Agptools: a utility suite for editing genome assemblies.

Summary: The AGP format is a tab-separated table format describing how components of a genome assembly fit together. A standard submission format for genome assemblies is a fasta file giving the sequence of contigs along with an AGP file showing how these components are assembled into larger pieces like scaffolds or chromosomes. For this reason, many scaffolding software pipelines output assemblies in this format.

Critical reproductive behaviors in Scaled Quail and Northern Bobwhite are affected by thermal variability and mean temperature.

Animals can respond differently to shifting thermal variability versus thermal averages, both of which are changing due to climate warming. How these thermal variables affect parental care behaviors can reveal the ability of parents to modify their behaviors to meet the competing demands of their offspring's thermal needs and self-maintenance, which becomes critical in suboptimal thermal conditions. Further, the time frame used to examine the interplay between temperature and behavioral shifts (e.

Carcinogenic air pollutants and breast cancer risk in the Arkansas rural community health study: A nested case-control study.

Background: Previous epidemiological studies on the associations between hazardous air pollutants (HAPs) and breast cancer (BC) have largely neglected rural, medically underserved areas in the United States, which differ in exposures and disparities compared to urban areas.

Objectives: We aimed to examine the associations between carcinogenic HAPs and BC risk in a rural population.

Methods: Using a nested case-control design, 574 cases and 2295 incidence density-sampled controls matched 1:4 on index age and race were included from the Arkansas Rural Community Health study.

Astyanax mexicanus surface and cavefish chromosome-scale assemblies for trait variation discovery.

The ability of organisms to adapt to sudden extreme environmental changes produces some of the most drastic examples of rapid phenotypic evolution. The Mexican Tetra, Astyanax mexicanus, is abundant in the surface waters of northeastern Mexico, but repeated colonizations of cave environments have resulted in the independent evolution of troglomorphic phenotypes in several populations. Here, we present three chromosome-scale assemblies of this species, for one surface and two cave populations, enabling the first whole-genome comparisons between independently evolved cave populations to evaluate the genetic basis for the evolution of adaptation to the cave environment.

A chromosome-scale fishing cat reference genome for the evaluation of potential germline risk variants.

The fishing cat, Prionailurus viverrinus, faces a population decline, increasing the importance of maintaining healthy zoo populations. Unfortunately, zoo-managed individuals currently face a high prevalence of transitional cell carcinoma (TCC), a form of bladder cancer. To investigate the genetics of inherited diseases among captive fishing cats, we present a chromosome-scale assembly, generate the pedigree of the zoo-managed population, reaffirm the close genetic relationship with the Asian leopard cat (Prionailurus bengalensis), and identify 7.

Astyanax mexicanus surface and cavefish chromosome-scale assemblies for trait variation discovery.

The ability of organisms to adapt to sudden extreme environmental changes produces some of the most drastic examples of rapid phenotypic evolution. The Mexican Tetra, , is abundant in the surface waters of northeastern Mexico, but repeated colonizations of cave environments have resulted in the independent evolution of troglomorphic phenotypes in several populations. Here, we present three chromosome-scale assemblies of this species, for one surface and two cave populations, enabling the first whole-genome comparisons between independently evolved cave populations to evaluate the genetic basis for the evolution of adaptation to the cave environment.

Single-haplotype comparative genomics provides insights into lineage-specific structural variation during cat evolution.

The role of structurally dynamic genomic regions in speciation is poorly understood due to challenges inherent in diploid genome assembly. Here we reconstructed the evolutionary dynamics of structural variation in five cat species by phasing the genomes of three interspecies F1 hybrids to generate near-gapless single-haplotype assemblies. We discerned that cat genomes have a paucity of segmental duplications relative to great apes, explaining their remarkable karyotypic stability.

Understanding the role of environmental and socioeconomic factors in the geographic variation of breast cancer risk in the US-wide Sister Study.

