Find research datasets worth reusing

opencc-by-4.0Feb 2020View details →

Head-Neck-Radiomics-HN1 data processed with Pyradiomics ready to use for data analysis

We downloaded <a href="https://wiki.cancerimagingarchive.net/display/Public/Head-Neck-Radiomics-HN1">Head-Neck-Radiomics-HN1, </a>align CT and segmentation images and use PyRadiomics to extract all kind of features for data analysis. CSV contains all the features. Some of them are settings information, setting information should be remove before any data analysis. By using feature extraction algorithm or... by checking values, all the settings have the same values in the columns. Each row is a patient.

opencc-by-sa-4.0Feb 2020View details →

Processed Saccharomyces cerevisiae transcriptomics and genomics data for machine learning

Genomic data including open reading frame (ORF) boundaries of Saccharomyces cerevisiae C288 was obtained from the Saccharomyces Genome Database (<a href="https://www.yeastgenome.org/">https://www.yeastgenome.org/</a>) (<a href="http://paperpile.com/b/QmuOBv/gg2yy">Cherry, J. M. et al. Saccharomyces Genome Database: the genomics resource of budding yeast. Nucleic Acids Res. 40, D700–5 (2012)</a>) and published data (<a href="http://paperpile.com/b/QmuOBv/g4EbQ">Xu, Z. et al. Bidirectional promoters generate pervasive transcription in yeast. Nature 457, 1033–1037 (2009)</a>, <a href="http://paperpile.com/b/QmuOBv/uJqAw">Nagalakshmi, U. et al. The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 320, 1344–1349 (2008)</a>). Coding regions were extracted based on ORF boundaries and codon frequencies were normalized to probabilities. Processed raw RNA sequencing Star counts were obtained from the Digital Expression Explorer V2 database (<a href="http://dee2.io/index.html">http://dee2.io/index.html</a>) (<a href="http://paperpile.com/b/QmuOBv/LCGD">Ziemann, M., Kaspi, A. & El-Osta, A. Digital expression explorer 2: a repository of uniformly processed RNA sequencing data. GigaScience vol. 8 (2019)</a>) and filtered for experiments that passed quality control. Raw mRNA data were transformed to transcripts per million (TPM) counts and genes with zero mRNA output (TPM < 5) were removed. Prior to modeling, the mRNA counts were Box-Cox transformed.

openother-openMay 2020View details →

Orthographic and phonological processing in Hong Kong deaf readers: Data and R Scripts

This data was reported on in an article titled "Orthographic and phonological processing in Hong Kong deaf readers: An eye-tracking study."

opencc-zeroMay 2020View details →

Data from: Combinatorial signal processing in an insect

Human language is combinatorial: phonemes are grouped into syllables, syllables into words, and so on. The capacity for combinatorial processing is present to different degrees in some mammals and birds. We tested for basic combinatorial processing in an insect against two competing hypotheses: beginning rule (where the early signal portions play a stronger role in acceptability); and no rule (where the order of signal elements plays no role in signal acceptability). We worked with Enchenopa treehoppers, whose vibrational signals consist of a whine (W) followed by pulses (P). The combinatorial rule hypothesis predicts females will prefer any stimuli containing the natural-combination (WP or PWP) over reverse-order stimuli (PW). The beginning rule hypothesis predicts that females will prefer stimuli with natural beginnings (WP or W) over stimuli with modified beginnings (PW or PWP). The no rules hypothesis predicts no preferences in stimuli acceptability. In playback experiments using laser vibrometry, females preferred natural-combination signals regardless of the beginning element (WP or PWP) and discriminated against reverse-order signals (PW) or individual elements (W or P). Finding support for the combinatorial rule hypothesis in insects suggests that this capability represents a common solution to the problems presented by complex communication.

opencc-by-4.0Mar 2020View details →

fMRI data of morphological processing in Hebrew dyslexic and typical readers

see the attached documentation file

opencc-by-4.0Jun 2020View details →

Data Accompanying "Fracturing process of concrete under uniaxial and triaxial compression: insights from in-situ x-ray mechanical tests"

