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1,157 results for “Limited data”
Data and codes related to the article: Horner et al. Streamflow uncertainty due to the limited sensitivity of controls at hydrometric stations
<p>The data files and R code files are related to the article Horner et al. "Streamflow uncertainty due to the limited sensitivity of controls at hydrometric stations" published in Hydrological Processes.</p> <p><strong>Data: </strong></p> <p>1/ Q_Craponne.txt</p> <p>Original streamflow time series of Craponne hydrometric station which was used to generate the synthetic stage time series using the theoretical equations of the 5 fictive hydrometric stations.</p> <p>Column separator: semi-colon (;)<br> Column 1 ==> Time (%Y-%m-%d %H:%M)<br> Column 2 ==> Streamflow (in m3/s)</p> <p>2/ h_Mercier.txt</p> <p>Original stage time series for Mercier hydrometric station</p> <p>Column separator: semi-colon (;)<br> Column 1 ==> Time (%Y-%m-%d %H:%M)<br> Column 2 ==> Stage(in mm)<br> Missing value code: NA</p> <p>3/ Gaugings_Mercier.txt</p> <p>Gaugings (date, stage, streamflow and associated uncertainty) of the Mercier hydrometric station before and after hydraulic control change which occured in November 2013.</p> <p>Column separator: semi-colon (;)<br> Column 1 ==> Date (%Y-%m-%d)<br> Column 2 ==> Stage_m (in m)<br> Column 3 ==> Streamflow_m3_per_s (in m3/s)<br> Column 3 ==> Uncertainty (unitless)</p> <p><strong>R codes:</strong></p> <p>0/ other ressources:<br> All the ressources related to the bayesian estimation of the rating curve can be found on github: <a href="https://github.com/BaM-tools">https://github.com/BaM-tools</a><br> Time aggregation of time series was done using the tAgg R package available on github: <a href="https://github.com/IvanHeriver/tAgg">https://github.com/IvanHeriver/tAgg</a></p> <p>1/ functions.R<br> This files contains several functions. Comments within the file explains each of the function:</p> <ul> <li>hydraulicEquations(): returns a list of the theoretical equations for the rating curves of the five fictive cases</li> <li>hydraulicEquationsInverter(): inverts of a theoretical rating curve (given a function Q=f(h), it returns a function h=f(Q))</li> <li>computeAM30(): computes the AM30</li> <li>generate_nonsyst_errors(): generates a matrix of non systematic errors</li> <li>generate_syst_errors(): generates a matrix of systematic errors</li> <li>get_resampling_indices_from_periodicity(): returns the indices of the resampling time steps used to generate systematic errors given a time vector and a periodicity</li> </ul> <p>Some of the code require the following packages: dplyr and RcppRoll</p> <p>2/ examples.R<br> This file contains some code illustrating the usage of the functions in the "functions.R" file.</p> <p> </p>
Data from: Forest degradation limits the complementarity and quality of animal seed dispersal
<p><span>Forest degradation changes the structural heterogeneity of forests and species communities, with potential consequences for ecosystem functions including seed dispersal by frugivorous animals. While the quantity of seed dispersal may be robust towards forest degradation, changes in the effectiveness of seed dispersal through qualitative changes are poorly understood. Here, we carried out extensive field sampling on the structure of forest microhabitats, seed deposition sites, and plant recruitment along three characteristics of forest microhabitats (canopy cover, ground vegetation, deadwood) in Europe's last lowland primeval forest (Białowieża, Poland). We then applied niche modelling to study forest degradation effects on multi-dimensional seed deposition by frugivores and recruitment of fleshy-fruited plants. Forest degradation was shown to (1) reduce the niche volume of forest microhabitat characteristics by half, (2) homogenize the spatial seed deposition within and among frugivore species, and (3) limit the regeneration of plants via changes in seed deposition and recruitment. Our study shows that the loss of frugivores in degraded forests is accompanied by a reduction in the complementarity and quality of seed dispersal by remaining frugivores. In contrast, structure-rich habitats, such as old-growth forests, safeguard the diversity of species interactions, forming the basis for high-quality ecosystem functions.</span></p>
