Find research datasets worth reusing

opencc-by-4.0Jun 2017View details →

Data: Muon Tomography sites for Colombia volcanoes for generate muon flux trought volcanic structures (arXiv:1705.09884v1)

Data: Muon Tomography sites for Colombia volcanoes (arXiv:1705.09884v1) The MuTe Collaboration Data for generating figure 6 Muon Tomography sites for Colombia volcanoes (arXiv:1705.09884v1) The files in this record contain data from Extensive Atmospheric Shower simulations made by CORSIKA and Magnetocosmic codes, in a muography of Machin Volcano (Colombia) [https://volcano.si.edu/volcano.cfm?vn=351040] for a particular observation point. The objective was to count muons crossing the volcanic structure for a fixed observation point. Muon transport through the volcanic edifice is calculated by using an algorithm taken Corsika-Magnetocosmic output and taking into account the energy losses with the muon stopping power  tables given by Particle Data Group (PDG). This dataset contains: <ul> <li>Six (6) Corsika output files of 4 hours of simulation each using a flat detector (equivalent to 12 hours of simulated cosmic rays).</li> <li>One (1) Corsika output file of 12 hours of simulation using flat detector (equivalent to 6 hours of simulated cosmic rays).</li> <li>One (1) Corsika output file of 48 hours of simulation using flat detector (equivalent to 24 hours of simulated cosmic rays).</li> <li>Two (2) Corsika output files of 24 hours of simulation each using volumetric detector (equivalent to 48 hours of simulated cosmic rays).</li> <li>Everything makes a total simulated time of 3.75 days.</li> </ul> The output files necessary for the determination of the muon flux through the volcanic structure are obtained through the following process: <ul> <li>From the .shw.bz2 files it is possible to obtain an output file with the momentum information of the particle in the x, y, and z directions, and also the total momentum of the muons, essentially a formatted file (px, py, pz, p). This file can be built by typing in a terminal shell (bash code):</li> </ul> > bzcat *.shw.bz2 | awk '{if($1==0006 ||$1==0005){j=sqrt(($2*$2)+($3*$3)+($4*$4));printf "%s %s %s %.s\n",$2, $3, $4, j }}' | sort -n > salida.out <ul> <li>Metadata in the showers file is as this type (for example):</li> </ul> # # # shw # # CURVED mode is ENABLED and observation level is 2750 m a.s.l. # # This is the Secondaries file - CrkTools v3r0 # # 12 column format is: # # CorsikaId px py pz x y z shower_id prm_id prm_energy prm_theta prm_phi 0001 +1.42146e-04 -3.96008e-05 +1.60247e-04 -1.31716e+03 -6.10051e+01 +2.44986e+03 00000001 0703 +1.25065e+02 +43.016 +021.768 0003 +1.80713e-04 +1.89560e-03 +4.49373e-03 -1.32279e+03 -5.62869e+01 +2.44986e+03 00000001 0703 +1.25065e+02 +43.016 +021.768 0003 +9.41713e-03 +2.38845e-03 +1.10020e-02 -1.32098e+03 -5.68323e+01 +2.44986e+03 00000001 0703 +1.25065e+02 +43.016 +021.768 <ul> <li>Concatenate all output files.</li> <li>Then, the muon flux trought rock can be calculated from two python codes, available in https://github.com/AstroparticulasBucaramanga/Propagacion-Muones-en-Roca. This step generates the final files to be graphed with any plotter, in our case, also using python.</li> </ul>

