Find research datasets worth reusing

opencc-by-4.0Jul 2021View details →

Data files for manuscript "Exome first approach to reduce diagnostic costs and time – retrospective analysis of 111 individuals with rare neurodevelopmental disorders"

#2021-07-23 #Summary This ZIP-file contains the Excel files used for the clinical and variant analyses for the manuscript "Exome first approach to reduce diagnostic costs and time – retrospective analysis of 111 individuals with rare neurodevelopmental disorders". #Folder structure ./                        (parent directory containing this README file and all subfolders) ./Clinical/                (contains an Excel sheets with complete clinical data, costs and criteria) ./Variants/                (contains an Excel sheet with all variant annotation) #Files and checksums 6DB0EF10BE7A7AF5A18E523F33FB662A  ./Clinical/FileS2_Clinical.xlsx 0B0C1AFA0751B63A35DC99DB25546A38  ./Variants/FileS3_Variants.xlsx

Data deposition of the article 'Multi-Omics analysis identifies a lncRNA-related prognostic signature to predict bladder cancer recurrence'

Data deposition of the article 'Multi-Omics analysis identifies a lncRNA-related prognostic signature to predict bladder cancer recurrence'

opencc-zeroAug 2021View details →

Data from: Plant-type dominates fine-root C:N:P stoichiometry across China: a meta-analysis

Aim: Fine roots play an important role in biogeochemical cycling in terrestrial ecosystems. However, our understanding of large scale biogeographic patterns and drivers of fine-root C:N:P stoichiometry is extremely limited. Location: China. Methods: We compiled data for fine-root carbon (C), nitrogen (N) and phosphorus (P) concentrations at 165 sites across China to explore large-scale biogeographic patterns and drivers of fine-root C:N:P stoichiometry. Results: The geometric means of fine-root C, N, and P concentrations were 448.81 mg g-1, 10.73 mg g-1, and 0.9 mg g-1, respectively, whereas C:N, C:P and N:P ratios were 41.84, 508.32 and 11.73, respectively. The fine-root elemental concentrations and their ratios varied widely among plant groups and biomes, and showed clear latitudinal and longitudinal trends, as a consequence of differences in climate, soil and plant-type. However, plant-type was the largest contributor to the total variance in fine-root C, N, and P and their ratios compared to climate factors or soil features. Main conclusions: The data reveal the existence of broad biogeographic patterns of fine-root C:N:P stoichiometry in China. These results advance our knowledge about the biogeochemical cycling of fine roots.

Natural history of Lafora Disease: A Prognostic Systematic Review and Individual Participant Data Meta-Analysis (Dataset)

Raw data used for statistical analysis of our paper "Natural history of Lafora Disease: A Prognostic Systematic Review and Individual Participant Data Meta-Analysis".

Training data for MaxQuant and Msstats TMT analysis in Galaxy

The files serve as input and intermediate results for a MaxQuant and MsstatsTMT training on  lysine methyl transferase 9 knockdown and control cell proteomics (https://doi.org/10.1186/s12935-020-1141-2) in the Galaxy training network (https://training.galaxyproject.org). Input files: human FASTA protein database for Maxquant. MaxQuant experimental design template, MSstatsTMT annotation file Intermediate result files: MaxQuant protein groups and evidence

opencc-zeroAug 2021View details →

Terrestrial green algae show higher tolerance to dehydration than do their aquatic sister-species: Raw data and analysis files

Diverse algae possess the ability to recover from extreme desiccation without forming specialized resting structures. Green algal genera such as Tetradesmus (Sphaeropleales, Chlorophyceae) contain temperate terrestrial, desert, and aquatic species, providing an opportunity to compare physiological traits associated with the transition to land in closely related taxa. We subjected six species from distinct habitats to three dehydration treatments varying in relative humidity (RH 5%, 65%, 80%) followed by short- and long-term rehydration. We tested the capacity of the algae to recover from dehydration using the effective quantum yield of photosystem II as a proxy for physiological activity. The degree of recovery was dependent both on the habitat of origin and the dehydration scenario, with terrestrial, but not aquatic species, recovering from dehydration. Distinct strains of each species responded similarly to dehydration and rehydration, with the exception of one aquatic strain that recovered from the mildest dehydration treatment. Cell ultrastructure was uniformly maintained in both aquatic and desert species during dehydration and rehydration, but staining with an amphiphilic styryl dye indicated damage to the plasma membrane from osmotically-induced water loss in the aquatic species. These analyses demonstrate that terrestrial Tetradesmus possess a vegetative desiccation tolerance phenotype, making these species ideal for comparative omics studies.

opengpl-2.0Aug 2021View details →

Complementary dataset of the paper "The viewing angle in AGN SED models, a data-driven analysis"

