Assessing the reproducibility of discriminant function analyses.

Data are the foundation of empirical research, yet all too often the datasets underlying published papers are unavailable, incorrect, or poorly curated. This is a serious issue, because future researchers are then unable to validate published results or reuse data to explore new ideas and hypotheses. Even if data files are securely stored and accessible, they must also be accompanied by accurate labels and identifiers. To assess how often problems with metadata or data curation affect the reproducibility of published results, we attempted to reproduce Discriminant Function Analyses (DFAs) from the field of organismal biology. DFA is a commonly used statistical analysis that has changed little since its inception almost eight decades ago, and therefore provides an opportunity to test reproducibility among datasets of varying ages. Out of 100 papers we initially surveyed, fourteen were excluded because they did not present the common types of quantitative result from their DFA or gave insufficient details of their DFA. Of the remaining 86 datasets, there were 15 cases for which we were unable to confidently relate the dataset we received to the one used in the published analysis. The reasons ranged from incomprehensible or absent variable labels, the DFA being performed on an unspecified subset of the data, or the dataset we received being incomplete. We focused on reproducing three common summary statistics from DFAs: the percent variance explained, the percentage correctly assigned and the largest discriminant function coefficient. The reproducibility of the first two was fairly high (20 of 26, and 44 of 60 datasets, respectively), whereas our success rate with the discriminant function coefficients was lower (15 of 26 datasets). When considering all three summary statistics, we were able to completely reproduce 46 (65%) of 71 datasets. While our results show that a majority of studies are reproducible, they highlight the fact that many studies still are not the carefully curated research that the scientific community and public expects

Recruitment of Reviewers Is Becoming Harder at Some Journals: A Test of the Influence of Reviewer Fatigue at Six Journals in Ecology and Evolution

Background: It is commonly reported by editors that it has become harder to recruit reviewers for peer review and that this is because individuals are being asked to review too often and are experiencing reviewer fatigue. However, evidence supporting these arguments is largely anecdotal. Main body: We examine responses of individuals to review invitations for six journals in ecology and evolution. The proportion of invitations that lead to a submitted review has been decreasing steadily over 13 years (2003–2015) for four of the six journals examined, with a cumulative effect that has been quite substantial (average decline from 56% of review invitations generating a review in 2003 to just 37% in 2015). The likelihood that an invitee agrees to review declines significantly with the number of invitations they receive in a year. However, the average number of invitations being sent to prospective reviewers and the proportion of individuals being invited more than once per year has not changed much over these 13 years, despite substantial increases in the total number of review invitations being sent by these journals—the reviewer base has expanded concomitant with this growth in review requests. Conclusions: The proportion of review invitations that lead to a review being submitted has been declining steadily for four of the six journals examined here, but reviewer fatigue is not likely the primary explanation for this decline

Analysis of ancestry heterozygosity suggests that hybrid incompatibilities in threespine stickleback are environment dependent

Hybrid incompatibilities occur when interactions between opposite ancestry alleles at different loci reduce the fitness of hybrids. Most work on incompatibilities has focused on those that are “intrinsic,” meaning they affect viability and sterility in the laboratory. Theory predicts that ecological selection can also underlie hybrid incompatibilities, but tests of this hypothesis using sequence data are scarce. In this article, we compiled genetic data for F(2) hybrid crosses between divergent populations of threespine stickleback fish (Gasterosteus aculeatus L.) that were born and raised in either the field (seminatural experimental ponds) or the laboratory (aquaria). Because selection against incompatibilities results in elevated ancestry heterozygosity, we tested the prediction that ancestry heterozygosity will be higher in pond-raised fish compared to those raised in aquaria. We found that ancestry heterozygosity was elevated by approximately 3% in crosses raised in ponds compared to those raised in aquaria. Additional analyses support a phenotypic basis for incompatibility and suggest that environment-specific single-locus heterozygote advantage is not the cause of selection on ancestry heterozygosity. Our study provides evidence that, in stickleback, a coarse—albeit indirect—signal of environment-dependent hybrid incompatibility is reliably detectable and suggests that extrinsic incompatibilities can evolve before intrinsic incompatibilities