These are the datasets analysed in "Fracturing process of concrete under uniaxial and triaxial compression: insights from in-situ x-ray  mechanical tests" by Stamati et. al. (submitted on June 2020 in Cement and Concrete Research) The datasets contain the reconstructed x-ray 3D images of selected tests and the corresponding DVC analysis. Note that details regarding the DVC analysis can be found in the paper. <ul> <li>Each folder contains a separate test; uniaxial compression ("C-02") and triaxial compression at 5MPa ("TX5-01"), 10MPa ("TX10-01") and 15MPa ("TX15-01") confining pressures.</li> <li>For each test, folder 01 contains the first scan, where 01 is the reference state for the DVC analyis. Folder 01 also contains the image of the labelled largest aggregates used for the discrete DVC. Folrders 02-XX contain the scans at intermediate loading steps and the corresponding DVC analysis; "reg" contains the registration result in downscaled 2-binning images. "ddic" contains the discrete DVC computation. "ldic" contains the local DVC computation, before and after the merge and filtering of the grid and discrete DVC fields. "strains" contains the strain fields coming from the corrected merged DVC field.</li> <li>Folder "stressStrain" contains the stress-strain curves measured during the tests after subtracting the displacement corresponding to the loading system.</li> <li>Folder "doubleScanUniaxial" contains the two reconstructed images of the "repeated scan" of the uniaxial tests, from which the DVC measurement uncertainties were evaluated.</li> </ul>

opencc-by-4.0Jul 2020View details →

Alzheimer's Disease versus Bipolar Disorder versus Health Control MRI data and processed results

README The data is structured as follows: Clinical_data folder contains the .csv that can be read by spreadsheet software, as well as from Python, Matlab or R. There are separate files for each biomarker. The file "clinical_data_id_age_gender.csv" contains the numerical random key of the patient for anonymity, diagnostic key, age and gender for each entry in the other files. The file "clinical_data_corrected.csv" can be ignored. Diagnostic keywords: "crl" == healthy control, "tb" == bipolar disorder, "ea" == Alheimer's disease Imaging data is nifti encoded. The name of the file starts with the diagnostic key followed by the numerical random key and some nemotechnic for the contents. For instance: "crl_132_diff_dti_FA_FA_to_target.nii.gz" is the spatially normalized FA data of healthy control 132. Imaging data can be read with FSL, SPM, and any other nifti reading soft. Imaging folders contain the following data DWI_origin - > the original diffusion weighted MRI data and their corresponding b-vector values FA - > the FA coefficients computed using FSL FA_to_target - > the FA volumes registered to MNI template using FSL tools T1_preprocessed - > the T1-weighted volumes at 1mm resolution registered to the MNI template using FSL no-linear registration tools T1_VBM_SPM_1mm - > the results of applying SPM implementation of voxel based morphometry (VBM) on the T1-weighted data, including results of the correlation between biomarkers and the detected clusters . Results can be checked using SPM (https://www.fil.ion.ucl.ac.uk/spm/) TBSS_results -> contains track based spatial statistics (TBSS) results obtained with FSL software (https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/TBSS)   Publications using this dataset M. Graña, M. Termenon, A. Savio, A. Gonzalez-Pinto, J. Echeveste, J. M. Pérez, A. Besga, Computer Aided Diagnosis system for Alzheimer Disease using brain Diffusion Tensor Imaging features selected by Pearson’s correlation,  Neuroscience letters,Volume 502, Issue 3, 20 September 2011, Pages 225-229 A. Besga, M. Termenon, M. Graña, J. Echeveste, J. M. Perez, A. Gonzalez-Pinto "Discovering Alzheimer's disease and bipolar disorder white matter effects building computer aided diagnostic systems on brain diffusion tensor imaging features, Neuroscience Letters, Volume 520, Issue 1, 27 June 2012, Pages 71–76. M. Termenon, M. Graña, A. Besga, J. Echeveste, A. Gonzalez-Pinto, Lattice Independent Component Analysis feature selection on Diffusion Weighted Imaging for Alzheimer’s Disease Classification, Neurocomputing (2013) Volume 114, 19 August 2013, Pages 132–141 Ariadna Besga, Itxaso González-Ortega, Enrique Echeburúa, Alexandre Savio, Borja Ayerdi, Darya Chyzhyk, Jose LM Madrigal, Juan C. Leza, Manuel Graña, Ana González-Pinto,  "Discrimination between Alzheimer’s Disease and Late Onset Bipolar Disorder using multivariate analysis" Frontiers in Aging Neuroscience, 7:231 Ariadna Besga-Basterra, Darya Chyzhyk, Itxaso González-Ortega, Alexandre Savio, Borja Ayerdi, Jon Echeveste, Manuel Graña, Ana González-Pinto,  Eigenanatomy on fractional anisotropy imaging provides white matter anatomical features discriminating between Alzheimer’s Disease and Late Onset Bipolar Disorder, Current Alzheimer Research, 13(5): 557 - 565 (2016) Ariadna Besga, Darya Chyzhyk, Itxaso Gonzalez Ortega, Jon Echeveste, Marina Grana-Lecuona, Manuel Grana, Ana González-Pinto, White Matter Tract Integrity in Alzheimer’s Disease versus Late Onset Bipolar Disorder and its Correlation with Systemic Inflammation and Oxidative Stress Biomarkers, Frontiers in Aging Neuroscience, 9:179 (2017)

opencc-by-4.0Jul 2020View details →

Data for: Wintertime coastal upwelling in Lake Geneva: An efficient transport process for deep-water renewal in a large, deep lake

