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5,990 results for “reproduction”
Survival, fecundity and reproductive tissue data from false killer whales (Pseudorca crassidens)
<p>These data come from specimens from false killer whales from combined strandings (South Africa, 1981) and harvest (Japan 1979-80). The South African material was collected from 65 false killer whales that stranded en masse on the west coast of the Western Cape Province. Scientists reached the site two days after the stranding event was reported, so the material was not fresh and fixation of tissue samples was suboptimal. Data are available from 41 (including 32 mature) females. The Japanese material (96 females, 57 mature) originated from 6 schools harvested during shore-drive fisheries operations at Iki Island. In each case, as many false killer whales as possible were randomly examined. Data presented here come from 91 females if which 89 were mature. The Japanese and South African data were combined to estimate survival, but fecundity information is available for each separately. These data are associated with the following publication: Theoni Photopoulou, Ines M. Ferreira, Peter B. Best, Toshio Kasuya and Helene Marsh. 2017. Evidence for a postreproductive phase in female false killer whales <em>Pseudorca crassidens. </em>Frontiers in Zoology. 14:30. DOI 10.1186/s12983-017-0208-y</p>
Data from: "Correlates of mid-winter pregnancy and early reproductive outcomes in a reintroduced elk (Cervus canadensis) population"
<p>Raw and processed datasets used for analysis in "Correlates of mid-winter pregnancy and early reproductive outcomes in a reintroduced elk (<em>Cervus canadensis</em>) population" by Hooven et al., published in <em>Mammalian Biology</em>. Datasets are as follows:</p> <p>Pregnancy.csv - Raw dataset detailing year and date of capture, individual identifier, and measured intrinsic variables, along with confirmed or predicted pregnancy/calf viability status.</p> <p>Pregnancy_final_mass.csv - Raw dataset after body mass estimation for individuals that were not weighed. </p> <p>all_confirmed_preg.csv - Subset of raw data for all individuals with confirmed pregnancy status (via lab PSPB assay).</p> <p>preg_ageclass.csv - Subset of all_confirmed_preg dataset including all individuals with general age classification (e.g., adult or subadult).</p> <p>preg_numeric.csv - Subset of all_confirmed_preg dataset including all individuals with numeric age value (from incisiform canine cementum annuli).</p> <p>all_fns.csv - Subset of dataset including all individuals with confirmed or predicted fetal/early neonatal survival ("offspring viability") status.</p> <p>fns_ageclass.csv - Subset of all_fns.csv including all individuals with general age classification.</p> <p>fns_numeric.csv - Subset of all_fns.csv including all individuals with numeric age values.</p> <p>parameter_est.csv - Parameter estimates from top-performing generalized linear mixed models for both pregnancy and offpsinrg viability, for plotting.</p>
Supplementary datasets for manuscript titled: Seasonal tissue-specific gene expression in wild crown-of-thorns starfish reveals reproductive and stress-related transcriptional systems
<p>Supplementary datasets for manuscript titled: Seasonal tissue-specific gene expression in wild crown-of-thorns starfish reveals reproductive and stress-related transcriptional systems</p>
The 2020 Comparison of Tools for the Analysis of Quantitative Formal Models: Results and Reproduction
<p>This archive contains detailed results from QComp 2020 as well as the necessary scripts and data to reproduce them.</p> <p>Visit http://qcomp.org for more information for QComp.</p> <p>Overview of Contents</p> <p>- `qcomp.org/` contains the state of our website from the timepoint of the competition. This includes:<br> - All benchmark files, browsable at `qcomp.org/benchmarks/index.html`<br> - Detailed competition results in a human-readable format, browsable at `https://qcomp.org/competition/2020/`<br> - `logs/` contains the raw logfiles and data gathered by our scripts<br> - `scripts/` contains scripts to replicate the whole competition<br> - `toolpackages/` contains a package for each participating tool which includes<br> - Instructions for obtaining and installing the tool<br> - a file `invocations.json` listing the commandlines used in QComp 2020<br> - a file `tool.py` providing functionalities to obtain the result from the tool output.</p>