Objective: To describe the geographic pattern of breast cancer incidence in a nationwide prospective cohort and investigate whether environmental exposures and/or neighborhood socioeconomic status explain observed geographic disparities.

Methods: Using accelerated failure time models with a spatial random effect term, we mapped the health region-level association between residential location and breast cancer incidence for 44,707 participants in the Sister Study after controlling for established individual-level breast cancer risk factors. We performed a variable selection process to select environmental exposures [i.

The Vocal Priorities of College Students With and Without Self-Reported Voice Problems.

Objectives/hypothesis: To determine if the Vocal Priorities Questionnaire (VPQ) could be used in people who were not seeking treatment for a voice problem. To determine if the VPQ could be used to compare groups based on self-reported voice problems. To determine if vocal priorities (loudness, clarity, pitch, pitch range) vary based on self-reported voice problems.

Supply and quality of colonoscopy according to the characteristics of gastroenterologists in the French population-based colorectal-cancer screening program.

Background: Since its complete roll-out in 2009, the French colorectal cancer screening program (CRCSP) experienced 3 major constraints [use of a less efficient Guaiac-test (gFOBT), stopping the supply of Fecal-Immunochemical-Test kits (FIT), and suspension of the program due to the coronavirus disease 2019 (COVID-19)] affecting its effectiveness.

Aim: To describe the impact of the constraints in terms of changes in the quality of screening-colonoscopy (Quali-Colo).

Methods: This retrospective cohort study included screening-colonoscopies performed by gastroenterologists between Jan-2010 and Dec-2020 in people aged 50-74 living in Ile-de-France (France).

Examining Mental Health Disorders in Overweight and Obese Pediatric Patients.

Introduction: We investigated the frequency and variation in three mental health diagnoses among obese or overweight children and adolescents.

Method: Logistic regression was used to examine the association between the outcome variables-anxiety, depression, and adjustment disorders-with the following covariates: overweight/obesity status, sex, age, and race.

Results: Findings show anxiety, depressive, and adjustment disorder diagnoses were significantly higher for overweight or obese youth in our sample.

Implications for health system resilience: Quantifying the impact of the COVID-19-related stay at home orders on cancer screenings and diagnoses in southeastern North Carolina, USA.

COVID-19 impacted hospital systems across the globe. Focus shifted to responding to increased healthcare demand while mitigating COVID-19 spread on their campuses. Mitigation efforts limited medical professional-patient interactions, including patient access to preventive cancer screenings.

Community vulnerability and mobility: What matters most in spatio-temporal modeling of the COVID-19 pandemic?

Community vulnerability is widely viewed as an important aspect to consider when modeling disease. Although COVID-19 does disproportionately impact vulnerable populations, human behavior as measured by community mobility is equally influential in understanding disease spread. In this research, we seek to understand which of four composite measures perform best in explaining disease spread and mortality, and we explore the extent to which mobility account for variance in the outcomes of interest.

The Quantitative Examination of the Relationship Between Job Satisfaction and Organizational Fit in Athletic Trainers.

Context: Athletic trainers' (ATs') job satisfaction has been extensively researched, yet little is known about how satisfaction relates to organizational culture.

Objective: To examine ATs' level of job satisfaction with and organizational-fit perceptions of their employment setting.

Design: Cross-sectional study.

Using spatial and temporal modeling to visualize the effects of U.S. state issued stay at home orders on COVID-19.

Coronavirus disease 2019 dominated and augmented many aspects of life beginning in early 2020. Related research and data generation developed alongside its spread. We developed a Bayesian spatio-temporal Poisson disease mapping model for estimating real-time characteristics of the coronavirus disease in the United States.

A systematic review of spatial habitat associations and modeling of marine fish distribution: A guide to predictors, methods, and knowledge gaps.

