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opencc-zeroJun 2020View details →

Data from: Transcriptome analysis reveals nutrition‐ and age‐related patterns of gene expression in the fat body of pre‐overwintering bumble bee queens

Many diapausing insects undergo a nutrient storage period prior to their entry into diapause. Bumble bee queens diapause as adults in the winter preceding their spring nest initiation period. Before diapause, they sequester glycogen and lipids, which they metabolize during the overwintering period. We used RNA sequencing to examine how age and nectar diet (specifically, the concentration of sucrose in nectar) impact gene expression in the pre-overwintering bumble bee queen fat body, the "liver-like" organ in insects with broad functions related to nutrient storage and metabolism. We found that diet on its own, and in combination with age, impacts the expression of genes involved in detoxification. Age was also a strong driver of gene expression, especially at earlier ages (up to 3 days). In addition to these molecular correlates of diet and age, we also found a putative molecular signature of diapause entry or preparation in adult queens in the oldest age group (12 days) fed the most sucrose-rich diet, based on comparisons between our data set and another transcriptome data set from bumble bee queens. This transcriptomic pattern suggests that preparation for (or entry into) diapause might be in part mediated by nutritional state in bumble bee queens. Collectively, these findings show that there are molecular processes in the fat body that are responsive to sucrose levels in the diet and/or associated with age-related maturational changes. A better understanding of these processes may shed light on important aspects of bumble bee biology, such as queen responses to nutritional and other forms of stress, and the factors that regulate their entrance into diapause.

opencc-by-4.0Jun 2020View details →

RadioGx: Analysis of Large-Scale Radio-Genomic Data

This dataset contains an index of RadioSet objects available for download using the RadioGx R package. Each of the RSet objects are hosted in their own separate Zenodo uploads. The RadioGx R package is available for download from Bioconductor.

opencc-zeroJun 2020View details →

Data from: Fish assemblage convergence along stream environmental gradients: an intercontinental analysis

Species that pass through similar environmental filters, regardless of geographic proximity or evolutionary history, are expected to share many traits, resulting in similar assemblage trait distributions. Convergence of assemblage trait distributions among different biotic regions would indicate that consistent ecological processes produce repeated patterns of adaptive evolution. This study analyzes trait-environment relationships across multiple stream fish assemblages representing evolutionarily divergent faunas. We hypothesized that trait-environment patterns converge across regional faunas in response to a common set of environmental filters acting on functional traits. One hundred and ninety-seven species and forty streams were sampled from five regions: Belize, Benin, Brazil, Cambodia, and United States of America. By examining trait-environment plots, multiple congruent trait-environment patterns were found across all regions, indicative of a consistent set of environmental filters acting on local community assembly. The consistency of these patterns strongly suggests that water velocity and habitat structural complexity function as universal environmental filters, producing similar assemblage trait distributions in streams across all regions. Bivariate relationships were not universal, and only one of the associations between a single functional trait and single environmental variable was statistically significant across all five regions. Strong phylogenetic signal was found in traits and habitat use, which implies that niche conservatism also influenced assemblage trait distributions. Overall, results support the idea that habitat templates structure trait distributions of stream fish assemblages and do so in a consistent manner.

opencc-zeroJun 2020View details →

Data from: Clinical management and mortality among COVID-19 cases in sub-Saharan Africa: a retrospective study from Burkina Faso and simulated case analysis.

Absolute numbers of COVID-19 cases and deaths reported to date in the sub-Saharan Africa (SSA) region have been relatively low. As a result, there has been limited investigation into deceased cases in the region, as well as the impacts of different case management strategies. We detail demographic, epidemiological, and clinical information derived from publicly available information on deceased cases in SSA and, for cases in Burkina Faso, from aggregate records at the Center Hospitalier Universitaire de Tengandogo. Logistic regression was conducted on a synthetic case population to evaluate the adjusted odds of survival for patients receiving oxygen therapy or convalescent plasma, based on therapeutic effectiveness observed for other respiratory illnesses. Across SSA, deceased cases have been predominantly male and over 50 years of age. After adjustment for sex, age, and underlying conditions, the odds of mortality among cases in the synthetic population not receiving oxygen therapy was significantly higher than those receiving oxygen (OR: 2.07; 95%CI: 1.56-2.75). Cases receiving convalescent plasma had 50% reduced odds of mortality (95%CI: 0.24-0.93). Investment in sustainable oxygen therapy could reduce COVID-19 deaths in SSA. Ongoing investigation into convalescent plasma is warranted, as data on its effectiveness specifically in treating COVID-19 becomes available.