Combining field measurements, 3D numerical modeling and Lagrangian particle tracking, we investigated wind-driven, Ekman-type coastal upwelling during the weakly stratified winter period 2017/2018 in Lake Geneva, a large and deep lake in western Europe. The data include measurements from moored Acoustic Doppler Current Profilers (ADCP) and vertical temperature profiles along with the corresponding 3D modeling and particle tracking results. The three-dimensional model used in this study is based on the MIT General Circulation Model (MITgcm, http://mitgcm.org/, https://doi.org/10.1029/96JC02775). The particle tracking code is based on ctracker (https://doi.org/10.5281/zenodo.1034118).

opencc-zeroJul 2020View details →

Data from: Along with intraspecific functional trait variation, individual performance is key to resolving community assembly processes

<ol> <li>Species contributing high proportions to community biomass strongly influence ecosystem processes within the community. Studies have shown that dominant species may serve as nurse plants, helping to ensure biomass stability of the subordinate species under stress conditions. The question is widely debated as to whether either niche differentiation or neutral processes drive the net outcome of plant interactions within a subordinate plant community. To answer this question, requires precise estimates of individual variation in functional traits and performance.</li> <li>In a five-year mesocosm experiment, the functional responses of a subordinate plant community to the removal of the dominant species were evaluated across two drought-stress scenarios. Small scale (i.e., large pots) wetland communities were constructed comprising one dominant species (Carex elata) and three subordinate species. Removal of the dominant species allowed evaluation of the net effects of drought and interspecific interactions. We estimated the functional divergences for three traits (specific leaf area, leaf dry matter content and height growth allocation) and compared these with performance differences quantified individually. This enabled distinctions to be made between deterministic (i.e., niche differentiation) and neutral processes driving the drought response of the subordinate community.</li> <li>We showed that the dominant species decreased relative performance differences within the subordinate plant community under conditions of permanent drought stress. These changes were associated with the convergence of traits related to resource acquisition and growth. The dominant species equalised species performance differences by supressing relatively drought-tolerant species with low competitive ability and by supporting the less drought-tolerant species with relatively high competitive ability. Meanwhile, under conditions of interannual drought, the subordinate species likely coexisted due to differentiation in resource-use strategies and the interaction with the dominant species.</li> <li>Inclusion of individual variation in performance with a functional trait approach provides valuable insights into the processes structuring plant communities. Ours is the first study to provide evidence that subordinate species exposed to drought may coexist via neutral processes arising from their interactions with the dominant species, leading to functional convergence of traits associated with the trade-off between stress tolerance and competitive ability.</li> </ol>

Data from: Dissecting the genetic architecture of a stepwise infection process

How a host fights infection depends on an ordered sequence of steps, beginning with attempts to prevent a pathogen from establishing an infection, through to steps that mitigate a pathogen's control of host resources, or minimising the damage caused during infection. Yet empirically characterising the genetic basis of these steps remains challenging. Although each step is likely to have a unique genetic and environmental signature, and may, therefore, respond to selection in a specific way, events that occur earlier in the infection process can mask or overwhelm the contributions of subsequent steps. In this study, we dissect the genetic architecture of a stepwise infection process using a quantitative trait loci (QTL) mapping approach. We control for variation at the first line of defence against a bacterial pathogen and expose downstream genetic variability related to the host's ability to mitigate the damage pathogens cause. In our model, the water-flea Daphnia magna, we found a single major effect QTL, explaining 64% variance, that is linked to the host's ability to completely block pathogen entry by preventing their attachment to the host oesophagus; consistent with the detection of this locus in prior studies. In susceptible hosts allowing attachment, however, a further 23 QTL, explaining between 5 to 16% variance, were mapped to traits related to the expression of disease. The general lack of pleiotropy and epistasis for traits related to the different stages of the infection process, together with the wide distribution of QTL across the genome, highlights the modular nature of a host's defence portfolio, and the potential for each different step to evolve independently. We discuss how isolating the genetic basis of individual steps can help resolve discussion over the genetic architecture of host resistance.

Data for Analysis of Keystone Predation - trait based or driven by extrinsic processes?

