The cycling and aging mouse female reproductive tract at single-cell resolution.

The female reproductive tract (FRT) undergoes extensive remodeling during reproductive cycling. This recurrent remodeling and how it shapes organ-specific aging remains poorly explored. Using single-cell and spatial transcriptomics, we systematically characterized morphological and gene expression changes occurring in ovary, oviduct, uterus, cervix, and vagina at each phase of the mouse estrous cycle, during decidualization, and into aging. These analyses reveal that fibroblasts play central-and highly organ-specific-roles in FRT remodeling by orchestrating extracellular matrix (ECM) reorganization and inflammation. Our results suggest a model wherein recurrent FRT remodeling over reproductive lifespan drives the gradual, age-related development of fibrosis and chronic inflammation. This hypothesis was directly tested using chemical ablation of cycling, which reduced fibrotic accumulation during aging. Our atlas provides extensive detail into how estrus, pregnancy, and aging shape the organs of the female reproductive tract and reveals the unexpected cost of the recurrent remodeling required for reproduction.

Do mammals have menopause?

Semantics and lack of data have clouded our understanding about menopause in non-human mammals. The traditional definition of menopause based on the last menstrual bleed is limited and hinders cross-species comparison. Here, we redefine it as the permanent cessation of ovulation and show menopause to be widespread across mammalian orders.

Waves of retrotransposon expansion remodel genome organization and CTCF binding in multiple mammalian lineages.

CTCF-binding locations represent regulatory sequences that are highly constrained over the course of evolution. To gain insight into how these DNA elements are conserved and spread through the genome, we defined the full spectrum of CTCF-binding sites, including a 33/34-mer motif, and identified over five thousand highly conserved, robust, and tissue-independent CTCF-binding locations by comparing ChIP-seq data from six mammals. Our data indicate that activation of retroelements has produced species-specific expansions of CTCF binding in rodents, dogs, and opossum, which often functionally serve as chromatin and transcriptional insulators. We discovered fossilized repeat elements flanking deeply conserved CTCF-binding regions, indicating that similar retrotransposon expansions occurred hundreds of millions of years ago. Repeat-driven dispersal of CTCF binding is a fundamental, ancient, and still highly active mechanism of genome evolution in mammalian lineages.

Single-cell reconstruction of the early maternal-fetal interface in humans.

During early human pregnancy the uterine mucosa transforms into the decidua, into which the fetal placenta implants and where placental trophoblast cells intermingle and communicate with maternal cells. Trophoblast-decidual interactions underlie common diseases of pregnancy, including pre-eclampsia and stillbirth. Here we profile the transcriptomes of about 70,000 single cells from first-trimester placentas with matched maternal blood and decidual cells. The cellular composition of human decidua reveals subsets of perivascular and stromal cells that are located in distinct decidual layers. There are three major subsets of decidual natural killer cells that have distinctive immunomodulatory and chemokine profiles. We develop a repository of ligand-receptor complexes and a statistical tool to predict the cell-type specificity of cell-cell communication via these molecular interactions. Our data identify many regulatory interactions that prevent harmful innate or adaptive immune responses in this environment. Our single-cell atlas of the maternal-fetal interface reveals the cellular organization of the decidua and placenta, and the interactions that are critical for placentation and reproductive success.

Bioactive Bismuth Compounds: Is Their Toxicity a Barrier to Therapeutic Use?

Bismuth compounds are considered relatively non-toxic, with their low solubility in aqueous solutions (e.g., biological fluids) being the major contributing factor to this property. Bismuth derivatives are widely used for the treatment of peptic ulcers, functional dyspepsia, and chronic gastritis. Moreover, the properties of bismuth compounds have also been extensively explored in two main fields of action: antimicrobial and anticancer. Despite the clinical interest of bismuth-based drugs, several side effects have also been reported. In fact, excessive acute ingestion of bismuth, or abuse for an extended period of time, can lead to toxicity. However, evidence has demonstrated that the discontinuation of these compounds usually reverses their toxic effects. Notwithstanding, the continuously growing use of bismuth products suggests that it is indeed part of our environment and our daily lives, which urges a more in-depth review and investigation into its possible undesired activities. Therefore, this review aims to update the pharmaco-toxicological properties of bismuth compounds. A special focus will be given to in vitro, in vivo, and clinical studies exploring their toxicity.