Reproduction package for paper "How far are we from reproducible research on code smell detection? A systematic literature review"
<p>Checklist and data extracted from publications analyzed for "How far are we from reproducible research on code smell detection? A systematic literature review" paper, together with processing scripts and calculations of Cohen's Kappa.</p> <p>Paper that describes details of the data is available here: https://doi.org/10.1016/j.infsof.2021.106783</p>
Data & R-Code for "Weather and food availability additively affect reproductive output in an expanding raptor population"
<p><strong>Abstract</strong></p> <p>The joint effects of interacting environmental factors on key demographic parameters can exacerbate or mitigate the separate factors’ effects on population dynamics. Given ongoing changes in climate and land use, assessing interactions between weather and food availability on reproductive performance is crucial to understand and forecast population dynamics. By conducting a feeding experiment in 4 years with different weather conditions, we were able to disentangle the effects of weather, food availability and their interactions on reproductive parameters in an expanding population of the red kite (<em>Milvus milvus</em>), a conservation-relevant raptor known to be supported by anthropogenic feeding. Brood loss occurred mainly during the incubation phase, and was associated with rainfall and low food availability. In contrast, brood loss during the nestling phase occurred mostly due to low temperatures. Survival of last-hatched nestlings and nestling development was enhanced by food supplementation and reduced by adverse weather conditions. However, we found no support for interactive effects of weather and food availability, suggesting that these factors affect reproduction of red kites additively. The results not only suggest that food-weather interactions are prevented by parental life-history trade-offs, but that food availability and weather conditions are crucial separate determinants of reproductive output, and thus population productivity. Overall, our results suggest that the observed increase in spring temperatures and enhanced anthropogenic food resources have contributed to the elevational expansion and the growth of the study population during the last decades.</p>
Data from: "Using low-fix rate GPS telemetry to expand estimates of ungulate reproductive success"
<p>Secondary datasets used for analysis in "Using low-fix rate GPS telemetry to expand estimates of ungulate reproductive success". Raw GPS relocation data are not publicly available due to potential ethical implications but are available from the corresponding author (Nathan Hooven, nathan.d.hooven@gmail.com) upon reasonable request. Datasets include:</p> <p>elk_days_part.csv: generated movement metrics and days from parturition for all cow elk for which reproductive success was confirmed</p> <p>elk_np.csv: generated movement metrics for non-parturient cow elk</p> <p>elk_unknowns.csv: generated movement metrics for cows with unknown reproductive status, but were confirmed pregnant in mid-winter</p> <p>elk_thisyear.csv: generated movement metrics for 2020 Vectronic cows monitored in 2021</p> <p>Part_dates.csv: Confirmed and predicted dates of parturition for all elk in training and testing sets</p> <p>all_prob_summary_parturient.csv: Confirmed and predicted dates of parturition and differences for confirmed successful elk</p> <p>Decision rules 1.xlsx: Spreadsheet with classification accuracy based upon varying decision rules</p> <p>Decision rules 2.csv: Plottable summary of classification accuracy based upon varying decision rules</p> <p> </p>
Supplementary material for "Long-term trends of reproductive success of black grouse Lyrurus tetrix in the southern Swiss Alps in relation to changes in climate and land use"