Data from: Different taxonomic and functional indices complement the understanding of herb-layer community assembly patterns in a southern-limit temperate forest
<p><span>The efficient conservation of vulnerable ecosystems in the face of global change requires a complete understanding of how plant communities respond to various environmental factors. We aim to demonstrate that a combined use of different approaches, traits, and indices representing each of the taxonomic and functional characteristics of plant communities will give complementary information on the factors driving vegetation assembly patterns. We analyzed variation across an environmental gradient in taxonomic and functional composition, richness, and diversity of the herb-layer of a temperate beech-oak forest that was located in northern Spain. We measured species cover and four functional traits: leaf dry matter content (LDMC), specific leaf area (SLA), leaf size, and plant height. We found that light is the most limiting resource influencing herb-layer vegetation. Taxonomic changes in richness are followed by equivalent functional changes in the diversity of leaf size but by opposite responses in the richness of SLA. Each functional index is related to different environmental factors even within a single trait (particularly for LDMC and leaf size). To conclude, each characteristic of a plant community is influenced by different and even contrasting factors or processes. Combining different approaches, traits, and indices simultaneously will help us understand how plant communities work.</span></p>
Text-fig. 8. Lanfrancia subglobosa E.REID et M.CHANDLER. a–c, e–g: Holotype V. 23014. a: reflected light. b, c: Surface renderings from micro-CT data. a, b: Lateral views with dorsal surface of locule facing forward and locule casts protruding in upper part. c: Apical view. d: Fruit showing two locule casts the dorsal surfaces of which face to the left and the right, V. 30417(1). e–g: Successive digital transverse sections showing four u to v to c-shaped locules from micro-CT data. h: Physical transverse section of specimen in (d). i–k: Physical transverse section, V. 30419 from Herne Bay, blue lines in K indicating limits of fibre layer lining the locule. l: Detail from (h), showing sclerenchyma composing the septa and central axis. m: Transverse section, enlargement from (i), showing anatomy of tissues adjacent to the dorsal infold. Blue lines indicate limits of the fibre layer lining the locule. n: Part of (m) recut, tangential section transecting the dorsal infold (central), both limbs of the locule cast, and peripheral parts of the pericarp on either side. o: Detail from (n), showing anatomy of the infold. Scale bars 5 mm in (a–h) (a–g share the same bar), 3 mm in (i), 1 mm in (j–m), 0.5 mm in (n), 0.2 mm in (o). in Mastixioid Fruits (Cornales) From The Early Eocene London Clay Flora: Morphology, Anatomy And Nomenclatural Revision
Text-fig. 8. Lanfrancia subglobosa E.REID et M.CHANDLER. a–c, e–g: Holotype V. 23014. a: reflected light. b, c: Surface renderings from micro-CT data. a, b: Lateral views with dorsal surface of locule facing forward and locule casts protruding in upper part. c: Apical view. d: Fruit showing two locule casts the dorsal surfaces of which face to the left and the right, V. 30417(1). e–g: Successive digital transverse sections showing four u to v to c-shaped locules from micro-CT data. h: Physical transverse section of specimen in (d). i–k: Physical transverse section, V. 30419 from Herne Bay, blue lines in K indicating limits of fibre layer lining the locule. l: Detail from (h), showing sclerenchyma composing the septa and central axis. m: Transverse section, enlargement from (i), showing anatomy of tissues adjacent to the dorsal infold. Blue lines indicate limits of the fibre layer lining the locule. n: Part of (m) recut, tangential section transecting the dorsal infold (central), both limbs of the locule cast, and peripheral parts of the pericarp on either side. o: Detail from (n), showing anatomy of the infold. Scale bars 5 mm in (a–h) (a–g share the same bar), 3 mm in (i), 1 mm in (j–m), 0.5 mm in (n), 0.2 mm in (o).