In this repository, you can find the SED data from the X-CIGALE estimates from the article: "<a href="https://academic.oup.com/mnras/article/510/1/687/6448487">The viewing angle in AGN SED models: a data-driven analysis</a>"

opencc-zeroAug 2021View details →

Data from: Computer-aided X-ray screening for tuberculosis and HIV testing among adults with cough in Malawi (the PROSPECT study): a randomized trial and cost-effectiveness analysis

Suboptimal tuberculosis (TB) diagnostics and HIV contribute to the high global burden of TB. We investigated costs and yield from systematic HIV-TB screening, including computer-aided digital chest X-ray (DCXR-CAD). Suboptimal tuberculosis (TB) diagnostics and HIV contribute to the high global burden of TB. We investigated costs and yield from systematic HIV-TB screening, including computer-aided digital chest X-ray (DCXR-CAD). In this open, three-arm randomised trial, adults (≥18 years) with cough attending acute primary services in Malawi were randomised (1:1:1) to standard-of-care (SOC); oral HIV testing (HIV screening) and linkage to care; or HIV testing and linkage to care plus DCXR-CAD with sputum Xpert for high CAD4TBv5 scores (HIV-TB screening). Participants and study staff were not blinded to intervention allocation, but investigator blinding was maintained until final analysis. The primary outcome was time to TB treatment. Secondary outcomes included proportion with same-day TB treatment; prevalence of undiagnosed/untreated bacteriologically-confirmed TB on day 56; and undiagnosed/untreated HIV. Analysis was done on an intention to treat basis. Cost-effectiveness analysis used a health-provider perspective. Between 15/11/2018-27/11/2019, 8236 were screened for eligibility, with 473, 492, and 497 randomly allocated to SOC, HIV, and HIV-TB screening arms; 53 (11%), 52 (9%), and 47 (9%) were lost to follow-up, respectively. At 56 days, TB treatment had been started in 5 (1.1%) SOC, 8 (1.6%) HIV-screening, and 15 (3.0%) HIV-TB screening participants. Median (IQR) time to TB treatment was 11 (6.5-38), 6 (1-22) and 1 (0-3) days (hazard ratio for HIV-TB vs. SOC: 2.86, 1.04-7.87), with same-day treatment of 0/5 (0%) SOC, 1/8 (12.5%) HIV, and 6/15 (40.0%) HIV-TB screening arm TB patients (p=0.03). At day 56, 2 SOC (0.5%), 4 HIV (1.0%), and 2 HIV-TB (0.5%) participants had undiagnosed microbiologically-confirmed TB. HIV screening reduced the proportion with undiagnosed or untreated HIV from 10 (2.7%) in the SOC arm to 2 (0.5%) in the HIV-screening arm (risk ratio [RR]: 0.18, 0.04-0.83), and 1 (0.2%) in the HIV-TB screening arm (RR: 0.09, 0.01-0.71). Incremental costs were US$3.58 and US$19.92 per participant screened for HIV and HIV-TB; the probability of cost-effectiveness at a US$1200/quality-adjusted life-year (QALY) threshold were 83.9% and 0%. Main limitations were the lower than anticipated prevalence of tuberculosis and short participant follow-up period; cost and quality of life benefits of this screening approach may accrue over a longer time horizon. DCXR-CAD with universal HIV screening significantly increased the timeliness and completeness of HIV and TB diagnosis. If implemented at scale this has potential to rapidly and efficiently improve TB and HIV diagnosis and treatment.

Data for "Advanced Structural Health Monitoring Method by Integrated Isogeometric Analysis and Distributed Fiber Optic Sensing"

This dataset includes the experiment and simulation data of a new structural health monitoring system using distributed fiber optic sensing (DFOS) and Isogeometric Analysis (IGA). The experiment setup was a 5mm thick PVC pipe with a fiber optic cable wrapped around the outer surface of the pipe. The PVC pipe was subjected to an applied deformation and the distributed strains along the optical fiber was measured with a Neubrescope (NBX7031) instrument using Rayleigh backscattering technology. The simulation was performed using the in-house code JWRIAN-IGA developed in Joining and Welding Research Institute, Osaka University. The simulated data includes deformation, stress and strain distributions of the pipe, and projected one-dimensional fiber strains. The visualization files are post-processed with ParaView software.