opencc-by-sa-4.0Jul 2017View details →

Protein Structure Initiative - TargetTrack 2000-2017 - all data files

Protein Structure Initiative - TargetTrack protein target registration database (795 MB, gzipped tarball) The Protein Structure Initiative was a high-throughput structural genomics effort from 2000-2015 focused on developing technologies to enable greater coverage of protein structure space. Over its 15-year tenure, over 100 investigators at 35 centers (see ContributingCenters.xls) declared over 350,000 protein sequences (targets) that they would study using state-of-the-art protein production and structure determination methods. Many of these targets were selected through bioinformatics-based methods to serve as representatives for sequence and structure clusters. From 2003-2010, these selected sequences and some basic identifying metadata were kept in a database called TargetDB, created at the Research Collaboratory for Structural Bioinformatics at Rutgers University. In 2008, a second database named PepcDB was created to track detailed experimental trial history and the standard protocols used by the PSI centers. These two databases became the principal structural genomics target databases, and were rolled into the PSI Structural Biology Knowledgebase in 2008. As part of the third phase of the PSI, TargetDB and PepcDB were merged into a single resource, TargetTrack, to facilitate one-stop access to the data as well as expanding the schema to include new required data items. Participating centers deposited the latest status on their active targets and the protocols that were used (along with any deviations) on a weekly or quarterly basis. TargetTrack provided a variety of pre-computed data downloads on a weekly basis as well. In July 2017, the Structural Biology Knowledgebase ceased operations. The files provided in this tarball represent the final datafiles generated by TargetTrack (timestamp June 30, 2017). Please read the README included in this dataset for descriptions of each file. The entire TargetTrack datafile in XML format can be found in /TargetTrack XML files/tt.xml.gz Key documentation can be found in the /Documentation folder. TargetTrack schema: targetTrack-v1.4.1.pdf Spreadsheet with TargetTrack enumerations for relevant fields: targetTrackEnumeratedDataItems-v1.4.1-1.xls Image depicted the XML data schema: targetTrack-v1.4.1.jpg These files are 868 MB in total size, uncompressed. To open the tarball, use the command 'tar -zxvf TargetTrack-1Jul2017.tar.gz' -- created by the PSI Structural Biology Knowledgebase, July 5, 2017

opencc-by-4.0Jan 2021View details →

Structures of FDA-approved drugs and their active metabolites and data sets of experimental PD and PK properties

Data sets are extracted from the 2024 release of the e-Drug3D Database (2118 FDA-approved drug structures) <ol> <li>e-Drug3D_2118.zip (contains e-Drug3D_2118.sdf) - Chemical Structures - The e-Drug3D collection in SDF format file -  one 3D conformer; ionization of carboxylic acid, phosphate, phosphonate, phosphonoamide, amidinium and guanidinium groups. The datablock contains the ID, name (INN), CAS number and Status.</li> <li>e-Drug3D_2118_PK.csv - Pharmacokinetics - Column/field value is separated by a semicolon. It contains the e-Drug3D ID, INN (drug name), CAS number, year of approval, Status, is_or_has a metabolite, routes of administration, Volume of distribution (VD), Clearance (Cl), Plasma Protein Binding (PPB), Half-life (t1/2), Bioavailability (F), Cmax/Tmax, comment on solubility.</li> <li>e-Drug3D_2118_PD.csv - Pharmacodynamics - Column/field value is separated by a semicolon. It contains the e-Drug3D ID, INN (drug name), CAS number, year of approval, Status, Primary target, ATC code(s), PDB codes and main list of drug targets.</li> <li>e-Drug3D_2118_RD.csv - FDA Registration Data - Column/field value is separated by a semicolon. It contains the ID, name (INN), CAS number, First year of approval, Status, <a href="http://www.knapsackfamily.com/knapsack_core/top.php">KNApSAcK</a> or <a href="https://www.npatlas.org">NPAtlas</a> Id if natural product, all associated NDA numbers [FDA approval number, name of the label file in PDF format, company name, year of approval and commercial name of the drug] and the Indication/Therapeutic class information.</li> <li>labels.tar.gz - The drug label files in PDF format (compressed directory). A label file is named with the NDA number. The NDA number is the approval number assigned by the FDA. A drug may possess several NDA numbers (see the above e-Drug3D-RD data set).</li> </ol>

opencc-by-4.0Oct 2023View details →

Agent-based model predicts that layered structure and 3D movement work synergistically to reduce bacterial load in 3D in vitro models of tuberculosis granuloma - Location Data