Chylothorax associated with pulmonary compressive atelectasis in an emperor tamarin (Saguinus imperator).

Chylothorax is the accumulation of lymph in the thoracic cavity, and it has never been reported in neotropical primates. An emperor tamarin died and at necropsy chylothorax associated with pulmonary compressive atelectasis was diagnosed. Idiopathic chylothorax can be a cause of respiratory insufficiency and death in tamarins.

Common genetic variation drives molecular heterogeneity in human iPSCs.

Technology utilizing human induced pluripotent stem cells (iPS cells) has enormous potential to provide improved cellular models of human disease. However, variable genetic and phenotypic characterization of many existing iPS cell lines limits their potential use for research and therapy. Here we describe the systematic generation, genotyping and phenotyping of 711 iPS cell lines derived from 301 healthy individuals by the Human Induced Pluripotent Stem Cells Initiative. Our study outlines the major sources of genetic and phenotypic variation in iPS cells and establishes their suitability as models of complex human traits and cancer. Through genome-wide profiling we find that 5-46% of the variation in different iPS cell phenotypes, including differentiation capacity and cellular morphology, arises from differences between individuals. Additionally, we assess the phenotypic consequences of genomic copy-number alterations that are repeatedly observed in iPS cells. In addition, we present a comprehensive map of common regulatory variants affecting the transcriptome of human pluripotent cells.

Corrigendum: Common genetic variation drives molecular heterogeneity in human iPSCs.

This corrects the article DOI: 10.1038/nature22403.

Fast identification of differential distributions in single-cell RNA-sequencing data with waddR.

MOTIVATION: Single-cell gene expression distributions measured by single-cell RNA-sequencing (scRNA-seq) often display complex differences between samples. These differences are biologically meaningful but cannot be identified using standard methods for differential expression. RESULTS: Here, we derive and implement a flexible and fast differential distribution testing procedure based on the 2-Wasserstein distance. Our method is able to detect any type of difference in distribution between conditions. To interpret distributional differences, we decompose the 2-Wasserstein distance into terms that capture the relative contribution of changes in mean, variance and shape to the overall difference. Finally, we derive mathematical generalizations that allow our method to be used in a broad range of disciplines other than scRNA-seq or bioinformatics. AVAILABILITY AND IMPLEMENTATION: Our methods are implemented in the R/Bioconductor package waddR, which is freely available at https://github.com/goncalves-lab/waddR, along with documentation and examples. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Extensive compensatory cis-trans regulation in the evolution of mouse gene expression.

Gene expression levels are thought to diverge primarily via regulatory mutations in trans within species, and in cis between species. To test this hypothesis in mammals we used RNA-sequencing to measure gene expression divergence between C57BL/6J and CAST/EiJ mouse strains and allele-specific expression in their F1 progeny. We identified 535 genes with parent-of-origin specific expression patterns, although few of these showed full allelic silencing. This suggests that the number of imprinted genes in a typical mouse somatic tissue is relatively small. In the set of nonimprinted genes, 32% showed evidence of divergent expression between the two strains. Of these, 2% could be attributed purely to variants acting in trans, while 43% were attributable only to variants acting in cis. The genes with expression divergence driven by changes in trans showed significantly higher sequence constraint than genes where the divergence was explained by variants acting in cis. The remaining genes with divergent patterns of expression (55%) were regulated by a combination of variants acting in cis and variants acting in trans. Intriguingly, the changes in expression induced by the cis and trans variants were in opposite directions more frequently than expected by chance, implying that compensatory regulation to stabilize gene expression levels is widespread. We propose that expression levels of genes regulated by this mechanism are fine-tuned by cis variants that arise following regulatory changes in trans, suggesting that many cis variants are not the primary targets of natural selection.