Data from: Limited intraspecific variation in drought resistance along a pronounced tropical rainfall gradient
<p>Assessing within-species variation in response to drought is crucial for predicting species responses to climate change and informing restoration and conservation efforts, yet experimental data are lacking for the vast majority of tropical tree species. We assessed intraspecific variation in response to water availability across a strong rainfall gradient for 16 tropical tree species using reciprocal transplant and common garden field experiments, along with measurements of gene flow and key functional traits linked to drought resistance.</p>
Raw data for: Self-Referencing for Quasi Shot-Noise-Limited Widefield Transient Microscopy
<p>The repository shares the data used to produce the figures in the paper "Self-Referencing for Quasi Shot-Noise-Limited Widefield Transient Microscopy", submitted 2024 in Optics Express. </p> <p>The upload includes for each Figure the raw and processed self-referenced transient normalized transmission data, (T_on-T_off) / T_off, from which all results and statistics are deduced.</p>
Data from: Mast fruiting in a large tropical African legume tree provides evidence for the nutrient resource limitation hypothesis
<p>The large grove-forming tropical tree <em>Microberlinia bisulcata</em> (Fabaceae subfamily Detarioideae) at Korup, Cameroon, shows strong mast fruiting. Reproductive allocation is considerable. The site has very nutrient-poor soil. To test the nutrient resource limitation hypothesis, phenological recordings between 1989 and 2017 were matched with climate variables and analyzed using logistic time-series regression. Masting happened mostly on 2- or 3-year cycles. A strong predictor was mean daily rainfall in the dry season: low in the current year of masting and high in the year prior. Less strongly predictive was the increase in dry season radiation between prior and mast years. Masting events showed no relationship to annual stem increment, nor with local plantation yields. Later, the normally heavy mastings became moderate after two attacks by caterpillars. Collated studies of fallen leaf nutrient concentrations showed that P increased markedly, K rose and fell, but N and Mg changed little, in the inter-mast interval. P and K were likely being accumulated and stored and then triggered masting events when internal thresholds were crossed. The drier season prior to masting enabled a rise in C, and the wetter season the year before, with higher soil moisture, enabled better acquisition and uptake of nutrients by roots and mycorrhizas. The main storage of P may be in bark and branches, that for K on soil organic-colloids. A rooting-fruiting trade-off in C allocated over a minimal 2-year cycle is implied. The hypothesis is that synchrony among masting trees may be achieved, in part, by equilibration of P across the mycorrhizal network. The long-term driver appears to be the inherent year-to-year stochasticity of dry-season rainfall, the realization of which leads to an important refinement of the hypothesis. Life history strategy linked to nutrient resource dynamics provides a plausible explanation and more advanced hypothesis for the masting events observed.</p>
Data from: The limit to evolutionary rescue depends on ploidy in yeast exposed to nystatin
<h4>Data package about haploid vs diploid adaptation to nystatin in yeast</h4> <div>This package contains files and scripts related to the publication "The limit to evolutionary rescue depends on ploidy in yeast exposed to nystatin". Raw data and analyses are included.</div>
Terrain variables used for ensemble distribution modelling of vulnerable marine ecosystems indicator taxa on data-limited seamounts of Cabo Verde (NW Africa)