This dataset is meant to be used with "Agent-based model predicts that layered structure and 3D movement work synergistically to reduce bacterial load in 3D in vitro models of tuberculosis granuloma - Results and Data". It provides spatial output data for 4 different setups (spheroid, traditional, 3d gravity, and traditional floating) of an agent-based model of in vitro tuberculosis infection models.

opencc-by-4.0Oct 2023View details →

POMFinder: Identifying polyoxometalate cluster structures from pair distribution function data using explainable machine learning

Databases that were used to train the POMFinder ML model.

opencc-zeroOct 2023View details →

Data from: Both the selection and complementarity effects underpin the effect of structural diversity on aboveground biomass in tropical forests

Aim: Despite mounting empirical evidence regarding the positive effects of forest structural diversity (STRDIV) on forest functioning, the underlying biotic mechanisms and controlling abiotic factors remain poorly understood. This study provides the first assessment of the interactive effects of STRDIV and diversity in species and functional traits on aboveground biomass (AGB) in natural forests in West and East Africa. Location: West and East Africa Time period: 2014-2020 Major taxa studied: Woody plants Methods: Using data from 276 plots and 7993 trees of 207 species distributed across various types of natural forests and major climatic zones of Africa, linear mixed-effects and structural equation models, we have evaluated how alternative causal relationships between STRDIV and taxonomic and functional diversity attributes influence AGB, while accounting for the effects of environmental covariates. We also assessed the consistency of these relationships across floristically and environmentally homogenous forest types. Results: We found that the positive effects of STRDIV on AGB were underpinned by both the community-weighted mean (CWM) of trait values (selection effects) and species richness (niche complementarity), but the relative importance of these effects varied depending on forest types. Across the forest types, STRDIV primarily mediated the effects of CWM of traits and species richness on AGB. We also found that STRDIV–AGB relationships were constrained by resource (water and nutrient) availability. Main conclusions: Our findings provide novel insights into the role of functional traits as key determinants of the effects of STRDIV on AGB in tropical forests. We suggest that forest management and climate change mitigation strategies aimed at conserving biodiversity and fostering biomass storage through increased STRDIV should focus on maintaining high levels of functionally dominant species while also increasing tree species diversity.

opencc-zeroOct 2023View details →

Data from: Pan-genome analysis highlights the role of structural variation in the evolution and environmental adaptation of Asian honeybees

The Asian honeybee, Apis cerana, is an ecologically and economically important pollinator. Mapping its genetic variation is key to understanding population-level health, histories, and potential capacities to respond to environmental changes. However, most efforts to date were focused on single nucleotide polymorphisms (SNPs) based on a single reference genome, thereby ignoring larger-scale genomic variation. We employed long-read sequencing technologies to generate a chromosome-scale reference genome for the ancestral group of A. cerana. Integrating this with 525 resequencing datasets, we constructed the first pan-genome of A. cerana, encompassing almost the entire gene content. We found that 31.32% of genes in the pan-genome were variably present across populations, providing a broad gene pool for environmental adaptation. We identified and characterized structural variations (SVs) and found that they were not closely linked with SNP distributions, however, the formation of SVs was closely associated with transposable elements. Furthermore, phylogenetic analysis using SVs revealed a novel A. cerana ecological group not recoverable from the SNP data. Performing environmental association analysis identified a total of 44 SVs likely to be associated with environmental adaptation. Verification and analysis of one of these, a 330 bp deletion in the Atpalpha gene, indicated that this SV may promote the cold adaptation of A. cerana by altering gene expression. Taken together, our study demonstrates the feasibility and utility of applying pan-genome approaches to map and explore genetic feature variations of honeybee populations, and in particular to examine the role of SVs in the evolution and environmental adaptation of A. cerana.

opencc-zeroOct 2023View details →

Data from: Social networks reveal sex- and age-patterned social structure in Butler's Gartersnakes