opencc-by-4.0Apr 2020View details →

Data for "Coherence-Guided InSAR Deformation Analysis in the Presence of Ongoing Land Surface Change in the Imperial Valley, California"

Interferometric Synthetic Aperture Radar (InSAR) observations of the surface velocity field in the Imperial Valley, California, over the period of 2015-2019, derived from the European Satellite Agency’s (ESA) Sentinel-1a/b satellite imagery. This dataset includes the following: 1. Downsampled results in geographic coordinates (a grid spacing of 2”). The average (secular) velocity (in mm/yr) is estimated along the satellite line-of-sight (LOS) directions from descending (D173) and ascending (A166) tracks over the spatial extent covering the Imperial Valley (S/N/W/E: 32.4/33.6/-116.2/-115). GeoTIFF files contain velocity values or color-coded RGB values using the Matplotlib colormap RdBu_r (ranging from -25 to 25 mm/yr). Masked pixels are assigned with NaN values. 2. Original high-resolution results processed in radar coordinates (~28 m in range and ~42 m in azimuth). HDF5 files contain matrices of the same size for the longitude, latitude, LOS secular velocity, and LOS residual displacements at each ground pixel from both tracks. The temporal error of displacement time series at each pixel (in mm) is represented by the root-mean-square residual of data fits to a linear trend. Masked pixels are assigned with NaN values.

opencc-by-4.0Jul 2020View details →

Extended data: Impact of admixture and ancestry on eQTL analysis and GWAS colocalization in GTEx

eQTL summary statistics and GWAS colocalization posterior probabilities from eQTL calling in an admixed subcohort of GTEx v8 with local and global ancestry adjustments. For the original, non-peer-reviewed preprint, see <a href="https://www.biorxiv.org/content/10.1101/836825v1">https://www.biorxiv.org/content/10.1101/836825v1</a>.  For the related source code, see <a href="https://doi.org/10.5281/zenodo.3924788">https://doi.org/10.5281/zenodo.3924788</a> or <a href="https://github.com/nicolerg/gtex-admixture-la">https://github.com/nicolerg/gtex-admixture-la</a>.

opencc-zeroJul 2020View details →

Data from: Comparative analysis of DNA repeats and identification of novel Fesreba centromeric element in fescues and ryagrasses

Background Cultivated grasses are an important source of food for domestic animals worldwide. Better knowledge of their genomes can speed up the development of new cultivars with better quality and resistance to biotic and abiotic stresses. The most widely grown grasses are tetraploid ryegrass species ( Lolium spp.) and diploid and hexaploid fescue species (Festuca spp.). In this work, we characterized repetitive DNA sequences and their contribution to genome size in five fescue and two ryegrass species, as well as one fescue and two ryegrass cultivars. Results Partial genome sequences produced by Illumina technology were used for genome-wide comparative analyses using RepeatExplorer pipeline. Retrotransposons were found to be the most abundant repeat types in all seven grass species. Athila element of Ty3/gypsy family showed the most striking differences in copy number between fescues and ryegrasses. The sequence data enabled the assembly of an LTR element Fesreba, which is highly enriched in centromeric and (peri)centromeric regions in all species. A combination of FISH with a probe specific to Fesreba element and immunostaining with CENH3 antibody showed their colocalization and indicated a possible role of Fesreba in centromere function. Conclusions Comparative repeatome analysis in a set of fescues and ryegrasses provided new insights into their genome organization and divergence, including the assembly of LTR element Fesreba. A new LTR element Fesreba was identified and found abundant in centromeric regions of the fescues and ryegrasses. It may have a role in the function of their centromeres.

opencc-zeroJul 2020View details →

Data from: A phylogenetic analysis of the dirt ants, Basiceros Schulz (Formicidae: Myrmicinae): inferring life histories through morphological convergence