<p><strong>Abstract</strong></p> <p>Breeding success of an Alpine black grouse <em>Lyrurus tetrix</em> population in southern Switzerland was monitored from 1981 to 2020. This long-term dataset allows exploring relationships of reproductive rates with climate and habitat, which have shown marked changes during this period. Over the 40 years, the average elevation of black grouse breeding sites increased by around 100 m in Central/Southern Ticino but showed only a slight increase in Northern Ticino, where black grouse occur at higher elevations. Average reproductive rates in Northern Ticino remained constant throughout the study period but declined in Central/Southern Ticino. Relationships between reproductive success and weather as well as habitat variables were analysed with a multiple regression model. Temperature during the early chick-rearing phase and the time of egg-laying was positively correlated with reproductive rate. Correlations between reproductive rates and precipitation were less clear, and only small proportions of the variance in reproductive rates could be explained by precipitation. Brush forest explained the greatest amount of variation in reproductive rate (6.2%). Forest, alpine agricultural areas, and unproductive vegetation all showed a positive relationship with reproductive rate, but the proportion of the variance explained was small. Year (5.1%) and its interaction with region (2.3%) explained considerable amounts of the variance. While in Northern Ticino reproductive success did not show a negative trend when correcting for weather and habitat changes, there remained a negative trend over the years in Central/Southern Ticino. Despite the positive correlations of reproductive rate with temperature, increasing temperatures do not appear to have improved reproductive success, likely as a result of habitat changes that forced black grouse towards higher elevations. Changes in reproductive success were limited to the southern region, indicating deteriorating conditions at the edge of the distribution range.</p> <p> </p>
Reproduction package for the publication 'Galaxy cluster photons alter the ionisation state of the nearby warm-hot intergalactic medium'
<p>The following files can be used to reproduce the figures and data from the paper <strong>Galaxy cluster photons alter the ionisation state of the nearby warm-hot intergalactic medium</strong><strong> </strong>by L. Štofanová, A. Simionescu, N. A. Wijers, J. Schaye, and J. Kaastra to be accepted in Monthly Notices of the Royal Astronomical Society (MNRAS).</p>
Data from: Reproductive success of the wood warbler Phylloscopus sibilatrix varies across Europe
<p><strong>Abstract</strong></p> <p>Differences in population trends across a species’ breeding range are ultimately linked to variation in demographic rates. In small songbirds, demographic rates related to fecundity typically have strong effects on population trends. Populations of a forest songbird, the wood warbler <em>Phylloscopus sibilatrix</em>, have been declining in many but not all regions of the European breeding range. We investigated if clutch size, hatching rate, nest survival, and number of fledglings vary across Europe, and if nest survival is related to differences in the regionally dominant nest predator class (birds vs. mammals). From 2009 to 2020, we monitored 1896 nests and used cameras at a subsample of 645 nests in six study regions: the United Kingdom (mid-Wales, Dartmoor, New Forest), Germany (Hessen), Switzerland (Jura mountains), and Poland (Białowieża National Park). Number of fledglings was lowest in New Forest (1.43±CI 0.23), intermediate in Jura (2.41±0.31) and Białowieża (2.26±0.24), and highest in mid-Wales (3.02±0.48) and Dartmoor (2.92±0.32). The reason for low reproductive success in New Forest, Jura, and Białowieża was low nest survival, and large clutch sizes in Białowieża did not compensate for high nest losses. High reproductive success in mid-Wales and Dartmoor was due to high nest survival and large clutch sizes. Overall predation rates were similar everywhere despite variation between the regions in the dominant nest predator class. Unsuccessful nests in mid-Wales were mainly predated by birds, in Dartmoor, New Forest, Hessen, and Jura similarly by birds and mammals, and in Białowieża exclusively by mammals. Regional reproductive success does not match the population trends recently reported for the wood warbler in the six study regions (i.e., high reproduction ≠ positive trend). Annual survival may be a decisive factor, but it is difficult to quantify for a nomadic species such as the wood warbler that rarely returns to the same breeding locations.</p>
Metabolic scaling, growth, and reproduction data for animals
<p>Data for the scaling of metabolic rate, rates of growth, and annual reproduction for animals. Data and R scripts associated with "Metabolic scaling is the product of life history optimization"</p>
Intraspecific variation in reproductive barriers between two closely-related Arabidopsis sister species