Input Data for "Assembly and Analysis of Cell-Scale Membrane Envelopes"

Input structures for a manuscript, along with selected output data and structures. This directory structure contains a cut-down copy of the directories used to generate the simulation data and the analysis. In order to make this fit into the 50GB Zenodo limit, it was constructed with the following tar command: `tar -zcvf protocellmodeling.tar.gz --exclude="*BAK" --exclude="*#" --exclude="*xtc" --exclude="*gro" --exclude="*trr" --exclude="*js" --exclude="*[0-9].out" --exclude="*old" --exclude="*dcd" --exclude="*tmp" --exclude="*xst" --exclude="*edr" --exclude="*state_prev.cpt" --exclude="*.o[0-9]*" cgDracula`, which intentionally excludes large files. The full 4.8TB dataset that includes trajectories is available upon request. The data is split into multiple subdirectories and largely undocumented, however here are the highlights: <ul> <li>The Analysis subdirectory is where the analysis in the paper lives. All other directories are related to building or running systems.</li> <li>getsources.py in the main directory is the script that downloads the initial structure from MemProtMD.</li> <li>transform.py builds the initial protein models from MemProtMD.</li> <li>vesiclebuilder.py builds the lipid ball.</li> <li>protpatchplacer.py sets up the ultra-coarse grained simulation, which is in the supercg directory.</li> <li>movepatches.py takes the results from the ultra-coarse grained simulation, and builds the protein ball.</li> <li>gendx.tcl generates the density maps from the protein ball.</li> <li>This is used in lipids/picklipids.py, which cuts out the pieces of the lipid that need to be removed.</li> <li>The water is added to the system with addwater/quicksolvate.sh</li> <li>The system is ionized by ionize.py</li> <li>And a topology is written by writetop.py</li> </ul>

LA-ICP-MS line scan data and time-series analysis outputs for Baltic Sea sediment core F80

The datafile contains two sheets: HTM and MCA, corresponding to geochemical data from the Holocene Thermal Maximum and Medieval Climate Anomaly intervals, respectively, of a sediment core from the Baltic Sea (site F80, 58°00.00N, 19°53.81E, water depth 191m, Fårö Deep, collected during the HYPER/COMBINE cruise of R/V Aranda, May/June 2009). In each sheet, columns A-J contain Laser Ablation (LA)-ICP-MS line scan data of element ratios in resin-embedded sediment (Mo/Al, Fe/Al and Br/P) presented in the time domain (Age in years BP). Dating of the sediment core is described in the accompanying manuscript and references therein. These profiles are presented in three forms: Raw= raw data resampled to 1 year resolution; Det= detrended and normalized to unit variance; Gau; Gaussian bandpass filter at a period of 20-100 years. Columns L-S contain time-series analysis results of the detrended, normalized elemental ratios in period domain, including power spectra of each ratio (Blackman-Tukey window, columns M-O) and cross-spectral analysis (Blackman-Tukey window, bandwidth 5 years) of Mo/Al vs Br/P (columns P-Q) and Mo/Al vs Fe/Al (columns R-S), respectively. All analyses were performed in Analyseries 1.1.1 (Paillard et al., 1996). Figures containing the data have been submitted as part of a manuscript to Geophysical Research Letters (Jilbert et al., forthcoming),   Paillard, D., Labeyrie, L., & Yiou, P. (1996). Macintosh program performs time‐series analysis. Eos, Transactions American Geophysical Union, 77(39), 379-379. <a href="https://doi.org/10.1029/96EO00259">https://doi.org/10.1029/96EO00259</a> Jilbert, T., Gustafsson, B.G., Veldhuijzen, S., Reed, D.C., van Helmond, N.A.G.M., Hermans, M., & Slomp, C.P (forthcoming). Iron-phosphorus feedbacks drive multidecadal oscillations in Baltic Sea hypoxia. Submitted to Geophysical Research Letters

FIGURE 1 in Are Monobia and Montezumia Monophyletic? A Cladistic Analysis of Their Species Groups Based on Morphological Data (Hymenoptera, Vespidae, Eumeninae)

FIGURE 1. Strict consensus cladogram of 35 most parsimonious trees

FIGURE 4 in Are Monobia and Montezumia Monophyletic? A Cladistic Analysis of Their Species Groups Based on Morphological Data (Hymenoptera, Vespidae, Eumeninae)

FIGURE 4. Single cladogram obtained with implied weighting of the characters (k =

FIGURE 3 in Are Monobia and Montezumia Monophyletic? A Cladistic Analysis of Their Species Groups Based on Morphological Data (Hymenoptera, Vespidae, Eumeninae)

FIGURE 3. Single cladogram obtained with implied weighting of the characters (k =

FIGURE 2 in Are Monobia and Montezumia Monophyletic? A Cladistic Analysis of Their Species Groups Based on Morphological Data (Hymenoptera, Vespidae, Eumeninae)

FIGURE 2. Strict consensus cladogram of nine most parsimonious trees using

opencc-zeroSep 2021View details →

Data and codes to replicate the analysis in: The spatial ecology of conflicts: Unravelling patterns of wildlife damage at multiple scales

