reported here provide kinetic information for most of the Pol II-driven genes in this organism, offering a rich resource for exploring the mechanistic relationships between PIC assembly, gene regulation, and transcription.

Outcomes After Induction of Labor Compared With Dilation and Evacuation for the Management of Rupture of Membranes in the Second Trimester.

Previable and periviable rupture of membranes is associated with significant morbidity for the pregnant patient. For those who have a choice of options and undergo active management, it is not known how the risks of induction of labor compare with those for dilation and evacuation (D&E). We performed a retrospective cohort study of patients with rupture of membranes between 14 0/7 and 23 6/7 weeks of gestation who opted for active management. Adverse events (52.2% vs 16.9%, P <.01) and time to uterine evacuation greater than 24 hours (26.7% vs 9.6%, P =.01) were more common among patients undergoing induction of labor. In a multivariable regression, induction of labor was an independent risk factor for complications (odds ratio 5.70, 95% CI, 2.35-13.82) compared with D&E. Severe complications were rare across both groups (4.4% for patients undergoing induction vs 2.6% for D&E, P =.63). Given the differing risks by termination method, access to D&E is an important treatment option for this patient population.

Comparison of Methods to Assess Adolescent Gender Identity in the ABCD Study.

This cross-sectional study assesses the reliability and validity of methods used to capture gender identity in Adolescent Brain Cognitive Development (ABCD) Study participants.

Genome-scale chromatin interaction dynamic measurements for key components of the RNA Pol II general transcription machinery.

Background: A great deal of work has revealed in structural detail the components of the machinery responsible for mRNA gene transcription initiation. These include the general transcription factors (GTFs), which assemble at promoters along with RNA Polymerase II (Pol II) to form a preinitiation complex (PIC) aided by the activities of cofactors and site-specific transcription factors (TFs). However, less well understood are the in vivo PIC assembly pathways and their kinetics, an understanding of which is vital for determining on a mechanistic level how rates of in vivo RNA synthesis are established and how cofactors and TFs impact them. Results: We used competition ChIP to obtain genome-scale estimates of the residence times for five GTFs: TBP, TFIIA, TFIIB, TFIIE and TFIIF in budding yeast. While many GTF-chromatin interactions were short-lived (< 1 min), there were numerous interactions with residence times in the several minutes range. Sets of genes with a shared function also shared similar patterns of GTF kinetic behavior. TFIIE, a GTF that enters the PIC late in the assembly process, had residence times correlated with RNA synthesis rates. Conclusions: The datasets and results reported here provide kinetic information for most of the Pol II-driven genes in this organism and therefore offer a rich resource for exploring the mechanistic relationships between PIC assembly, gene regulation, and transcription. The relationships between gene function and GTF dynamics suggest that shared sets of TFs tune PIC assembly kinetics to ensure appropriate levels of expression.

Importance of internal vaginal pelvic floor muscle exams for women with external lumbar/hip/pelvic girdle pain.

INTRODUCTION AND HYPOTHESIS: The relationship between external lumbar, hip, and/or pelvic girdle pain and internal vaginal pelvic floor myofascial pain is not well described. We assessed this relationship in a cohort of adult women. METHODS: The cohort included women ≥ 18 years old who received care for external lumbar, hip, and/or pelvic girdle pain (reported or elicited on physical examination) who then underwent internal vaginal myofascial levator ani pain assessments, in a tertiary care Female Pelvic Medicine and Reconstructive Surgery pelvic pain clinic over a 2-year period (2013 and 2014). RESULTS: The cohort of 177 women had an average age of 44.9±16.0 years, an average body mass index of 27.2±7.0 kg/m2, and the majority (79.2%) were white. Most patients presented with a chief complaint of pelvic (51.4%), vulvovaginal (18.6%), and/or lumbar (15.3%) pain. Women who reported symptoms of lumbar, hip, or pelvic girdle pain were more likely to have pain on vaginal pelvic floor muscle examination than women without this history (OR, 7.24; 95% CI, 1.95-26.93, p=0.003). The majority (85.9%) of women had bilateral internal vaginal pelvic floor myofascial pain on examination. CONCLUSIONS: Although participants did not describe "vaginal pelvic floor myofascial pain," the high detection rate for internal vaginal pelvic floor myofascial pain on clinical examination highlights an opportunity to improve treatment planning. These findings suggest that the vaginal pelvic floor muscle examination should be part of the assessment of all women with lumbar, hip, and/or pelvic girdle pain. The relationship between this finding and clinical outcomes following directed treatment warrants additional study.