<p><em>Aim:</em> Seamounts are conspicuous geological features with an important ecological role and can be considered Vulnerable Marine Ecosystems (VMEs). Since many deep-sea regions remain largely unexplored, investigating the occurrence of VME taxa on seamounts is challenging. Our study aimed to predict the distribution of four cold-water coral (CWC) taxa, indicators for VMEs, in a region where occurrence data is scarce.</p> <p><em>Location: </em>Seamounts around the Cabo Verde Archipelago (NW Africa).</p> <p><em>Methods:</em> We used species presence-absence data obtained from Remotely Operated Vehicle (ROV) footage collected during two research expeditions. Terrain variables calculated using a multiscale approach from a 100 m resolution bathymetry grid, as well as physical oceanographical data from the VIKING20X model, at a native resolution of 1/20°, were used as environmental predictors. Two modelling techniques (Generalized Additive Model (GAM) and Random Forest (RF)) were employed and single-model predictions were combined into a final weighted-average ensemble model. Model performance was validated using different metrics through cross-validation.</p> <p><em>Results</em>: Terrain orientation, at broad-scale, presented one of the highest relative variable contributions to the distribution models of all CWC taxa, suggesting that hydrodynamic-topographic interactions on the seamounts could benefit CWCs by maximizing food supply. However, changes at finer scales in terrain morphology and bottom salinity were important for driving differences in the distribution of specific CWCs. The ensemble model predicted the presence of VME taxa on all seamounts and consistently achieved the highest performance metrics, outperforming individual models. Nonetheless, model extrapolation and uncertainty, measured as the coefficient of variation, were high, particularly, in least surveyed areas across seamounts, highlighting the need to collect more data in future surveys.</p> <p><em>Main conclusions:</em> Our study shows how data-poor areas may be assessed for the likelihood of VMEs and provides important information to guide future research in Cabo Verde, which is fundamental to advise ongoing conservation planning.</p>
Code from: Enhancing data-limited assessments with random effects: A case study on Korea chub mackerel (Scomber japonicus)
<div> <div> <div> <p>In a state-space framework, temporal variations in fishery-dependent processes can be modeled as random effects. This modeling flexibility makes state-space models (SSMs) powerful tools for data-limited assessments. Though SSMs enable the model-based inference of the unobserved processes, their flexibility can lead to overfitting and non-identifiability issues. To address these challenges, we developed a suite of state-space length-based age-structured models and applied them to the Korean chub mackerel (<em>Scomber japonicus</em>) stock. Our research demonstrated that incorporating temporal variations in fishery-dependent processes can rectify model mis-specification but may compromise robustness, which can be diagnosed through a series of model checking processes. To tackle non-identifiability, we used a non- degenerate estimator, implementing a gamma distribution as a penalty for the standard deviation parameters of observation errors. This penalty function enabled the simultaneous estimation of both process and observation error variances with minimal bias, a notably challenging task in SSMs. These results highlight the importance of model checking and the effectiveness of the penalized approach in estimating SSMs. Additionally, we discussed novel assessment outcomes for the mackerel stock.</p> </div> </div> </div>
Data from: Caught in the act: Incipient speciation at the southern limit of Viburnum in the Central Andes