Sex-Dependent Effects of Prenatal Food and Protein Restriction on Offspring Physiology in Rats and Mice: Systematic Review and Meta-Analyses

Background:  Males and females may experience different effects of early-life adversity on life-long health. One hypothesis is that male foetuses invest more in foetal growth and relatively less in placental growth, and that this makes them susceptible to poor nutrition in utero, particularly if nutrition is reduced part-way through gestation. Objectives:  Our objectives were to examine whether (1) food and/ or protein restriction in rats and mice has consistent sex-dependent effects, (2) sex-dependency differs between types of outcomes, and (3) males are more severely affected when restriction starts part-way through gestation. Data sources:  PubMed and Web of Science were searched to identify eligible studies. Study eligibility criteria:  Eligible studies described controlled experiments that restricted protein or food during gestation in rats or mice, examined physiological traits in offspring from manipulated pregnancies, and tested whether effects differed between males and females. Results:  Our search identified 292 articles, of which the full texts of 72 were assessed, and 65 were included for further synthesis. A majority (50) used Wistar or Sprague-Dawley rats and so these were the primary focus. Among studies in which maternal diet was restricted for the duration of gestation, no type of trait was consistently more severely affected in one particular sex, although blood pressure was generally increased in both sexes. Meta-analysis found no difference between sexes in the effect of protein restriction throughout gestation on blood pressure. Among studies restricting food in the latter half of gestation only, there were again few consistent sex-dependent effects, although three studies found blood pressure was increased in males only. Meta-analysis found that food restriction in the second half of gestation increased adult blood pressure in both sexes, with a significantly greater effect in males. Birthweight was consistently reduced in both sexes, a result confirmed by meta-analysis. Conclusions:  We found little support for the hypotheses that males are more affected by food and protein restriction, or that effects are particularly severe if nutrition is reduced part-way through gestation. However, less than half of the studies tested for sex by maternal diet interactions to identify sex-dependent effects. As a result, many reported sex-specific effects may be false positives

Assessing the reproducibility of discriminant function analyses

Data are the foundation of empirical research, yet all too often the datasets underlying published papers are unavailable, incorrect, or poorly curated. This is a serious issue, because future researchers are then unable to validate published results or reuse data to explore new ideas and hypotheses. Even if data files are securely stored and accessible, they must also be accompanied by accurate labels and identifiers. To assess how often problems with metadata or data curation affect the reproducibility of published results, we attempted to reproduce Discriminant Function Analyses (DFAs) from the field of organismal biology. DFA is a commonly used statistical analysis that has changed little since its inception almost eight decades ago, and therefore provides an opportunity to test reproducibility among datasets of varying ages. Out of 100 papers we initially surveyed, fourteen were excluded because they did not present the common types of quantitative result from their DFA or gave insufficient details of their DFA. Of the remaining 86 datasets, there were 15 cases for which we were unable to confidently relate the dataset we received to the one used in the published analysis. The reasons ranged from incomprehensible or absent variable labels, the DFA being performed on an unspecified subset of the data, or the dataset we received being incomplete. We focused on reproducing three common summary statistics from DFAs: the percent variance explained, the percentage correctly assigned and the largest discriminant function coefficient. The reproducibility of the first two was fairly high (20 of 26, and 44 of 60 datasets, respectively), whereas our success rate with the discriminant function coefficients was lower (15 of 26 datasets). When considering all three summary statistics, we were able to completely reproduce 46 (65%) of 71 datasets. While our results show that a majority of studies are reproducible, they highlight the fact that many studies still are not the carefully curated research that the scientific community and public expects

Abortion services and providers in Canada in 2019: results of a national survey.