Ants of the genus Basiceros (Hymenoptera: Formicidae: Myrmicinae) are elusive species known only from Neotropical rainforests. Little information is available regarding their natural history, and nothing is known about the phylogenetic relationships among species within the genus. The genus has been the subject of some controversy regarding generic delimitation but is currently a member of the "Basiceros-genus group" following recent classification changes. For mouthparts, labral and mandibular morphologies present considerable variation in the Basiceros-genus group, likely a result of adaptive evolution. In Basiceros, those differences can be observed in the labrum shape and the various degrees of development of the labral cleft and the clypeomandibular space. Here, in an attempt to illuminate the evolution of the group, species boundaries are tested for Basiceros. The evolutionary relationships of its species are investigated using molecular and morphological data. Bayesian inference (BI) and maximum likelihood (ML) analyses of a molecular dataset consisting of up to nine genes (three mitochondrial, six nuclear) and including samples from multiple populations of all known Basiceros taxa recovered the monophyly of the genus and of its species, with two well resolved internal clades: the singularis clade and the disciger clade. Focusing on the female castes of Basiceros, an ancestral state reconstruction is presented for mandibles and labrum morphology. The results suggest that the labrum and clypeomandibular morphologies are highly labile, although phylogenetically important characters in the genus. Mouthpart traits indicate a strong correlated evolutionary history potentially associated with specialized feeding habits.

opencc-by-4.0Dec 2019View details →

Analysis data for ""Integration of time-series meta-omics data reveals how microbial ecosystems respond to disturbance""

Analysis data for the manuscript: "Integration of meta-omics data reveals how microbial ecosystems respond to disturbance" Files used with the repository:  https://git-r3lab.uni.lu/malte.herold/laots_niche_ecology_analysis/ The archive was split into multiple parts for uploading to zenodo which need to be joined in order to extract the files: <pre><code class="language-bash">cat resultsdir_laots.tar.gz.part_* > resultsdir_laots.tar.gz tar xvfz resultsdir_laots.tar.gz</code></pre> Version 2 contains additional files generated in the revision.

opencc-zeroJul 2020View details →

Data from: Comparing traditional and Bayesian approaches to ecological meta-analysis

1. Despite the wide application of meta-analysis in ecology, some of the traditional methods used for meta-analysis may not perform well given the type of data characteristic of ecological meta-analyses. 2. We reviewed published meta-analyses on the ecological impacts of global climate change, evaluating the number of replicates used in the primary studies (ni) and the number of studies or records (k) that were aggregated to calculate a mean effect size. We used the results of the review in a simulation experiment to assess the performance of conventional frequentist and Bayesian meta-analysis methods for estimating a mean effect size and its uncertainty interval. 3. Our literature review showed that ni and k were highly variable, distributions were right-skewed, and were generally small (median ni =5, median k=44). Our simulations show that the choice of method for calculating uncertainty intervals was critical for obtaining appropriate coverage (close to the nominal value of 0.95). When k was low (<40), 95% coverage was achieved by a confidence interval based on the t-distribution that uses an adjusted standard error (the Hartung-Knapp-Sidik-Jonkman, HKSJ), or by a Bayesian credible interval, whereas bootstrap or z-distribution confidence intervals had lower coverage. Despite the importance of the method to calculate the uncertainty interval, 39% of the meta-analyses reviewed did not report the method used, and of the 61% that did, 94% used a potentially problematic method, which may be a consequence of software defaults. 4. In general, for a simple random-effects meta-analysis, the performance of the best frequentist and Bayesian methods were similar for the same combinations of factors (k and mean replication), though the Bayesian approaches had higher than nominal (>95%) coverage for the mean effect when k was very low (k<15). Our literature review suggests that many meta-analyses that used z-distribution or bootstrapping confidence intervals may have over-estimated the statistical significance of their results when the number of studies was low; more appropriate methods need to be adopted in ecological meta-analyses.

opencc-zeroSep 2020View details →

Data from: A framework for the integrated analysis of the magnitude, selectivity, and biotic effects of extinction and origination

