long-read-tools.org: an interactive catalogue of analysis methods for long-read sequencing data.

Background: The data produced by long-read third-generation sequencers have unique characteristics compared to short-read sequencing data, often requiring tailored analysis tools for tasks ranging from quality control to downstream processing. The rapid growth in software that addresses these challenges for different genomics applications is difficult to keep track of, which makes it hard for users to choose the most appropriate tool for their analysis goal and for developers to identify areas of need and existing solutions to benchmark against.

Findings: We describe the implementation of long-read-tools.

Covering all your bases: incorporating intron signal from RNA-seq data.

RNA-seq datasets can contain millions of intron reads per library that are typically removed from downstream analysis. Only reads overlapping annotated exons are considered to be informative since mature mRNA is assumed to be the major component sequenced, especially for poly(A) RNA libraries. In this study, we show that intron reads are informative, and through exploratory data analysis of read coverage that intron signal is representative of both pre-mRNAs and intron retention.

International approaches to protecting and retaining trees on private urban land.

Most studies of urban forest management look at vegetation on public land. Yet, to meet ambitious urban forest targets, cities must attempt to maintain or increase trees and canopy cover on private urban land too. In this study, we review and evaluate international approaches to protecting and retaining trees on private urban land.

Rates of COVID-19-Related Outcomes in Cancer Compared With Noncancer Patients.

Cancer patients are a vulnerable population postulated to be at higher risk for severe coronavirus disease 2019 (COVID-19) infection. Increased COVID-19 morbidity and mortality in cancer patients may be attributable to age, comorbidities, smoking, health care exposure, and cancer treatments, and partially to the cancer itself. Most studies to date have focused on hospitalized patients with severe COVID-19, thereby limiting the generalizability and interpretability of the association between cancer and COVID-19 severity.

Multi-trait association studies discover pleiotropic loci between Alzheimer's disease and cardiometabolic traits.

Background: Identification of genetic risk factors that are shared between Alzheimer's disease (AD) and other traits, i.e., pleiotropy, can help improve our understanding of the etiology of AD and potentially detect new therapeutic targets.

76-year decline and recovery of aspen mediated by contrasting fire regimes: Long-unburned, infrequent and frequent mixed-severity wildfire.

Quaking aspen (Populus tremuloides) is a valued, minor component on northeastern California landscapes. It provides a wide range of ecosystem services and has been in decline throughout the region for the last century. This decline may be explained partially by the lack of fire on the landscape due to heavier fire suppression, as aspen benefit from fire that eliminates conifer competition and stimulates reproduction through root suckering.

Sex-specific responses to cold in a very cold-tolerant, northern Drosophila species.

Organisms can plastically alter resource allocation in response to changing environmental factors. For example, in harsh conditions, organisms are expected to shift investment from reproduction toward survival; however, the factors and mechanisms that govern the magnitude of such shifts are relatively poorly studied. Here we compared the impact of cold on males and females of the highly cold-tolerant species Drosophila montana at the phenotypic and transcriptomic levels.

Interviews with health professionals about the National Child Protection Alert System.

Aim: The New Zealand National Child Protection Alert System is administered by multidisciplinary teams in every district health board. The aim of this study was to investigate the factors that influence multidisciplinary child protection teams' (MDTs') decisions about whether to place a child protection alert.

Method: Members of the Child Protection Alert System teams were invited to participate in semi-structured interviews.

Exome-wide evaluation of rare coding variants using electronic health records identifies new gene-phenotype associations.

The clinical impact of rare loss-of-function variants has yet to be determined for most genes. Integration of DNA sequencing data with electronic health records (EHRs) could enhance our understanding of the contribution of rare genetic variation to human disease. By leveraging 10,900 whole-exome sequences linked to EHR data in the Penn Medicine Biobank, we addressed the association of the cumulative effects of rare predicted loss-of-function variants for each individual gene on human disease on an exome-wide scale, as assessed using a set of diverse EHR phenotypes.

Lossless integration of multiple electronic health records for identifying pleiotropy using summary statistics.

Increasingly, clinical phenotypes with matched genetic data from bio-bank linked electronic health records (EHRs) have been used for pleiotropy analyses. Thus far, pleiotropy analysis using individual-level EHR data has been limited to data from one site. However, it is desirable to integrate EHR data from multiple sites to improve the detection power and generalizability of the results.

Association between triglycerides, known risk SNVs and conserved rare variation in SLC25A40 in a multi-ancestry cohort.

Background: Elevated triglycerides (TG) are associated with, and may be causal for, cardiovascular disease (CVD), and co-morbidities such as type II diabetes and metabolic syndrome. Pathogenic variants in APOA5 and APOC3 as well as risk SNVs in other genes [APOE (rs429358, rs7412), APOA1/C3/A4/A5 gene cluster (rs964184), INSR (rs7248104), CETP (rs7205804), GCKR (rs1260326)] have been shown to affect TG levels. Knowledge of genetic causes for elevated TG may lead to early intervention and targeted treatment for CVD.