Rapid turnover of long noncoding RNAs and the evolution of gene expression.

A large proportion of functional sequence within mammalian genomes falls outside protein-coding exons and can be transcribed into long RNAs. However, the roles in mammalian biology of long noncoding RNA (lncRNA) are not well understood. Few lncRNAs have experimentally determined roles, with some of these being lineage-specific. Determining the extent by which transcription of lncRNA loci is retained or lost across multiple evolutionary lineages is essential if we are to understand their contribution to mammalian biology and to lineage-specific traits. Here, we experimentally investigated the conservation of lncRNA expression among closely related rodent species, allowing the evolution of DNA sequence to be uncoupled from evolution of transcript expression. We generated total RNA (RNAseq) and H3K4me3-bound (ChIPseq) DNA data, and combined both to construct catalogues of transcripts expressed in the adult liver of Mus musculus domesticus (C57BL/6J), Mus musculus castaneus, and Rattus norvegicus. We estimated the rate of transcriptional turnover of lncRNAs and investigated the effects of their lineage-specific birth or death. LncRNA transcription showed considerably greater gain and loss during rodent evolution, compared with protein-coding genes. Nucleotide substitution rates were found to mirror the in vivo transcriptional conservation of intergenic lncRNAs between rodents: only the sequences of noncoding loci with conserved transcription were constrained. Finally, we found that lineage-specific intergenic lncRNAs appear to be associated with modestly elevated expression of genomically neighbouring protein-coding genes. Our findings show that nearly half of intergenic lncRNA loci have been gained or lost since the last common ancestor of mouse and rat, and they predict that such rapid transcriptional turnover contributes to the evolution of tissue- and lineage-specific gene expression.

Clonal heterogeneity in ER+ breast cancer reveals the proteasome and PKC as potential therapeutic targets.

Intratumoral heterogeneity impacts the success or failure of anti-cancer therapies. Here, we investigated the evolution and mechanistic heterogeneity in clonal populations of cell models for estrogen receptor positive breast cancer. To this end, we established barcoded models of luminal breast cancer and rendered them resistant to commonly applied first line endocrine therapies. By isolating single clones from the resistant cell pools and characterizing replicates of individual clones we observed inter- (between cell lines) and intra-tumor (between different clones from the same cell line) heterogeneity. Molecular characterization at RNA and phospho-proteomic levels revealed private clonal activation of the unfolded protein response and respective sensitivity to inhibition of the proteasome, and potentially shared sensitivities for repression of protein kinase C. Our in vitro findings are consistent with tumor-heterogeneity that is observed in breast cancer patients thus highlighting the need to uncover heterogeneity at an individual patient level and to adjust therapies accordingly.

Low level of antioxidant capacity biomarkers but not target overexpression predicts vulnerability to ROS-inducing drugs.

Despite a strong rationale for why cancer cells are susceptible to redox-targeting drugs, such drugs often face tumor resistance or dose-limiting toxicity in preclinical and clinical studies. An important reason is the lack of specific biomarkers to better select susceptible cancer entities and stratify patients. Using a large panel of lung cancer cell lines, we identified a set of "antioxidant-capacity" biomarkers (ACB), which were tightly repressed, partly by STAT3 and STAT5A/B in sensitive cells, rendering them susceptible to multiple redox-targeting and ferroptosis-inducing drugs. Contrary to expectation, constitutively low ACB expression was not associated with an increased steady state level of reactive oxygen species (ROS) but a high level of nitric oxide, which is required to sustain high replication rates. Using ACBs, we identified cancer entities with a high percentage of patients with favorable ACB expression pattern, making it likely that more responders to ROS-inducing drugs could be stratified for clinical trials.