Fetomaternal hemorrhage assessment in Rh-negative patients undergoing dilation and evacuation between 20 and 24 weeks' gestational age: A retrospective cohort study.

OBJECTIVE: To estimate the rate of requiring more than one 300-mcg Rh D immune globulin dose for fetomaternal hemorrhage (FMH) at the time of second-trimester dilation and evacuation (D + E). STUDY DESIGN: We performed a retrospective cohort analysis of patients at greater than 20 weeks' gestation who underwent D + E, had Rh D-negative blood type, and received FMH quantification testing. RESULTS: Of 25 eligible patients, 24 had negative quantification of FMH; one had positive quantification that did not meet the clinical threshold for additional dosing. CONCLUSIONS: The absolute risk of requiring additional Rh D immune globulin after D+E for pregnancies greater than 20 weeks' gestation was 0%.

The yeast Dbf4 Zn2+ finger domain suppresses single-stranded DNA at replication forks initiated from a subset of origins.

Dbf4 is the cyclin-like subunit for the Dbf4-dependent protein kinase (DDK), required for activating the replicative helicase at DNA replication origin that fire during S phase. Dbf4 also functions as an adaptor, targeting the DDK to different groups of origins and substrates. Here we report a genome-wide analysis of origin firing in a budding yeast mutant, dbf4-zn, lacking the Zn2+ finger domain within the C-terminus of Dbf4. At one group of origins, which we call dromedaries, we observe an unanticipated DNA replication phenotype: accumulation of single-stranded DNA spanning ± 5kbp from the center of the origins. A similar accumulation of single-stranded DNA at origins occurs more globally in pri1-m4 mutants defective for the catalytic subunit of DNA primase and rad53 mutants defective for the S phase checkpoint following DNA replication stress. We propose the Dbf4 Zn2+ finger suppresses single-stranded gaps at replication forks emanating from dromedary origins. Certain origins may impose an elevated requirement for the DDK to fully initiate DNA synthesis following origin activation. Alternatively, dbf4-zn may be defective for stabilizing/restarting replication forks emanating from dromedary origins during replication stress.

Measurement of gender and sexuality in the Adolescent Brain Cognitive Development (ABCD) study.

The Adolescent Brain Cognitive DevelopmentSM (ABCD) study is a longitudinal study of adolescent brain development and health that includes over 11,800 youth in the United States. The ABCD study includes broad developmental domains, and gender and sexuality are two of these with noted changes across late childhood and early adolescence. The Gender Identity and Sexual Health (GISH) workgroup recommends measures of gender and sexuality for the ABCD study, prioritizing those that are developmentally sensitive, capture individual differences in the experience of gender and sexuality, and minimize participant burden. This manuscript describes the gender and sexuality measures used in ABCD and provides guidance for researchers using these data. Data showing the utility of these measures and longitudinal trends are presented. Including assessment of gender and sexuality in ABCD allows for characterization of developmental trajectories of gender and sexuality, and the broad scope of ABCD data collection allows examination of identity development in an intersectional manner.

The meaning of regular participation in vigorous-intensity exercise among men with Parkinson's disease.

PURPOSE: To understand the meaning of regular participation in multiple types of vigorous-intensity exercise for those with Parkinson's disease (PD). MATERIALS AND METHODS: Using a qualitative phenomenological approach, in-depth individual interviews were conducted with eight male participants who engaged in at least two modes of vigorous-intensity exercise, including Rock Steady Boxing, about their experiences with exercise and the multifaceted role it played in their lives. Interview data were analyzed using systematic coding and organized into primary themes. RESULTS: Three primary themes emerged from the interview data: (1) the unique importance of social connections with others diagnosed with PD, (2) a sense of purpose, and (3) determination and confidence. Specifically, for those with a minimal history of engagement in exercise, regular participation in multiple types of vigorous-intensity exercise accompanied life-affirming social connections that served to boost feelings of hope and foster a clear sense of purpose in the face of disease. Participation in regular vigorous-intensity exercise fueled determination and confidence to engage in even more vigorous activities. CONCLUSIONS: Implications for rehabilitation practice include the importance of collaboration between health care professionals and community programs for people with PD. Promotion of group-based community activities, vigorous-intensity modes of exercise, and consideration of a patient's exercise history will be essential for the successful delivery of future services.IMPLICATIONS FOR REHABILITATIONSocial connections built through Rock Steady Boxing, a group exercise program, served as a catalyst for increasing hope, sense of purpose and motivation for people with Parkinson's disease;Vigorous-intensity exercise at Rock Steady Boxing fueled determination and confidence to engage in additional vigorous exercise regimens;Collaboration between health care providers and community partners is essential for long-term service provision for individuals with disability;Exercise history should be considered when making recommendations for physical activity.