A genome-wide investigation of adaptive signatures in protein-coding genes related to tool behaviour in New Caledonian and Hawaiian crows.

Very few animals habitually manufacture and use tools. It has been suggested that advanced tool behaviour co-evolves with a suite of behavioural, morphological and life history traits. In fact, there are indications for such an adaptive complex in tool-using crows (genus Corvus species).

Single-Cell Transcriptomic Analysis Reveals BCMA CAR-T Cell Dynamics in a Patient with Refractory Primary Plasma Cell Leukemia.

Chimeric antigen receptor T cell (CAR-T) therapy has revolutionized the clinical treatment of hematological malignancies due to the prominent anti-tumor effects. B cell maturation antigen (BCMA) CAR-T cells have demonstrated promising effects in patients with relapsed/refractory multiple myeloma. However, the dynamics of CAR-T cell proliferation and cytotoxicity in clinical patients remains unexplored.

A simple and dynamic thermal gradient device for measuring thermal performance in small ectotherms.

The body temperature of ectothermic animals is heavily dependent on environmental temperature, impacting fitness. Laboratory exposure to favorable and unfavorable temperatures is used to understand these effects, as well as the physiological, biochemical, and molecular underpinnings of variation in thermal performance. Although small ectotherms, like insects, can often be easily reared in large numbers, it can be challenging and expensive to simultaneously create and manipulate several thermal environments in a laboratory setting.

Antibiotics for Uncomplicated Diverticulitis.

Learn more about the benefits and harms of antibiotics for uncomplicated diverticulitis.

is a maternal effect gene required for genomic imprinting.

Genomic imprinting establishes parental allele-biased expression of a suite of mammalian genes based on parent-of-origin specific epigenetic marks. These marks are under the control of maternal effect proteins supplied in the oocyte. Here we report epigenetic repressor as a novel maternal effect gene that regulates the imprinted expression of ten genes in mice.

A new lymphoid-primed progenitor marked by Dach1 downregulation identified with single cell multi-omics.

A classical view of blood cell development is that multipotent hematopoietic stem and progenitor cells (HSPCs) become lineage-restricted at defined stages. Linc-KitSca-1Flt3 cells, termed lymphoid-primed multipotent progenitors (LMPPs), have lost megakaryocyte and erythroid potential but are heterogeneous in their fate. Here, through single-cell RNA sequencing, we identify the expression of Dach1 and associated genes in this fraction as being coexpressed with myeloid/stem genes but inversely correlated with lymphoid genes.

Within-population sperm competition intensity does not predict asymmetry in conpopulation sperm precedence.

Postcopulatory sexual selection can generate evolutionary arms races between the sexes resulting in the rapid coevolution of reproductive phenotypes. As traits affecting fertilization success diverge between populations, postmating prezygotic (PMPZ) barriers to gene flow may evolve. Conspecific sperm precedence is a form of PMPZ isolation thought to evolve early during speciation yet has mostly been studied between species.

Genetics of height and risk of atrial fibrillation: A Mendelian randomization study.

Background: Observational studies have identified height as a strong risk factor for atrial fibrillation, but this finding may be limited by residual confounding. We aimed to examine genetic variation in height within the Mendelian randomization (MR) framework to determine whether height has a causal effect on risk of atrial fibrillation.

Methods And Findings: In summary-level analyses, MR was performed using summary statistics from genome-wide association studies of height (GIANT/UK Biobank; 693,529 individuals) and atrial fibrillation (AFGen; 65,446 cases and 522,744 controls), finding that each 1-SD increase in genetically predicted height increased the odds of atrial fibrillation (odds ratio [OR] 1.

Genetic Architecture of Abdominal Aortic Aneurysm in the Million Veteran Program.

Background: Abdominal aortic aneurysm (AAA) is an important cause of cardiovascular mortality; however, its genetic determinants remain incompletely defined. In total, 10 previously identified risk loci explain a small fraction of AAA heritability.

Methods: We performed a genome-wide association study in the Million Veteran Program testing ≈18 million DNA sequence variants with AAA (7642 cases and 172 172 controls) in veterans of European ancestry with independent replication in up to 4972 cases and 99 858 controls.

Parental fatigue before and after ventilation tube insertion in their children.

Objective: To determine if there is a difference in fatigue for caregivers of children with otitis media pre and post ventilation tube insertion (VTI).

Methods: Consecutive parents presenting with children at a pediatric otolaryngology practice at an academic medical center with recurrent otitis media who met criteria for VTI or who were following up within 6 weeks of VTI were surveyed with the Chalder Fatigue Scale (CFQ), a Visual Analogue Fatigue Scale (VAS-F), and demographic questions.

Results: No significant demographic differences were found (P < 0.