A pipeline for RNA-seq data processing and quality assessment.

SUMMARY: We present an R based pipeline, ArrayExpressHTS, for pre-processing, expression estimation and data quality assessment of high-throughput sequencing transcriptional profiling (RNA-seq) datasets. The pipeline starts from raw sequence files and produces standard Bioconductor R objects containing gene or transcript measurements for downstream analysis along with web reports for data quality assessment. It may be run locally on a user's own computer or remotely on a distributed R-cloud farm at the European Bioinformatics Institute. It can be used to analyse user's own datasets or public RNA-seq datasets from the ArrayExpress Archive. AVAILABILITY: The R package is available at www.ebi.ac.uk/tools/rcloud with online documentation at www.ebi.ac.uk/Tools/rwiki/, also available as supplementary material.

Adherence to the CONSORT statement of randomized clinical trials on ART restorations in children: current status and reporting characteristics.

Appropriate research reports are important to facilitate the evaluation of studies and the decision-making by dentists and policymakers. This meta-research study assessed the conformity of randomized clinical trials (RCTs) on atraumatic restorative treatment (ART) restorations with the CONSORT recommendations and their risk of bias (RoB). Cochrane Library, MEDLINE, BBO, LILACS, Scopus, and Web of Science databases were searched from April 2019 to June 2021 for RCTs that assessed the longevity of ART restorations in children. A specific tool was used to assess adherence to the CONSORT recommendations; RoB was evaluated with the Cochrane risk-of-bias tool. Descriptive analyses included the number of studies by journal, follow-up period, country, and quality assessments. A total of 2,181 papers were retrieved and 36 of them were analyzed qualitatively. The overall CONSORT mean score (CONms) was 22.52 ± 6.17 out of 32 points. The best described items were intervention and outcomes, whereas allocation concealment was described in only 22% of the papers. Significant differences in CONms were detected in the analysis by country and publication dates. High CONms were observed in recently published papers (26.7 ± 3.1) when compared to first ART studies (18.1 ± 4.6; p < 0.001). RoB was low in four studies, unclear in 11, and high in 21. Adherence of the papers to the CONSORT recommendations was not fully achieved and most of the papers had unclear and high RoB (PROSPERO registration #CRD42020201460).

Why do they engage in such hard programs? The search for excellence in youth basketball.

Excellent performance in sport has a strong positive relationship with the accumulated hours of practice. The specialization years are seen as a decisive moment to lift the skill level, athletic readiness and commitment but the selection and orientation of talent has been strongly dependent of biological and motor variables. The purpose of this study is to describe the achievement and motivation variables that can explain the belonging to an elite competitive level of young basketball players. Eighty-two basketball players under 16 years fulfilled the WOFO Questionnaire (Spence and Helmreich, 1983), and an adapted version of the DPMQ (De Bruin, Rikers and Schmidt, 2007). Forty players (mean age 15. 8 ± 0.96) were engaged in high performance centres and forty-two (mean age 15.6 ± 1.01) played in national level clubs. A decision tree and a random forest analysis between elite and national level players were performed. The most discriminant variable was Will to Excel, with 85,2% true positives in elite or national level. Mastery and competitiveness did not enter the final model. The will to reach excellence in performance can be considered as a condition to engage in more specialized and demanding practice. The assessment of the path to expertise only through motor variables or through the accumulated hours of deliberate practice is limited and can lead to mistaken identification or orientation of young sport talents. The use of a more comprehensive model is needed. Key pointsExcellent performance in sport has a strong positive relationship with the accumulated hours of practice.It seems reasonable that if the young athletes are better selected, have better training conditions and practice and compete more time with better teammates and opponents, the chance of becoming competent adult athletes is greater.A self orientation to excellence may play a crucial role in persistence in practice, in order to achieve higher standards in competition.The specific motivation that underpins participation at different levels and help the coaches to be sensitive to non-biological or non-functional variables, leading to a better knowledge and caring of the adolescents they teach.The assessment of the path to expertise only through motor variables or through the accumulated hours of deliberate practice is limited and can lead to mistaken identification or orientation of young sport talents.