The taxonomic and ecologic composition of Earth's biota has shifted dramatically through geologic time, with some clades going extinct while others diversified. Here, we derive a metric that quantifies the change in biotic composition due to extinction or origination and show that it equals the product of extinction/origination magnitude and selectivity (variation in magnitude among groups). We also define metrics that describe the extent to which a recovery (1) reinforced or reversed the effects of extinction on biotic composition and (2) changed composition in ways uncorrelated with the extinction. To demonstrate the approach, we analyzed an updated compilation of stratigraphic ranges of marine animal genera. We show that mass extinctions were not more selective than background intervals at the phylum level; rather, they tended to drive greater taxonomic change due to their higher magnitudes. Mass extinctions did not represent a separate class of events with respect to either strength of selectivity or effect. Similar observations apply to origination during recoveries from mass extinctions, and on average, extinction and origination were similarly selective and drove similar amounts of biotic change. Elevated origination during recoveries drove bursts of compositional change that varied considerably in effect. In some cases, origination partially reversed the effects of extinction, returning the biota towards the pre-extinction composition; in others, it reinforced the effects of the extinction, magnifying biotic change. Recoveries were as important as extinction events in shaping the marine biota, and their selectivity deserves systematic study alongside that of extinction.

Data from: Characteristics of university students supported by counseling services: analysis of psychological tests and pulse rate variability

Objective Mental health is an essential issue during adolescence. The number of students who use counseling services is increasing in universities. We attempted to confirm the characteristics of the students who access counseling services using both psychological tests and pulse rate variability (PRV) for better support for students' academic success. Methods We recruited the participants for this study from the students who had counseling sessions at Kanazawa University (Group S). As a control group, we also recruited students who had no experience in counseling services (Group H). We obtained health information from the database of annual health checkups. Participants received the Wechsler Adult Intelligence Scale (WAIS) III, Autism-Spectrum Quotient (AQ), Sukemune-Hiew (S-H) Resilience Test, and State-Trait Anxiety Inventory-JYZ (STAI). We also studied the SF-12v2 Health Survey. As a physiological test, we examined the spectral analyses of pulse rate variability (PRV) by accelerating plethysmography. We performed a linear analysis of PRV for LF, HF, and LF/HF as indexes of autonomic nervous function. We also conducted a non-linear analysis of PRV for the largest Lyapunov exponent (LLE). Additionally, we examined participants' blood for autoantibodies against glutamate decarboxylase (GAD) 65. Results A total of 105 students participated in this study. Group S had 37 participants (Male: 26, Female: 11), and Group H had 68 participants (Male: 27, Female 41). <a name="_Hlk24561145">There were five males and one female who had diagnoses of autism spectrum disorder (ASD), and three males and no female with attention deficit hyperactivity disorder (ADHD) by medical institutes in Group S. Additionally, four males and two females had diagnoses of ASD with ADHD by medical institutes in Group S.</a> A male with ASD in Group S had epilepsy. The students of Group S had characteristics as follows: 1) lower power of WMI despite high Full-Scale IQ, 2) higher ASD traits especially in Male, 3) lower resilience powers, 4) higher anxiety trait, 5) lower QOL in Role/social component in both Male and Female, 6) lower QOL in Mental component in Male 7) shifting of autonomic nervous balance toward higher sympathetic activity. Conclusion We could confirm the characteristics of students who visited counseling rooms for mental support. We also found gender differences in specificities of Group S. The educational system is changing rapidly to adjust social requests. These changes make conflict with the features of students of Group S. We should think about appropriate supports for the students who would pioneer the future of humanity.