<p>A fundamental objective of evolutionary biology is to understand the origin of independently evolving species. Phylogenetic studies of species radiations rarely are able to document ongoing speciation; instead, modes of speciation, entailing geographic separation and/or ecological differentiation, are posited retrospectively. The Oreinotinus clade of <em>Viburnum </em>has radiated recently from north to south through the cloud forests of Mexico and Central America to the Central Andes. Our analyses support a hypothesis of incipient speciation in Oreinotinus at the southern edge of its geographic range, from central Peru to northern Argentina. Although several species and infraspecific taxa of have been recognized in this area, multiple lines of evidence and analytical approaches (including analyses of phylogenetic relationships, genetic structure, leaf morphology, and climatic envelopes) favor the recognition of just a single species, V. seemenii. We show that what has previously been recognized as <em>V. seemenii </em>f. <em>minor </em>has recently occupied the drier Tucuman-Bolivian forest region from Samaipata in Bolivia to Salta in northern Argentina. Plants in these populations form a well-supported clade with a distinctive genetic signature and they have evolved smaller, narrower leaves. We interpret this as the beginning of a within-species divergence process that has elsewhere in the neotropics resulted repeatedly in Viburnum species with a particular set of leaf ecomorphs. Specifically, the southern populations are in the process of evolving the small, glabrous, and entire leaf ecomorph that has evolved in four other montane areas of endemism. As predicted based on our studies of leaf ecomorphs in Chiapas, Mexico, these southern populations experience generally drier conditions, with large diurnal temperature fluctuations. In a central portion of the range of <em>V. seemenii</em>, characterized by wetter climatic conditions, we also document what may be the initial differentiation of the leaf ecomorph with larger, pubescent, and toothy leaves. The emergence of these ecomorphs thus appears to be driven by adaptation to subtly different climatic conditions in separate geographic regions, as opposed to parapatric differentiation along elevational gradients as suggested by Viburnum species distributions in other parts of the neotropics.</p>
Reference data for "Limitations of alignment-free tools in total RNA-seq quantification"
<p>This repository contains reference data for "Limitations of alignment-free tools in total RNA-seq quantification"</p>
Extended data for the paper "Reliable generation of native-like decoys limits predictive ability in fragment-based protein structure prediction"
<p>Extended data for the paper:<br> Reliable generation of native-like decoys limits predictive ability in fragment-based protein structure prediction</p> <p>Authors:<br> Shaun M Kandathil, Mario Garza-Fabre, Simon C Lovell and Julia Handl</p> <p>--------------------------------</p> <p>Contents of the zip file:</p> <p> </p> <p>Directory 'ECDFplots':<br> ----------------------<br> Data corresponding to Figure 3 for all targets, for the bilevel and ILS protocols. Data are available following stages 3 and 4 of the low-resolution protocol.</p> <p>Directory 'ScoreRMSDplots_3archivers':<br> --------------------------------------<br> Data corresponding to Figures 6 and 9 for all targets. Data corresponding to decoys obtained after low-resolution stages 3 and 4 can be found in subdirectories 'Stage3' and 'Stage4', respectively.<br> </p>
Figure 2. A in Pushing the Limits: New Data on the Morphology of Geophilus impressus C. L. Koch, 1847 (Geophilomorpha: Geophilidae)
Figure 2. A – Apex of right forcipule, ventral view, B – Leg-bearing segment 9, ventral view, C – Last leg-bearing and postpedal segments of female, ventral view.
Figure 1. A in Pushing the Limits: New Data on the Morphology of Geophilus impressus C. L. Koch, 1847 (Geophilomorpha: Geophilidae)
Figure 1. A – Cephalic capsule and antennae, dorsal view, B – Maxillae I and II, ventral view, C – Forcipular segment, ventral view, D – Clypeus and labrum, ventral view.
Data for: Widespread forest-savanna coexistence but limited bistability at a landscape scale in Central Africa