Early Adolescent Substance Use Before and During the COVID-19 Pandemic: A Longitudinal Survey in the ABCD Study Cohort.

PURPOSE: Evaluate changes in early adolescent substance use during the coronavirus disease 2019 (COVID-19) pandemic using a prospective, longitudinal, nationwide cohort. METHODS: Participants were enrolled in the Adolescent Brain Cognitive Development Study. A total of 7,842 youth (mean age = 12.4 years, range = 10.5-14.6) at 21 study sites across the U.S. completed a three-wave assessment of substance use between May and August 2020. Youth reported whether they had used alcohol, nicotine, cannabis, or other substances in the past 30 days. Data were linked to prepandemic surveys that the same youth had completed in the years 2018-2020, before the advent of the COVID-19 pandemic. RESULTS: Past-30-day substance use remained stable in the 6 months since stay-at-home orders were first issued in U.S. states/counties; was primarily episodic (1-2 days in the past month); and was typically limited to a single substance. Using pretest/posttest and age-period designs, we found that compared to before the pandemic, fewer youth were using alcohol and more youth were using nicotine or misusing prescription drugs. During the pandemic, youth were more likely to use substances when they were more stressed by pandemic-related uncertainty; their family experienced material hardship; their parents used alcohol or drugs; or they experienced greater depression or anxiety. Neither engagement in social distancing nor worry about COVID-19 infection was associated with substance use. Several risk factors were stronger among older (vs. younger) adolescents. CONCLUSIONS: Among youth in early adolescence, advent of the COVID-19 pandemic was associated with decreased use of alcohol and increased use of nicotine and misuse of prescription drugs.

Meaningful associations in the adolescent brain cognitive development study.

The Adolescent Brain Cognitive Development (ABCD) Study is the largest single-cohort prospective longitudinal study of neurodevelopment and children's health in the United States. A cohort of n = 11,880 children aged 9-10 years (and their parents/guardians) were recruited across 22 sites and are being followed with in-person visits on an annual basis for at least 10 years. The study approximates the US population on several key sociodemographic variables, including sex, race, ethnicity, household income, and parental education. Data collected include assessments of health, mental health, substance use, culture and environment and neurocognition, as well as geocoded exposures, structural and functional magnetic resonance imaging (MRI), and whole-genome genotyping. Here, we describe the ABCD Study aims and design, as well as issues surrounding estimation of meaningful associations using its data, including population inferences, hypothesis testing, power and precision, control of covariates, interpretation of associations, and recommended best practices for reproducible research, analytical procedures and reporting of results.

Rates of Incidental Findings in Brain Magnetic Resonance Imaging in Children.