Sex- and age-based social structures have been well-documented in animals with visible aggregations. However, very little is known about the social structures of snakes. This is most likely because snakes are often considered non-social animals and are particularly difficult to observe in the wild. Here, we show that wild Butler's Gartersnakes have an age and sex assorted social structure similar to more commonly studied social animals. To demonstrate this, we use data from a 12-year capture-mark-recapture study to identify social interactions using social network analyses. We find that the social structures of Butler's Gartersnakes comprise sex- and age-assorted intra-species communities with older females often central and age segregation partially due to patterns of study site use. In addition, we find that females tended to increase in sociability as they aged while the opposite occurred in males. We also present evidence that social interaction may provide fitness benefits, where snakes that were part of a social network were more likely to have improved body condition. We demonstrate that conventional capture data can reveal valuable information on social structures in cryptic species. This is particularly valuable as research has consistently demonstrated that understanding social structure is important for conservation efforts. Additionally, research on the social patterns of animals without obvious social groups provides valuable insight into the evolution of group living.

Data from: Investigating the spatial, demographic, and genetic structures of Cylicodiscus gabunensis Harms, a light-demanding African timber species

Most Central African rainforest canopies consist of light-demanding tree species that hold high commercial value but also suffer locally from regeneration deficits, raising concerns about the sustainability of logging. Regeneration is influenced by factors such as past perturbations (including human activity), mating systems, and seed/pollen dispersal processes that impact demographic, spatial, and genetic structures within populations. To gain a better understanding of these interactions, we studied the spatial distribution and trunk diameter structure of Cylicodiscus gabunensis (Fabaceae) - a wind-dispersed, insect-pollinated, timber species - in three plots ranging from 400 to 839 ha situated in various environmental contexts (e.g. forest types and elephant densities) across Central Africa. We also genotyped adults and juveniles using microsatellite markers to analyze the spatial genetic structure of each population and infer the selfing rate, seed and pollen dispersal capacities and selection gradients using the 'neighborhood model'. The selfing rate was low (3 – 4 %), and seed dispersal distances (ds = 184 m) were much shorter than pollen dispersal distances (dp > 2 km). The three populations displayed contrasted spatial, demographic and genetic structures. One population showed no spatial aggregation or genetic structure, and a multimodal diameter structure indicating pulses of regeneration events. Two populations showed strong spatial aggregation and genetic structures. One exhibited a unimodal diameter structure indicating one ancient pulse of regeneration, while the other displayed a 'reverse J-shaped' diameter structure, typical of ongoing regeneration. In the latter, reproductive success appeared leptokurtic, three mother trees accounting for over 90 % of the regeneration and no tree below the minimum cutting diameter implemented by logging companies had offspring. The idiosyncratic nature of population characteristics observed in C. gabunensis suggests that, for sustainable management, a nuanced approach is needed. This involves protecting productive seed trees in areas where natural regeneration is occurring and actively supporting regeneration in areas exhibiting deficits, especially in contexts with low elephant densities.

opencc-by-4.0Oct 2023View details →

Data associated with "Robust Structured Illumination Microscopy with Bayesian Noise Control"

Experimental and synthetic data saved in tiff and/or zarr formats and SIM reconstruction scripts written in Python (Wiener and FISTA-SIM0. These also include estimated SIM patterns which are needed for B-SIM<ul><li>Synthetic data consisting of variably spaced line pairs. Found in <a href="https://zenodo.org/uploads/10037823">2023_10_02_synthetic_line_pairs.zip</a></li><li>Experimental data. Fluorescence images of one of the variably spaced line pair patterns on an ArgoSIM calibration slide. Found in <a href="https://zenodo.org/uploads/10037823">2023_08_02_folder=002_argosim_slide.zip</a></li><li>Experimental data. MitoTracker Red labelled mitochondria in live HeLa cells. Found in <a href="2023_08_07_folder=011_mitos_live_hela.zip">2023_08_07_folder=011_mitos_live_hela.zip</a></li><li>Camera calibration maps, including gain, variance, and offset. Found in <a href="camera_calibration.zip">camera_calibration.zip</a></li></ul>