Human encroachment into natural habitats is typically followed by conflicts derived from wildlife damages to agriculture and livestock. Spatial risk modelling is a useful tool to gain understanding of wildlife damage and mitigate conflicts. Although resource selection is a hierarchical process operating at multiple scales, risk models usually fail to address more than one scale, which can result in the misidentification of the underlying processes. Here, we addressed the multi-scale nature of wildlife damage occurrence by considering ecological and management correlates interacting from household to landscape scales. We studied brown bear (Ursus arctos) damage to apiaries in the North-eastern Carpathians as our model system. Using generalized additive models, we found that brown bear tendency to avoid humans and the habitat preferences of bears and beekeepers determine the risk of bear damage at multiple scales. Damage risk at fine scales increased when the broad landscape context also favoured damages. Furthermore, integrated-scale risk maps resulted in more accurate predictions than single-scale models. Our results suggest that principles of resource selection by animals can be used to understand the occurrence of damages and help mitigate conflicts in a proactive and preventive manner.

openother-openSep 2021View details →

Meta Analysis of Conservation Games Data

This is the first release of Meta Analysis of Conservation Games Dataset. This was created for the analysis in the paper "Payments don't reconcile agriculture and conservation" by Andrew Reid Bell, O. Sarobidy Rakotonarivo, Apurva Bhargava, A. Bradley Duthie, Wei Zhang, Becca Sargent, Spike Lewis, and Adams Kipchumba.

opencc-by-4.0Sep 2021View details →

Raw data for: Stable Isotope Trajectory Analysis (SITA): A new approach to quantify and visualize dynamics in stable isotope studies. Sturbois et al., in revision in Ecological Monographs

These data sets are used as ecological applications in Sturbois et al., in revision, Stable Isotope Trajectory Analysis (SITA): A new approach to quantify and visualize dynamics in stable isotope studies. submitted in Ecological Monographs. - DataS1_furseals.Rdata originates from:  Kernaléguen, L., Cazelles, B., Arnould, J.P.Y., Richard, P., Guinet, C., Cherel, Y., 2012. Long-Term Species, Sexual and Individual Variations in Foraging Strategies of Fur Seals Revealed by Stable Isotopes in Whiskers. PLoS ONE 7, e32916. https://doi.org/10.1371/journal.pone.0032916 - DataS2_Pike.Rdata  originates from: Cucherousset, J., Paillisson, J.-M., Roussel, J.-M., 2013. Natal departure timing from spatially varying environments is dependent of individual ontogenetic status. Naturwissenschaften 100, 761–768. https://doi.org/10.1007/s00114-013-1073-y - DataS4_GT1.Rdata and DataS5_GT2.Rdata originate from: Quillien, N., Nordström, M.C., Schaal, G., Bonsdorff, E., Grall, J., 2016. Opportunistic basal resource simplifies food web structure and functioning of a highly dynamic marine environment. Journal of Experimental Marine Biology and Ecology 477, 92–102. - DataS6_Lakes.Rdata originates from: Zhao, T., Villéger, S., Cucherousset, J., 2019. Accounting for intraspecific diversity when examining relationships between non-native species and functional diversity. Oecologia 189, 171–183. https://doi.org/10.1007/s00442-018-4311-3 Information about respective sampling strategies and sample preparation are available in these original articles. All use of this data sets must cite original article as well as the SITA article.

opencc-zeroDec 2020View details →

Data from: Genome-wide analysis reveals associations between climate and regional patterns of adaptive divergence and dispersal in American pikas

Understanding the role of adaptation in species responses to climate change is important for evaluating the evolutionary potential of populations and informing conservation efforts. Population genomics provides a useful approach for identifying putative signatures of selection and the underlying environmental factors or biological processes that may be involved. Here, we employed a population genomic approach within a space-for-time study design to investigate the genetic basis of local adaptation and reconstruct patterns of movement across rapidly changing environments in a thermally-sensitive mammal, the American pika (Ochotona princeps). Using genotypic data at 49,074 single nucleotide polymorphisms (SNPs), we analyzed patterns of genome-wide diversity, structure, and migration along three independent elevational transects located at the northern extent (Tweedsmuir South Provincial Park, British Columbia, Canada) and core (North Cascades National Park, Washington, USA) of the Cascades lineage. We identified 899 robust outlier SNPs within- and among-transects. Of those annotated to genes with known function, many were linked with cellular processes related to climate stress including ATP-binding, ATP citrate synthase activity, ATPase activity, hormone activity, metal ion-binding, and protein-binding. Moreover, we detected evidence for contrasting patterns of directional migration along transects across geographic regions that suggest an increased propensity for American pikas to disperse among lower elevation populations at higher latitudes where environments are generally cooler. Ultimately, our data indicate that fine-scale demographic patterns and adaptive processes may vary among populations of American pikas, providing an important context for evaluating biotic responses to climate change in this species and other alpine-adapted mammals.