BACKGROUND: Since 2016, abortion care has undergone several important changes, particularly related to the provision of medical abortion using mifepristone. We aimed to document characteristics of the abortion care workforce in Canada after the update of clinical practice guidelines of mifepristone use for medical abortion. METHODS: We conducted a national, web-based, anonymized, bilingual (English/French) survey. We collected demographics and clinical care characteristics of physicians and nurse practitioners who provided abortion care in 2019. Between July and December 2020, we distributed the survey through professional organizations, including The College of Family Physicians of Canada and The Society of Obstetricians and Gynaecologists of Canada. We present descriptive statistics. RESULTS: Overall, 465 respondents representing all 10 provinces and 3 territories in Canada completed the survey. Of these, 388 (83.4%), including 30 nurse practitioners, provided first-trimester medical abortion, of which 350 (99.4%) used mifepristone. Two hundred and nineteen (47.1%) respondents provided first-trimester surgical abortion, 109 (23.4%) provided second-trimester surgical abortion and 115 (24.7%) provided second- or third-trimester medical abortion. Half of respondents reported fewer than 5 years of experience with any abortion care. Respondents reported providing a total of 48 509 abortions in 2019, including 32 345 (66.7%) first-trimester surgical abortions and 13 429 (27.7%) first-trimester medical abortions. In Quebec, only 1918 (12.5%) of reported abortions were first-trimester medical abortions. Primary care providers provided 34 540 (71.2%) of the total abortions. First-trimester medical abortions represented 44.4% (n = 2334) of all abortions in rural areas, as opposed to 25.6% (n = 11 067) in urban areas. INTERPRETATION: The increased availability of medical abortion facilitates abortion access, especially in primary care and rural settings, and where surgical abortion is not available. Rejuvenation of the workforce is a critical contributor to equitable access to abortion services

The genetics of adaptive shape shift in stickleback: pleiotropy and effect size.

The distribution of effect sizes of genes underlying adaptation is unknown (Orr 2005

Age, gender and disability predict future disability in older people: the Rotterdam Study

<p>Abstract</p> <p>Background</p> <p>To develop a prediction model that predicts disability in community-dwelling older people. Insight in the predictors of disability is needed to target preventive strategies for people at increased risk.</p> <p>Methods</p> <p>Data were obtained from the Rotterdam Study, including subjects of 55 years and over. Subjects who had complete data for sociodemographic factors, life style variables, health conditions, disability status at baseline and complete data for disability at follow-up were included in the analysis. Disability was expressed as a Disability Index (DI) measured with the Health Assessment Questionnaire.</p> <p>We used a multivariable polytomous logistic regression to derive a basic prediction model and an extended prediction model. Finally we developed readily applicable score charts for the calculation of outcome probabilities.</p> <p>Results</p> <p>Of the 5027 subjects included, 49% had no disability, 18% had mild disability, 16% had severe disability and 18% had deceased at follow-up after six years. The strongest predictors were age and prior disability. The contribution of other predictors was relatively small. The discriminative ability of the basic model was high; the extended model did not enhance predictive ability.</p> <p>Conclusion</p> <p>As prior disability status predicts future disability status, interventive strategies should be aimed at preventing disability in the first place.</p

Effects of eight neuropsychiatric copy number variants on human brain structure

Many copy number variants (CNVs) confer risk for the same range of neurodevelopmental symptoms and psychiatric conditions including autism and schizophrenia. Yet, to date neuroimaging studies have typically been carried out one mutation at a time, showing that CNVs have large effects on brain anatomy. Here, we aimed to characterize and quantify the distinct brain morphometry effects and latent dimensions across 8 neuropsychiatric CNVs. We analyzed T1-weighted MRI data from clinically and non-clinically ascertained CNV carriers (deletion/duplication) at the 1q21.1 (n = 39/28), 16p11.2 (n = 87/78), 22q11.2 (n = 75/30), and 15q11.2 (n = 72/76) loci as well as 1296 non-carriers (controls). Case-control contrasts of all examined genomic loci demonstrated effects on brain anatomy, with deletions and duplications showing mirror effects at the global and regional levels. Although CNVs mainly showed distinct brain patterns, principal component analysis (PCA) loaded subsets of CNVs on two latent brain dimensions, which explained 32 and 29% of the variance of the 8 Cohen’s d maps. The cingulate gyrus, insula, supplementary motor cortex, and cerebellum were identified by PCA and multi-view pattern learning as top regions contributing to latent dimension shared across subsets of CNVs. The large proportion of distinct CNV effects on brain morphology may explain the small neuroimaging effect sizes reported in polygenic psychiatric conditions. Nevertheless, latent gene brain morphology dimensions will help subgroup the rapidly expanding landscape of neuropsychiatric variants and dissect the heterogeneity of idiopathic conditions