Data from: Relict stands of Central European oaks: unravelling autochthony and genetic structure based on a multi-population study

Central European white oaks expanded rapidly after the last glacial period and reached their current distribution range during the early Holocene. They have been an important resource of timber, fuelwood and animal feed for humans, who actively promoted their presence in forests and other landscape types at least since the early historical times. Besides stands with intensive management, putatively relict populations of three native oak species can be found on unproductive sites with restricted accessibility. Here, we apply chloroplast and nuclear microsatellite markers in order to address the autochthony of relict and managed stands and compare the spatial distribution of genetic variation between them. Based on data from more than 150 populations, we demonstrate that oak autochthony was preserved throughout historical times which is likely the result of traditional silvicultural treatment. This is supported by the fact that the spatial pattern of chloroplast haplotype distribution still reflects the post-glacial recolonization in both relict and old managed stands. We observed significant admixture of haplotypes only in stands established after the Second World War, which is attributable to the transfer of reproductive material used for afforestation. In terms of nuclear genetic variation, we observed marked differences among species. Quercus pubescens exhibited a pronounced genetic structure. Genetic drift and limited gene flow among its small and isolated populations in our study area might have contributed to this pattern. Varying extent of genetic introgression with other sympatric oak species could offer an additional explanation. On the contrary, the gene pools of Q. petraea and Q. robur are highly homogenous, displaying only weak isolation-by-distance. We found no significant differences of genetic diversity and differentiation between relict and managed stands. This suggests that seed transfer mostly occurred within our study area, even in those stands established in post-war times, verifying previous findings that point out limited human interference. We recommend consideration of population genetic structure for gene conservation, with a finer resolution of gene conservation units needed for Q. pubescens due to its spatial genetic structure. Both relict and old managed stands, species-pure or mixed, are suitable for conservation, as they host autochthonous gene pools. Coppice-with-standard management could contribute to preservation of autochthony. In the face of climate change, it is also important to maintain the evolutionary potential of the stands, by facilitating generative reproduction and allowing for hybridization in mixed stands.

Replication Data for "Inverse-designed low-index-contrast structures on silicon photonics platform for vector-matrix multiplication"

COMSOL files and Python post-processing code.

Data for: Horizontal viewsheds of large herbivores as a function of woodland structure

This dataset contains values of tree stem density per hectare of different size classes (Sapling: > 0.3m, < 1.3m height, Small stem: >=1.3m height, < 10cm DBH, Medium stem: 10-20cm DBH, Large: 21-30cm DBH, Very large: >=31cm DBH), Viewshed Coefficient values (vc), Leaf Area Index (LAI) values for 0.75 - 1.5m above the ground and average percentage cover of bramble (Rubus frutocisus agg.). These data have come from 71 circular 15m-radius sampling plots (four-character codes in plotID column across ten woodland sites (three-character codes in site column). The "raw_data" tab contains the untransformed, unscaled raw data. The "transformed_scaled_data" tab contains the transformed, scaled data that were used in the modelling approach in the associated manuscript.

Figs 53–56. Metaventrite structure. 53 in ON SPLITTING OF THE GENUS NOTOCUPES (COLEOPTERA: ARCHOSTEMATA): NEW DATA ON MORPHOLOGY AND TAXONOMY

Figs 53–56. Metaventrite structure. 53 – Conexicoxa crassa; 54 – Notocupes excellens;

opencc-by-4.0Sep 2023View details →

Data from: Protection promotes energetically efficient structures in marine communities