<p>This directory contains the data used in the article **Zwaan et al. (2024) Widespread forest-savanna coexistence but limited bistability at a landscape scale in Central Africa** (DOI: <span><a href="https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdoi.org%2F10.1088%2F1748-9326%2Fad8cef&data=05%7C02%7Ca.zwaan%40uu.nl%7C66d868876ad44e69715608dcf9c1c197%7Cd72758a0a4464e0fa0aa4bf95a4a10e7%7C0%7C0%7C638659857776731023%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=3Bk8nBksr5ZBWJF4nfBvx3yp1tbyZiy%2FLlnfwDCZwfE%3D&reserved=0">https://doi.org/10.1088/1748-9326/ad8cef</a></span>).</p> <p>This repository provides the datasets used for the figures and statistics in our research article. We hope that this data can be useful for other researchers. Feel free to explore and analyze the data as needed. If you use this data in your own research, please cite our article.</p> <p><br>**Contact**: For any questions or further information, please contact:<br>* Aart Zwaan<br>* Email: a.zwaan@uu.nl</p>
Data release: Whole-genome sequencing of Schistosoma mansoni reveals extensive diversity with limited selection despite mass drug administration
<p>Source data used in the publication: Berger et al. (2021) - Provisional title: 'Whole-genome sequencing of <em>Schistosoma mansoni</em> reveals extensive diversity with limited selection despite mass drug administration'. These data were used to generate all figures used in the publication and all files are organised and labelled specifically to run with the custom code that uses these data can be found at: http://doi.org/10.5281/zenodo.4975908. </p> <p><br> <strong>File descriptions:</strong></p> <p><strong>SOURCE DATA.zip - All source data for all figures. </strong></p> <p><strong>Figure 1b:</strong></p> <ul> <li>supplementary_data_9.txt - Metadata</li> </ul> <p><strong>Figure 2a&b:</strong></p> <ul> <li>207_PCA.eigenvec - PCA eigenvectors</li> <li>207_PCA.eigenval - PCA eigenvalues</li> </ul> <p><strong>Figure 2c:</strong></p> <ul> <li>autosomes.mdist - PLINK distance matrix used to build the neighbour joining phylogeny</li> </ul> <p><strong>Figure 2d:</strong></p> <ul> <li>all.pi.pixy.schools.txt - Nucleotide diversity results for each school subpopulation.</li> </ul> <p><strong>Figure 2e:</strong></p> <ul> <li>autosomes.dxy.5kb.schools.txt - Autosomal D<sub>XY</sub> results between school subpopulations. </li> <li>autosomes.fst.5kb.schools.txt - Autosomal F<sub>ST</sub> results between school subpopulations.</li> </ul> <p><strong>Figure 2f:</strong></p> <ul> <li>admixture_all.txt - ADMIXTURE results for each sample and population sizes, column 1 represents number of populations (K), columns 3-8 represent admixture values for each population. </li> </ul> <p><strong>Figure 3a, Supplementary figure 10a:</strong></p> <ul> <li>sfs.csv - Site frequency spectra (allelic proportions at each frequency bin) for each school. </li> </ul> <p><strong>Figure 3b:</strong></p> <ul> <li>TD.all.txt - Tajima's D values calculated in 5 kb windows for each school subpopulation. </li> </ul> <p><strong>Figure 4a, Supplementary figures 13-18: </strong></p> <ul> <li>ALL.MAYUGE.IHS.ihs.out.100bins.norm.txt.zip - Normalised iHS scores for the Mayuge district parasite populations (Selscan output).</li> </ul> <p><strong>Figure 4b, Supplementary figures 13-18: </strong></p> <ul> <li>ALL.TORORO.IHS.ihs.out.100bins.norm.txt.zip -<strong> - </strong>Normalised iHS scores for the Tororo district parasite populations (Selscan output).</li> </ul> <p><strong>Figure 4c, Supplementary figures 13-18: </strong></p> <ul> <li>ALL.MAYUGEvsTORORO.xpehh.xpehh.out.norm.txt.zip - - Normalised XP-EHH scores between Mayuge and Tororo parasite populations.</li> </ul> <p><strong>Figure 4d, Supplementary figures 13-18:</strong></p> <ul> <li>MAYUGE_TORORO_2000.windowed.weir.txt.zip - F<sub>ST</sub> values calculated between Mayuge and Tororo populations in 2kb windows. </li> </ul> <p><strong>Figure 4e, Supplementary figures 12a&c:</strong></p> <ul> <li>MAYUGE_PI.windowed.pi.zip - Nucleotide diversity values calculated in 2 kb windows for Mayuge populations. </li> <li>TORORO_PI.windowed.pi.zip - Nucleotide diversity values calculated in 2 kb windows for Kocoge populations (Tororo district).