Importance: Incidental findings (IFs) are unexpected abnormalities discovered during imaging and can range from normal anatomic variants to findings requiring urgent medical intervention. In the case of brain magnetic resonance imaging (MRI), reliable data about the prevalence and significance of IFs in the general population are limited, making it difficult to anticipate, communicate, and manage these findings. Objectives: To determine the overall prevalence of IFs in brain MRI in the nonclinical pediatric population as well as the rates of specific findings and findings for which clinical referral is recommended. Design, Setting, and Participants: This cohort study was based on the April 2019 release of baseline data from 11 810 children aged 9 to 10 years who were enrolled and completed baseline neuroimaging in the Adolescent Brain Cognitive Development (ABCD) study, the largest US population-based longitudinal observational study of brain development and child health, between September 1, 2016, and November 15, 2018. Participants were enrolled at 21 sites across the US designed to mirror the demographic characteristics of the US population. Baseline structural MRIs were centrally reviewed for IFs by board-certified neuroradiologists and findings were described and categorized (category 1, no abnormal findings; 2, no referral recommended; 3; consider referral; and 4, consider immediate referral). Children were enrolled through a broad school-based recruitment process in which all children of eligible age at selected schools were invited to participate. Exclusion criteria were severe sensory, intellectual, medical, or neurologic disorders that would preclude or interfere with study participation. During the enrollment process, demographic data were monitored to ensure that the study met targets for sex, socioeconomic, ethnic, and racial diversity. Data were analyzed from March 15, 2018, to November 20, 2020. Main Outcomes and Measures: Percentage of children with IFs in each category and prevalence of specific IFs. Results: A total of 11 679 children (52.1% boys, mean [SD] age, 9.9 [0.62] years) had interpretable baseline structural MRI results. Of these, 2464 participants (21.1%) had IFs, including 2013 children (17.2%) assigned to category 2, 431 (3.7%) assigned to category 3, and 20 (0.2%) assigned to category 4. Overall rates of IFs did not differ significantly between singleton and twin gestations or between monozygotic and dizygotic twins, but heritability analysis showed heritability for the presence or absence of IFs (h2 = 0.260; 95% CI, 0.135-0.387). Conclusions and Relevance: Incidental findings in brain MRI and findings with potential clinical significance are both common in the general pediatric population. By assessing IFs and concurrent developmental and health measures and following these findings over the longitudinal study course, the ABCD study has the potential to determine the significance of many common IFs.

Early adolescent gender diversity and mental health in the Adolescent Brain Cognitive Development study.

BACKGROUND: There are known associations between mental health symptoms and transgender identity among adults. Whether this relationship extends to early adolescents and to gender domains other than identity is unclear. This study measured dimensions of gender in a large, diverse, sample of youth, and examined associations between diverse gender experiences and mental health. METHODS: The ABCD study is an ongoing, longitudinal, US cohort study. Baseline data (release 2.0) include 11,873 youth age 9/10 (48% female); and the 4,951 1-year follow-up visits (age 10/11; 48% female) completed prior to data release. A novel gender survey at the 1-year visit assessed felt-gender, gender noncontentedness, and gender nonconformity using a 5-point scale. Mental health measures included youth- and parent-reports. RESULTS: Roughly half a percent of 9/10-year-olds (n = 58) responded 'yes' or 'maybe' when asked, 'Are you transgender' at baseline. Recurrent thoughts of death were more prevalent among these youth compared to the rest of the cohort (19.6% vs. 6.4%, χ2  = 16.0, p < .001). At the 1-year visit, when asked about the three dimensions of gender on a 5-point scale, 33.2% (n = 1,605) provided responses that were not exclusively and totally aligned with one gender. Significant relationships were observed between mental health symptoms and gender diversity for all dimensions assessed. CONCLUSIONS: Similar to adult studies, early adolescents identifying as transgender reported increased mental health symptoms. Results also point to considerable diversity in other dimensions of gender (felt-gender, gender noncontentedness, gender nonconformity) among 10/11-year-olds, and find this diversity to be related to critical mental health symptoms. These findings add to our limited understanding of the relationship between dimensions of gender and wellness for youth.

Replication Stress Induces Global Chromosome Breakage in the Fragile X Genome.

Fragile X syndrome (FXS) is a neurodevelopmental disorder caused by mutations in the FMR1 gene and deficiency of a functional FMRP protein. FMRP is known as a translation repressor whose nuclear function is not understood. We investigated the global impact on genome stability due to FMRP loss. Using Break-seq, we map spontaneous and replication stress-induced DNA double-strand breaks (DSBs) in an FXS patient-derived cell line. We report that the genomes of FXS cells are inherently unstable and accumulate twice as many DSBs as those from an unaffected control. We demonstrate that replication stress-induced DSBs in FXS cells colocalize with R-loop forming sequences. Exogenously expressed FMRP in FXS fibroblasts ameliorates DSB formation. FMRP, not the I304N mutant, abates R-loop-induced DSBs during programmed replication-transcription conflict. These results suggest that FMRP is a genome maintenance protein that prevents R-loop accumulation. Our study provides insights into the etiological basis for FXS.