The sustainability of marine communities is critical for supporting many biophysical processes that provide ecosystem services that promote human well-being. It is expected that anthropogenic disturbances such as climate change and human activities will tend to create less energetically-efficient ecosystems that support less biomass per unit energy flow. It is debated, however, whether this expected development should translate into bottom-heavy (with small basal species being the most abundant) or top-heavy communities (where more biomass is supported at higher trophic levels with species having larger body sizes). Here, we combine ecological theory and empirical data to demonstrate that full marine protection promotes shifts towards top-heavy energetically-efficient structures in marine communities. First, we use metabolic scaling theory to show that protected communities are expected to display stronger top-heavy structures than disturbed communities. Similarly, we show theoretically that communities with high energy transfer efficiency display stronger top-heavy structures than communities with low transfer efficiency. Next, we use empirical structures observed within fully protected marine areas compared to disturbed areas that vary in stress from thermal events and adjacent human activity. Using a nonparametric causal-inference analysis, we find a strong, positive, causal effect between full marine protection and stronger top-heavy structures. Our work corroborates ecological theory on community development and provides a quantitative framework to study the potential restorative effects of different candidate strategies on protected areas.

Data from "Compact Disks in a High-resolution ALMA Survey of Dust Structures in the Taurus Molecular Cloud"

Continuum fits images for all disks in our ALMA Cycle 4 Taurus disk survey - see details in Long et al., 2018, ApJ, 869, 17 and Long et al., 2019, ApJ, 882, 49

Data presented in Crustal structure and anisotropy measured by CHINArray and implications for complicated deformation mechanisms beneath the eastern Tibetan margin

The dataset includes the raw waveforms and receiver functions presented in the paper  Crustal structure and anisotropy measured by CHINArray and implications for complicated deformation mechanisms beneath the eastern Tibetan margin, submitted to JGR Solid Earth.Contact: Zengsijia@cug.edu.cn

Data from: Fine-scale genetic structure in the orchid Gymnadenia conopsea is not associated with local density of flowering plants

Premise: Density-dependent pollinator visitation can lead to density-dependent mating patterns and within-population genetic structure. In Gymnadenia conopsea, individuals in low-density patches receive more self-pollen than individuals in high-density patches, suggesting higher relatedness at low density. Ongoing fragmentation is also expected to cause more local matings, potentially leading to biparental inbreeding depression. Methods: To evaluate whether relatedness decreases with local density, we analysed 1315 SNP loci in 113 individuals within two large populations. We quantified within-population genetic structure in one of the populations, recorded potential habitat barriers, and visualized gene flow using estimated effective migration surfaces (EEMS). We further estimated the magnitude of biparental inbreeding depression that would result from matings restricted to within 5 m. Results: There was no significant relationship between local density and relatedness in any population. We detected significant fine-scale genetic structure consistent with isolation-by-distance, with positive kinship coefficients at distances below 10 m. Kinship coefficients were low, and predicted biparental inbreeding depression resulting from matings within the closest 5 m was a modest 1–3%. EEMS suggested that rocks and bushes may act as barriers to gene flow within a population. Conclusions: The results suggest that increased self-pollen deposition in sparse patches does not necessarily cause higher selfing rates, or that inbreeding depression results in low establishment success of inbred individuals. The modest relatedness suggests that biparental inbreeding depression is unlikely to be an immediate problem following fragmentation of large populations. The results further indicate that habitat structure may contribute to governing fine-scale genetic structure in G. conopsea.

Smoother: a unified and modular framework for incorporating structural dependency in spatial omics data: intermediate results

This directory contains all intermediate results generated in the "Smoother: a unified and modular framework for incorporating structural dependency in spatial omics data" for reproducibility purpose. Associated scripts are available at https://github.com/JiayuSuPKU/Smoother_paper. Raw and processed data can be downloaded at https://zenodo.org/records/10223862.Note that some intermediate results and figures in the notebooks may not be exactly the same as those in the paper due to the randomness in some analysis steps, but should be very close.

Smoother: a unified and modular framework for incorporating structural dependency in spatial omics data: raw and processed data files

This directory contains all spatial and single-cell omics datasets analyzed in the "Smoother: a unified and modular framework for incorporating structural dependency in spatial omics data". Associated scripts are available at https://github.com/JiayuSuPKU/Smoother_paper. See https://github.com/JiayuSuPKU/Smoother_paper/blob/main/data/README.md for details on folder structure and data sources.