Quality of Work Life and Contribution to Productivity: Assessing the Moderator Effects of Burnout Syndrome.

This study is focused on assessing the effects of burnout as a moderator of the relationship between employees' quality of work life (QWL) and their perceptions of their contribution to the organization's productivity by integrating the QWL factors into the trichotomy of (de)motivators of productivity in the workplace. The empirical findings resulting from an OLS multiple regression, with interaction terms, applied to a survey administered at 514 employees in 6 European countries, point out two important insights: (i) QWL hygiene factors (e.g., safe work environment and occupational healthcare) positively and significantly influence the contribution to productivity; and (ii) burnout de-motivator factors (that is, low effectiveness, cynicism, and emotional exhaustion) significantly moderate the relationship between QWL and the contribution to productivity. Combining burnout with other QWL components, such as occupational health, safe work, and appropriate salary, new insights are provided concerning the restricting (i.e., low effectiveness and cynicism) and catalyzing (emotional exhaustion) burnout components of contribution to productivity. These findings are particularly relevant given the increased weight of burnout, mental disorders and absenteeism in the labor market, affecting individuals' quality of life and organizations' performance and costs.

Signatures of TSPAN8 variants associated with human metabolic regulation and diseases.

Here, with the example of common copy number variation (CNV) in the TSPAN8 gene, we present an important piece of work in the field of CNV detection, that is, CNV association with complex human traits such as 1H NMR metabolomic phenotypes and an example of functional characterization of CNVs among human induced pluripotent stem cells (HipSci). We report TSPAN8 exon 11 (ENSE00003720745) as a pleiotropic locus associated with metabolomic regulation and show that its biology is associated with several metabolic diseases such as type 2 diabetes (T2D) and cancer. Our results further demonstrate the power of multivariate association models over univariate methods and define metabolomic signatures for variants in TSPAN8.

The portfolio as an evaluation tool: an analysis of its use in an undergraduate nursing program.

This qualitative study was carried out between April and August 2007. It analyzed the use of portfolios in the academic community. A total of nine full-time professors and 119 students enrolled in their third semester were interviewed through a semi-structured interview. Content analysis was used to analyze data. Learning evaluations are seen as a verification of knowledge and efficacy of pedagogical method, and also as an incentive to study. Evaluations are procedural, that is, evaluation is continuous, or one-time, e.g. semester end tests. The portfolio is defined as a gradual and continuous evaluation tool. The faculty members and students need to accept the use of portfolios and evaluate the possibilities of this resource. This study is a first attempt to appraise the evaluation process of an undergraduate program, and the use of portfolios and other strategies needs to be consolidated in order to improve the educational process in undergraduate nursing programs.

Quality of Work Life and Organizational Performance: Workers' Feelings of Contributing, or Not, to the Organization's Productivity.

This is a pioneering study on the relationship between quality of work life and the employee's perception of their contribution to organizational performance. It unveils the importance of subjective and behavioral components of quality of work life and their influence on the formation of the collaborator's individual desire to contribute to strengthening the organization's productivity. The results obtained indicate that for workers: feeling their supervisors' support through listening to their concerns and by sensing they take them on board; being integrated in a good work environment; and feeling respected both as professionals and as people; positively influence their feeling of contributing to organizational performance. The results are particularly relevant given the increased weight of services in the labor market, together with intensified automation and digitalization of collaborators' functions. The findings also contribute to the ongoing debate about the need for more work on the subjective and behavioral components of so-called smart and learning organizations, rather than focusing exclusively on remuneration as the factor stimulating organizational productivity based on the collaborator's contribution.