Data from: Quality of stroke care and outcomes by sex: a pooled analysis including 19,000 participants

Objective: To explore the sex differences in outcomes and management after stroke using a large sample with high-quality international trial data. Methods: Individual participant data were obtained from five acute stroke randomized controlled trials. Data were obtained on demographics, medication use, in-hospital treatment and functional outcome. Study-specific crude and adjusted models were used to estimate sex differences in outcomes and management, and then pooled using random-effects meta-analysis. Results: There were 19,652 participants of whom 7721 (40%) were women. After multivariable adjustments, women with ischemic stroke had higher survival at 3 to 6 months (odds ratio [OR] 0.82; 95% confidence interval [CI] 0.70-0.97), higher likelihood of disability (OR 1.20; 95% CI 1.06-1.36) and worse quality of life (weighted mean difference -0.07, 95% CI -0.09—0.04). For management, women were more likely admitted to an acute stroke unit (OR 1.17, 95% CI 1.01-1.34), but less likely intubated (OR 0.58, 95% CI 0.36-0.93), treated for fever (OR 0.82, 95% CI 0.70-0.95) and admitted to an intensive care unit (OR 0.83, 95% CI 0.74-0.93). For pre-admission medications, women had higher odds of being prescribed antihypertensive agents (OR 1.22, 95% CI 1.13-1.31) and lower odds of being prescribed antiplatelets (OR 0.86; 95% CI 0.79-0.93), glucose lowering (OR 0.86; 95% CI 0.78-0.94) and lipid lowering agents (OR 0.85; 95% CI 0.77-0.94). Conclusions: This analysis suggest that women who had ischemic stroke had better survival but were also more disabled and had poorer quality of life. Variations in hospital and out-of-hospital management may partly explain the disparities.

opencc-zeroDec 2019View details →

Data from: A meta-analysis of global avian survival across species and latitude

Tropical birds are thought to be longer lived than many temperate species. We explored the idea of higher survival at tropical latitudes and whether extrinsic climate factors and intrinsic traits helped explain this pattern using a meta-analytical approach. The dataset consists of 949 estimates from 204 studies of avian survival from both New World and Old World biogeographical realms.

opencc-by-4.0Aug 2020View details →

Supporting Information for "How long is too long? Variogram analysis of AERONET data to aid aerosol validation and intercomparison studies"

This contains data sets and their description for the paper "How long is too long? Variogram analysis of AERONET data to aid aerosol validation and intercomparison studies" submitted to the journal Earth and Space Science by this author. This study investigates the uncertainty introduced into comparisons (between e.g. AERONET ground observations, satellite retrievals, or model simulations) of aerosol optical properties due to differences in time of observation between the data sets. This uncertainty source has historically been neglected but is potentially important in some situations.   Journal policies are that Supporting Information data sets can no longer be archived with the paper, but instead should be uploaded to a separate repository. As a result, I have uploaded these data here.   This data set consists of one pdf file describing the data sets, and then two zip archives containing the data (ASCII format). The total size is approximately 10 MB. These data files allow the reproduction of analysis results in this paper, and enable researchers to estimate temporal mismatch uncertainties in their own analyses involving AERONET sites.

Data from: Reptile responses to anthropogenic habitat modification: a global meta-analysis

Aim To determine how reptile populations respond to anthropogenic habitat modification and determine if species traits and environmental factors influence such responses. Location Global. Time period 1981–2018. Major taxa studied Squamata. Methods We compiled a database of 56 studies reporting how habitat modification affects reptile abundance, and calculated standardised mean differences in abundance (Hedges' g). We used Bayesian meta-analytical models to test whether responses to habitat modification depended on body size, clutch size, reproductive mode, habitat specialisation, range size, disturbance type, vegetation type, temperature and precipitation. Results Based on 815 effect sizes from 376 species, we found an overall negative effect of habitat modification on reptile abundance (mean Hedges' g = -0.43, 95% credible intervals = -0.61 to -0.26). Reptile abundance was, on average, one-third lower in modified compared to unmodified habitats. Small range sizes and small clutch sizes were associated with more negative responses to habitat modification, although the responses were weak and the credible intervals overlapped zero. We detected no effects of body size, habitat specialisation, reproductive mode (egg-laying or live-bearing), temperature, or precipitation. Some families exhibited more negative responses than others, although overall there was no phylogenetic signal in the data. Mining had the most negative impacts on reptile abundance, followed by agriculture, grazing, plantations and patch size reduction, whereas the mean effect of logging was neutral. Main conclusions Habitat modification is a key cause of reptile population declines, although there is variability in responses both within and between species, families, and vegetation types. The effect of disturbance type appeared to be related to intensity of habitat modification. Ongoing development of environmentally sustainable practices that ameliorate anthropogenic impacts is urgently needed to prevent reptile population declines.

opencc-zeroMay 2021View details →

Data from: Avian developmental rates are constrained by latitude and migratoriness – a global analysis.