</li> </ul> <p><strong>Figure 5a:</strong></p> <ul> <li>all.pi.treat.fix.txt.zip - Nucleotide diversity results for each treatment subpopulation</li> </ul> <p><strong>Figure 5b</strong></p> <ul> <li>autosomes.dxy.5kb.treatment.txt - <strong> </strong>- Autosomal D<sub>XY</sub> results between clearance phenotype subpopulations. </li> <li>autosomes.fst.5kb.treatment.txt<strong> </strong>- Autosomal F<sub>ST</sub> results between clearance phenotype subpopulations. </li> </ul> <p><strong>Figure 5c:</strong></p> <ul> <li>fst.windows.2kb.treatment.txt.zip - F<sub>ST</sub> values for comparisons between different treatment groups (Pre-treatment, post-treatment (good clearers), post-treatment (poor clearers))</li> </ul> <p><strong>Figure 5d: </strong></p> <ul> <li>assoc_err_binary.txt.zip - Results of binary trait association between miracidia sampled from hosts with good clearance phenotypes (where treatment appeared to be highly effective) and miracidia isolated post-treatment from hosts with poor clearance phenotypes (where miracidia are potentially derived from parasites that survived treatment.</li> </ul> <p><strong>Figure 5e:</strong></p> <ul> <li>assoc_err_linear.txt.zip - - Results of linear regression genome-wide association study with the ERR estimates for all 198 samples, using the mean of the posterior ERR estimates from Crellen et al. (2016) as a quantitative trait.</li> </ul> <p><strong>Supplementary figure 1:</strong></p> <ul> <li>median.coverage.txt - Normalised depth of read coverage (column 4) calculated in 25 kb windows (columns 2&3) across all samples for all chromosomes (column 1).</li> </ul> <p><strong>Supplementary figure 2a-f: </strong></p> <ul> <li>cohort.genotyped.txt.zip - <strong> </strong>- Variant quality site values (used to inform variant site retention or removal). </li> </ul> <p><strong>Supplementary figure 2g:</strong></p> <ul> <li>hard_filtered.imiss.txt - Per sample variant missingness (used to inform quality control).</li> </ul> <p><strong>Supplementary figure 2h:</strong></p> <ul> <li>hard_filtered_filtindv.lmiss.txt.zip - Per site missingness (used to inform quality control).</li> </ul> <p><strong>Supplementary figure 3a, 4a, 4b:</strong></p> <ul> <li>prunedData.eigenvec - PCA eigenvectors</li> <li>prunedData.eigenval - PCA eigenvalues</li> </ul> <p><strong>Supplementary figure 3b:</strong></p> <ul> <li>pruned_data.mdist.csv - Distance matrix used as the basis for the neighbour joining phylogeny.</li> </ul> <p><strong>Supplementary figure 5:</strong></p> <ul> <li>cv_scores.txt - ADMIXTURE coefficient of variation scores (column 2) for each population size (1).</li> </ul> <p><strong>Supplementary figure 6:</strong></p> <ul> <li>*_SMC_SE.csv - SMC++ results (from 25 subsampled replicates) for each school subpopulation and outgroup samples. </li> </ul> <p><strong>Supplementary Figure 7:</strong></p> <ul> <li>smcpp.csv - SMC++ results for each school subpopulation and outgroup samples. </li> </ul> <p><strong>Supplementary Figure 8a-d</strong></p> <ul> <li>pi.per_host.txt.zip - Nucleotide diversity values for each host infrapopulation. </li> </ul> <p><strong>Supplementary Figure 9:</strong></p> <ul> <li>sexing.csv - inferred sex (based on differential read coverage over pseudoautosomal and Z-specific regions of the Z chromosome). </li> </ul> <p><strong>Supplementary Figure 10b:</strong></p> <ul> <li>sfs_res.csv - residuals for the SFS analysis in 3a/10a.</li> </ul> <p><strong>Supplementary Figure 11:</strong></p> <ul> <li>MAYUGE_TAJIMA_D.Tajima.D.2kb.txt.zip - Tajima's D values calculated for the Mayuge population in 2kb windows. </li> <li>Tororo_TAJIMA_D.Tajima.D.2kb.txt.zip - Tajima's D values calculated for the Tororo population in 2kb windows. </li> </ul> <p><strong>Supplementary Figures 13-18:</strong></p> <ul> <li>genes.bed - Coordinates of gene models (<em>S. mansoni </em>v7 annotation).