Correspondence Between Perceived Pubertal Development and Hormone Levels in 9-10 Year-Olds From the Adolescent Brain Cognitive Development Study.

Aim: To examine individual variability between perceived physical features and hormones of pubertal maturation in 9-10-year-old children as a function of sociodemographic characteristics. Methods: Cross-sectional metrics of puberty were utilized from the baseline assessment of the Adolescent Brain Cognitive Development (ABCD) Study-a multi-site sample of 9-10 year-olds (n = 11,875)-and included perceived physical features via the pubertal development scale (PDS) and child salivary hormone levels (dehydroepiandrosterone and testosterone in all, and estradiol in females). Multi-level models examined the relationships among sociodemographic measures, physical features, and hormone levels. A group factor analysis (GFA) was implemented to extract latent variables of pubertal maturation that integrated both measures of perceived physical features and hormone levels. Results: PDS summary scores indicated more males (70%) than females (31%) were prepubertal. Perceived physical features and hormone levels were significantly associated with child's weight status and income, such that more mature scores were observed among children that were overweight/obese or from households with low-income. Results from the GFA identified two latent factors that described individual differences in pubertal maturation among both females and males, with factor 1 driven by higher hormone levels, and factor 2 driven by perceived physical maturation. The correspondence between latent factor 1 scores (hormones) and latent factor 2 scores (perceived physical maturation) revealed synchronous and asynchronous relationships between hormones and concomitant physical features in this large young adolescent sample. Conclusions: Sociodemographic measures were associated with both objective hormone and self-report physical measures of pubertal maturation in a large, diverse sample of 9-10 year-olds. The latent variables of pubertal maturation described a complex interplay between perceived physical changes and hormone levels that hallmark sexual maturation, which future studies can examine in relation to trajectories of brain maturation, risk/resilience to substance use, and other mental health outcomes.

Increasing Compliance with a New Interunit Handoff Process: A Quality Improvement Project.

INTRODUCTION: Current literature demonstrates that standardizing interunit patient handoff improves communication, information transfer, and patient safety. However, few studies have focused on increasing staff compliance with new handoff processes. The purpose of this quality improvement project was to incorporate both user input into process design and on-the-job coaching with a newly introduced nurse handoff process between the postanesthesia care unit and Medical/Surgical units. We hypothesized that staff compliance would be 100% within 90 days. METHODS: The team's intervention consisted of (1) involving representative frontline nursing staff in the standardization and modification of the handoff process and (2) providing on-the-job coaching as the new process was being trialed at the bedside. We designed the handoff process during a 2-day workshop and a 1.5-week pilot. Data included the number of observed noncompliant process elements and handoff duration. Three sequential 30-day plan-do-study-act cycles were followed, during which compliance observations and user feedback were used to refine the design and coaching iteratively. RESULTS: A total of 1,800 process elements were observed and coached throughout a 90-day trial period. The number of observed noncompliant elements decreased from 15% (92) to 4% (22) from the first 30-day interval to the final 30-day interval. There was no undesirable increase in handoff duration (mean, 8.05 ± 4.72 minutes), and several potential errors-related to orders, charting, and patient placement-were prevented by using the new handoff. CONCLUSIONS: User input and on-the-job coaching resulted in iteratively increasing frontline compliance with a new standardized handoff process.

Stress exposures, neurodevelopment and health measures in the ABCD study.

The Adolescent Brain Cognitive Development (ABCD) Study, a large, longitudinal study of brain development and child health, is uniquely positioned to explore relationships among stress, neurodevelopment, and psychiatric symptomatology, including substance use and addiction. There is much we do not know about how adverse experiences affect the developing brain and cognitive, social, emotional, and academic outcomes. The data collected by the ABCD Study will allow the examination of the relationships among these variables in adolescence, including the effects of stressors (e.g., abuse, neglect, household challenges, parental substance use) on psychological adjustment and other stress responses. A comprehensive protocol that includes physical and mental health, substance use, culture and environment, neurocognitive assessments, biospecimen analyses, and structural and functional neuroimaging will provide opportunities for learning about the impacts of stressors on health and other outcomes in the context of adolescent development. This knowledge could lead to the development of interventions that reduce or even reverse the impacts of stressors.