<p>Reproductive isolation (RI) is a critical component of speciation and varies strongly in timing and strength among different sister taxa, depending e.g.<em>,</em> on the geography of speciation and divergence time. However, these factors may also produce variation in timing and strength among populations within species. Here we tested for variation in the expression of RI among replicate population pairs between the sister taxa <em>Arabidopsis lyrata</em> subsp. <em>lyrata</em> and <em>A. arenicola</em>. While the former is predominantly outcrossing, the latter is predominantly selfing<em>.</em> We focused on intrinsic prezygotic and postzygotic RI as both species occur largely in allopatry. We assessed RI by performing within-population crosses and interspecific between-population crosses, and by raising offspring. RI was generally high between all interspecific population pairs, but it varied in timing and strength depending on population history. Prezygotic isolation was strongest between the closest-related population pair, while early postzygotic isolation was high for all other population pairs. Furthermore, the timing and strength of RI depended strongly on cross direction. Our study provides empirical support that reproductive barriers between species are highly variable among population pairs and asymmetric within population pairs, and this variation seems to follow patterns typically described across species pairs.</p>
Separate-sex GWAS for reproductive fitness in Drosophila melanogaster (Sussex LHM sample)
<p>Code, data, logs, and graphs for GWAS on seperate-sex reproductive fitness in Drosophila melanogaster, Sussex LHM population sample.</p> <p>The shell script, code_drive_basic_gwas.sh, downloads input data files from the internet, drives Plink to select LD-independent SNPs, and then perform a genome-wide association test against female and male fitness, separately. Plink is also used to assign functions and gene names to SNPs. Bash/Unix code is used for formatting/compatibility adjustments, and also to add NCBI-dbSNP IDs to results. The shell script starts an R script that generates basic diagnostic graphs. This updated version differs from the first in that three large unconfirmed snRNA genes have been omitted to improve assignment of SNPs to genes.</p> <p>See https://f1000research.com/articles/5-2644/v3 and http://www.sussex.ac.uk/lifesci/morrowlab/</p>
False discovery rate calculations for genome-wide association study of reproductive fitness in Drosophila melanogaster (Sussex LHM sample)
<p>R code and results of applying false discovery (FDR) rate calculations to establish statistical signficance in a genome-wide association study of reproductive fitness in Drosophila melanogaster. Phenotype values were generated on hemiclone female and male lines from an outbred, laboratory adapted population. Thus, GWAS were previously performed seperately on the phenotype values for each sex, and also using a bivariate GWAS implemented in the R package multiPhen.</p> <p>FDR calculations were performed using the R package 'fdrtool' on all SNPs, and on LD-independent SNPs, the latter of which was used to determine p-value thresholds for genome-wide significance when all SNPs were considered.</p> <p>This version differs from the original in that: i) Some gene positions/names have been reassigned for accuaracy in the input data. ii) A file containing the p-value thresholds corresponding to an FDR of 0.1 has been added. The 95% credible intervals for each SNP association have been added to the results data files.</p>
Quantifying the basic reproduction number and the under-estimated fraction of mpox cases around the world at the onset of the outbreak: a mathematical modeling and machine learning- based study
<p><span>In 2022, there was a global resurgence of mpox, with different clinico-epidemiological features compared with previous</span><br><span>outbreaks. During this resurgence, sexual contact was hypothesized as the primary transmission route, with the community</span><br><span>of men having sex with men (MSM) being disproportionately affected. Because of the stigma associated with sexually</span><br><span>transmitted infections, especially those impacting MSM, the real burden of mpox could be masked.