Aim: It has long been recognized that tropical bird species demonstrate a wide range of traits characteristic for slow life histories, as indicated by lower investment in reproduction, slower senescence or slower physiological pace of life. Nevertheless, evidence for latitudinal variation in avian developmental rates has, so far, been inconclusive and based on limited geographic or phylogenetic sampling. The aim of this study was to test for global associations of avian developmental rates with latitude and migratoriness. Location: Global. Taxon: Birds. Methods: We compiled data on developmental (incubation and fledging) periods of 3500 passerine and non-passerine bird species distributed worldwide, which represented nearly all extant avian orders and families. Associations of developmental periods with latitude and migratoriness were analysed with phylogenetically-informed comparative models that controlled for major sources of variation in developmental rates (body mass, clutch size, and developmental mode across altricial-precocial spectrum). Results: Our analyses provided support for a negative latitudinal gradient in the duration of fledging, but not incubation period. After controlling for latitude, we also found that migratory birds showed faster developmental rates than resident species. Finally, we found that developmental rates were non-linearly associated with clutch size (fastest developmental rates at intermediate clutch size) and that duration of fledging period had higher evolutionary lability than incubation period. Main conclusions: Our global comparative analysis provided convincing and phylogenetically-robust evidence for a long-held hypothesis on latitudinal variation in avian developmental rates, although the pattern was apparent only at the post-embryonic stage of development (fledging period). This challenges a common belief on longer incubation periods in tropics and indicates that incubation and fledging periods may differently respond to external environmental factors, which can possibly be driven by their different evolutionary lability. The results may contribute to our understanding of biogeographic variation in species diversity.

Data from: The costs and benefits of paternal care in fish: a meta-analysis

Male-only parental care, while rare in most animals, is a widespread strategy within teleost fish. The costs and benefits to males of acting as sole carer are highly variable between fish species making it challenging to determine the selective pressures driving the evolution of male-only care to such a high prevalence. We conducted a phylogenetic meta-analysis to examine the costs and benefits of paternal care across fish species. We found no evidence that providing care negatively affects male condition. In contrast to other taxa, we also found limited evidence that male care has evolved as a strategy to improve offspring survival. Instead, we found that males already caring for a brood are preferred by females and that this preference is strongest in those species in which males work harder to care for larger broods. Thus, in fish, investment in offspring care does not constrain a male's mating success but rather augments it, suggesting that the relatively high prevalence of male-only care in fish may be in part explained by sexual selection through female preference for caring males.

Data from: How relatedness between mates influences reproductive success: an experimental analysis of self-fertilization and biparental inbreeding in a marine bryozoan

Kin associations increase the potential for inbreeding. The potential for inbreeding does not, however, make inbreeding inevitable. Numerous factors influence whether inbreeding preference, avoidance, or tolerance evolves, and, in hermaphrodites where both self-fertilization and biparental inbreeding are possible, it remains particularly difficult to predict how selection acts on the overall inbreeding strategy, and to distinguish the type of inbreeding when making inferences from genetic markers. Therefore, we undertook an empirical analysis on an understudied type of mating system (spermcast mating in the marine bryozoan, Bugula neritina) that provides numerous opportunities for inbreeding preference, avoidance, and tolerance. We created experimental crosses, containing three generations from two populations to estimate how parental reproductive success varies across parental relatedness, ranging from self, siblings, and non-siblings from within the same population. We found that the production of viable selfed offspring was extremely rare (only one colony produced three selfed offspring), and biparental inbreeding more common. Paternity analysis using 16 microsatellite markers confirmed outcrossing. The production of juveniles was lower for sib mating compared to non-sib mating. We found little evidence for consistent inbreeding, in terms of non-random mating, in adult samples collected from three populations, using multiple population genetic inferences. Our results suggest several testable hypotheses that potentially explain the overall mating and dispersal strategy in this species, including early inbreeding depression, inbreeding avoidance through cryptic mate choice, and differential dispersal distances of sperm and larvae.