As species distribution models, and similar techniques, have emerged in marine ecology, a vast array of predictor variables have been created and diverse methodologies have been applied. Marine fish are vital food resources worldwide, yet identifying the most suitable methodology and predictors to characterize spatial habitat associations, and the subsequent distributions, often remains ambiguous. Our objectives were to identify knowledge gaps in fish guilds, identify research themes, and to determine how data sources, statistics, and predictor variables differ among fish guilds.

Successful Perioperative Management of Orthotopic Cardiac Transplantation in a Pediatric Patient With Concurrent Congenital von Willebrand Disease and Acquired von Willebrand Syndrome Using Recombinant von Willebrand Factor.

Von Willebrand disease (VWD) is the most common bleeding disorder and reportedly affects 1:1,000 of the world's population. There are three subtypes of VWD characterized by a quantitative defect (types 1 and 3 VWD) or a qualitative defect (type 2 VWD). Type 1 VWD results in a partial deficiency of von Willebrand factor (VWF) and affects approximately 75% of individuals with VWD, whereas type 3 VWD results in a severe or complete deficiency of VWF.

Use of Factor VIIa and Anti-inhibitor Coagulant Complex in Pediatric Cardiac Surgery Patients.

Objectives: Postoperative bleeding is a common cause of morbidity and mortality in cardiac patients who undergo cardiopulmonary bypass (CPB). Pediatric patients are especially at risk for adverse effects of surgery and CPB on the coagulation system. This can result in bleeding, transfusions, and poor outcomes.

An analysis of hurricane impact across multiple cancers: Accessing spatio-temporal variation in cancer-specific survival with Hurricane Katrina and Louisiana SEER data.

Considering the impact of events such as natural disasters on disease risk is important. For this study, we examined temporal trends in multiple cancers available via Louisiana SEER data to understand how event impacts differ in timing and strength by cancer type. The specific event of interest for these Louisiana residents diagnosed with lung and bronchus, prostate, breast, colorectal, leukemia, or ovarian cancer in during the years 2000-2013 was Hurricane Katrina (August 2005).

Spatial patterns in prostate Cancer-specific mortality in Pennsylvania using Pennsylvania Cancer registry data, 2004-2014.

Background: Spatial heterogeneity of prostate cancer-specific mortality in Pennsylvania remains unclear. We utilized advanced geospatial survival regressions to examine spatial variation of prostate cancer-specific mortality in PA and evaluate potential effects of individual- and county-level risk factors.

Methods: Prostate cancer cases, aged ≥40 years, were identified in the 2004-2014 Pennsylvania Cancer Registry.

Latent classes for chemical mixtures analyses in epidemiology: an example using phthalate and phenol exposure biomarkers in pregnant women.

Latent class analysis (LCA), although minimally applied to the statistical analysis of mixtures, may serve as a useful tool for identifying individuals with shared real-life profiles of chemical exposures. Knowledge of these groupings and their risk of adverse outcomes has the potential to inform targeted public health prevention strategies. This example applies LCA to identify clusters of pregnant women from a case-control study within the LIFECODES birth cohort with shared exposure patterns across a panel of urinary phthalate metabolites and parabens, and to evaluate the association between cluster membership and urinary oxidative stress biomarkers.

Air Pollution, Clustering of Particulate Matter Components, and Breast Cancer in the Sister Study: A U.S.-Wide Cohort.

Background: Particulate matter (PM) is a complex mixture. Geographic variations in PM may explain the lack of consistent associations with breast cancer.

Objective: We aimed to evaluate the relationship between air pollution, PM components, and breast cancer risk in a United States-wide prospective cohort.

A mobile app identifies momentary psychosocial and contextual factors related to mealtime self-management in adolescents with type 1 diabetes.

Effective diabetes problem solving requires identification of risk factors for inadequate mealtime self-management. Ecological momentary assessment was used to enhance identification of factors hypothesized to impact self-management. Adolescents with type 1 diabetes participated in a feasibility trial for a mobile app called MyDay.