</li> <li>KOCOGE_SITE_PI.sites.pi.txt.zip - Per site nucleotide diversity values</li> <li>MAYUGE_TORORO_sites.weir.fst.txt.zip - Per site F<sub>ST</sub> values between Mayuge and Tororo populations. </li> <li>coverage_5kb.windows.txt.zip - Per sample depth of read coverage in 5 kb windows. Columns 4,5,6 represent the median, mean and sstev of coverage for each 5kb window (columns 2&3) along each chromosome (column 1). </li> <li>median.sample.coverage.txt - Median chromosomal depth of read coverage for each sample. </li> </ul> <p><strong>Supplementary Figure 19:</strong></p> <ul> <li>kocoge_median.ld.txt.zip - <strong> </strong>- The decay of linkage disequilibrium with genomic distance between all sites within 50 kb for the Kocoge parasite samples. Chromosomes are shown in column 1, distance in column 2, median values in column 3. </li> <li>mayuge_median.ld.txt.zip - The decay of linkage disequilibrium with genomic distance between all sites within 50 kb for the Mayuge parasite samples. Chromosomes are shown in column 1, distance in column 2, median values in column 3. </li> </ul> <p><strong>Misc files:</strong></p> <p>schools.list - List of samples and schools where they were sampled. </p> <p> </p>
Data from: Female-limited X-chromosome evolution effects on male pre- and post-copulatory success
<p>In our article, entitled "Female-limited X-chromosome evolution effects on male pre- and post-copulatory success", we carried out a female-limited X chromosome evolution experiment to study the effect of X-linked sexually antagonistic genetic variance on male reproductive traits.</p> <p>By limiting expression of the X chromosome to females for multiple generations, we removed male selective constraints, which should allow X-linked female-beneficial alleles to increase in frequency. </p> <p>As a result, expressing the experimentally evolved X chromosome in males, we found a small reduction in male fitness caused by the trade-off between male attractiveness and sperm competitiveness. These results indicate that the X chromosome in <i>D. melanogaster</i> harbors sexually antagonistic genetic variance for pre- and post- copulatory success in males.</p>
Data and Results for: Comparing Apples with Apples: Robust Detection Limits for Exoplanet High-Contrast Imaging in the Presence of non-Gaussian Noise
<p>This collection of data and results contains everything needed to reproduce the results in the paper:</p> <p>Comparing Apples with Apples: Robust Detection Limits for Exoplanet \\ High-Contrast Imaging in the Presence of non-Gaussian Noise</p> <p>The <a href="/api/files/53bfc05e-f632-443a-9c07-590b9bf860e1/apples_root_dir.zip?versionId=d41f6d1e-ef44-497c-ae2a-a5b291a8c9b9">apples_root_dir.zip</a> is further needed to run the examples of the python package Applefy.</p>
Data for Measurement report: Air pollution emission factors of inland river ships under compliance with the 10 parts per million limit for sulfur content in fuel
<p>Since July 1, 2019, China’s domestic diesel fuel has been limited to 10 ppm of sulfur. Hence, to explore the applicability of the “sniffer” method and the distribution and level of inland river ships (IRSs) emission factors (EFs) under this limitation, we installed “sniffer” monitoring equipment, from August 2020 to June 2022, at the Gezhou Dam of the Yangtze River in China and monitored emissions from 8,238 IRSs in total passing through the lock. We partnered with the maritime department to select 100 ships passing through the lock to extract fuel oilsamples for direct fuel sulfur content detection, which determined the true fuel sulfur content of the passing ships. fuel sulfur content.</p> <p>The “sniffer” monitoring equipment included SO<sub>2</sub>, CO<sub>2</sub>, NO, and NO<sub>2</sub> gas sensors, PM<sub>2.5</sub> and PM<sub>10</sub> particulate matter sensors, as well as wind speed, wind direction, temperature, humidity, and pressure sensors.</p>
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.