</span><br><span>We quantified the basic reproduction number (R</span><span>0</span><span>) and the under-estimated fraction of mpox cases in 16 countries, from the</span><br><span>onset of the outbreak until early September 2022, using Bayesian inference and a compartmentalized, risk-structured (high-</span><br><span>and low-risk populations), two-route (sexual and non-sexual transmission) mathematical model. Machine learning (ML) was</span><br><span>leveraged to identify under-estimation determinants.</span><br><span>Estimated R</span><span>0</span><span> </span><span>ranged between 1·37 (Canada) and 3·68 (Germany). The under-estimation rates for the high- and low-risk</span><br><span>populations varied between 25-93% and 65-85%, respectively. The estimated total number of mpox cases, relative to the</span><br><span>reported cases, is highest in Colombia (3·60) and lowest in Canada (1·08). In the ML analysis, two clusters of countries could</span><br><span>be identified, differing in terms of attitudes towards the 2SLGBTQIAP+ community and importance of religion.</span><br><span>Given the substantial mpox under-estimation, surveillance should be enhanced and campaigns against the stigmatization of</span><br><span>MSM should be organized. Countries have different social characteristics, potentially explaining the various degrees of under-</span><br><span>reporting in mpox cases, which should be considered by studies assessing the effectiveness of community-based</span><br><span>interventions.</span></p>
Reproduction package for the paper "Exploring the directly imaged HD 1160 system through spectroscopic characterization and high-cadence variability monitoring"
<p>This is a basic reproduction package for the paper <a href="https://doi.org/10.1093/mnras/stae1315">"Exploring the directly imaged HD 1160 system through spectroscopic characterization and high-cadence variability monitoring" by Sutlieff et al. (2024)</a>. It aims to provide the most important data products to check and reproduce the main results of the paper.</p>
MicroCT slices of reproductions of Minoan ceramic cups
<p>MicroCT data have been acquired at the Multidisciplinary Laboratory of the Abdus Salam International Centre for Theoretical Physics. The microCT scans were carried out by using a sealed X-ray source (Hamamatsu L8121–03) with a focal spot size of 5 μm and a flat panel detector (Hamamatsu C7942SK-25; pixel size of 50μm) according to the following parameters: 110kV, 90μA, exposure time/projection of 2 s, 1440 projections of the samples over 360°. The X-ray beam was filtered by a 0.01 mm-thick copper absorber. The final slices were reconstructed using the commercial software DigiXCT (Digisens) in 32-bit format at an isotropic voxel size of 40 μm. The uploaded slices have been converted in 8-bit format.</p>
Figure reproduction for "Accelerating small angle scattering experiments on anisotropic samples using kernel density estimation"
<p>These datasets and a Jupyter notebook reproduce figures in <a href="https://www.nature.com/articles/s41598-018-37345-5">a publication by Saito et al in Scientific Reports</a>. The notebook also serves as a demo for kernel density estimation (smoothing) of 2D data using Python. Details are described in the notebook. If you have no idea about ipynb format, please see HTML version with your web browser instead. It contains exactly the same codes and results as ipynb version.</p>
Large cortical bone pores in the tibia are associated with proximal femur strength - data for reproduction
<p>Results tables for the reproduction of:</p> <p>Iori G, Schneider J, Reisinger A, Heyer F, Peralta L, Wyers C, et al. Large cortical bone pores in the tibia are associated with proximal femur strength. PLOS ONE. doi:10.1371/journal.pone.0215405</p>
Reproduction package for: 'A NICER View of the Nearest and Brightest Millisecond Pulsar: PSR J0437–4715'
<div>Posterior sample files for the headline result associated with the publication "A NICER View of the Nearest and Brightest Millisecond Pulsar: PSR J0437–4715" by Choudhury et al. (2024; <a href="https://doi.org/10.3847/2041-8213/ad5a6f" target="_blank" rel="noopener"><em>ApJL</em> <strong>971</strong> L20</a>; <a href="https://arxiv.org/abs/2407.06789" target="_blank" rel="noopener">arXiv:2407.06789</a>).</div> <div> </div> <div>Also included are: the data products; the numeric model files including the telescope calibration products; model modules in the Python language using the X-PSI framework; and Jupyter analysis notebooks.</div> <div> </div> <div> <div> <p>Please refer to the README for detailed information.</p> </div> </div>
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.