Keystone predation can be a determinant of community structure, including species diversity, but factors underlying "keystoneness" have been minimally explored. Using the system in which the original keystone, the sea star Pisaster ochraceus, was discovered, we focused on two potential (but overlapping) determinants of keystoneness: intrinsic traits or state variables of the species (e.g., size, density), and extrinsic environmental parameters (e.g., prey productivity) that may provide conditions favorable for keystone predator evolution. Using a comparative-experimental approach, with repeated field experiments at multiple sites across a variable coastal environment, we tested predation rates, or how quickly predators consumed prey, and predation effects, or community response to predator presence or absence. We tested five hypotheses: (H1) predation rates and effects will vary in space but not time; (H2) per population predation rates will vary primarily with individual traits and population variables; (HJHH3) per capita predation rates will vary only with individual traits; (H4) predation effects will vary with traits, variables, and external drivers; and (H5) as predicted by the keystone predation hypothesis, diversity will vary unimodally with predation pressure. As hypothesized, predation rates differed among sites but not over time (H1), and in caging exclusion experiments, predation effect varied with both intrinsic and extrinsic factors (H4). Unexpectedly, predation rates varied with both intrinsic and extrinsic (H2, per population), or only with extrinsic (H3, per capita) factors. Further, in large-plot exclusion experiments, predation effect was most closely associated with individual traits (contra H4). Finally, taxon diversity varied unimodally with proxies of predation pressure (sessile prey abundance) and was sensitive to extrinsic factors (mussel growth, temperature, and upwelling) (H5). Hence, keystoneness depended on predator individual traits, predator population variables, and environmental parameters. However, temporal differences in caging experiments suggested that environmental characteristics underlying prey dynamics may be preeminent. Compared to prior experiments, predation was weaker with low prey input compared to periods with high prey input. Collectively, our results suggest that keystone predator evolution depends on the coalescence of species-specific characteristics, and environmental parameters favoring high prey productivity. Our approach may be a model for future studies exploring the generality of keystoneness.

Data from: Visualizing mineralization processes and fossil anatomy using synchronous synchrotron X-ray fluorescence and X-ray diffraction mapping

Fossils, including those that occasionally preserve decay-prone soft-tissues, are mostly made of minerals. Accessing their chemical composition provides unique insight into their past biology and/or the mechanisms by which they preserve, leading to a series of developments in chemical and elemental imaging. However, the mineral composition of fossils, particularly where soft-tissues are preserved, is often only inferred indirectly from elemental data, while X-ray diffraction that specifically provides phase identification received little attention. Here, we show the use of synchrotron radiation to generate not only X-ray fluorescence elemental maps of a fossil, but also mineralogical maps in transmission geometry using a two-dimensional area detector placed behind the fossil. This innovative approach was applied to millimetre-thick cross-sections prepared through three-dimensionally preserved fossils, as well as to compressed fossils. It identifies and maps mineral phases and their distribution at the microscale over centimetre-sized areas, benefitting from the elemental information collected synchronously, and further informs on texture (preferential orientation), crystallites size and local strain. Probing such crystallographic information is instrumental in defining mineralization sequences, reconstructing the fossilization environment and constraining preservation biases. Similarly, this approach could potentially provide new knowledge on other (bio)mineralization processes in environmental sciences. We also illustrate that mineralogical contrasts between fossil tissues and/or the encasing sedimentary matrix can be used to visualize hidden anatomies in fossils.

opencc-zeroSep 2020View details →

Anonymized source data files for figures in: Recurrent processes support a cascade of hierarchical decisions

Perception depends on a complex interplay between feedforward and recurrent processing. Yet, while the former has been extensively characterized, the computational organization of the latter remains largely unknown. Here, we use magneto-encephalography to localize, track and decode the feedforward and recurrent processes of reading, as elicited by letters and digits whose level of ambiguity was parametrically manipulated. We first confirm that a feedforward response propagates through the ventral and dorsal pathways within the first 200 ms. The subsequent activity is distributed across temporal, parietal and prefrontal cortices, which sequentially generate five levels of representations culminating in action-specific motor signals. Our decoding analyses reveal that both the content and the timing of these brain responses are best explained by a hierarchy of recurrent neural assemblies, which both maintain and broadcast increasingly rich representations. Together, these results show how recurrent processes generate, over extended time periods, a cascade of decisions that ultimately accounts for subjects' perceptual reports and reaction times.

Processed data of grasshoppers, butterflies and moths for analyses of species trend models for the regional WWF Living Planet Index for Belgium

This archive contains pre-processed datasets used for the analysis of species occupancy models, the results of which were used in the calculation of multi-species indices as part of the regional WWF Living Planet Index for Belgium. The datasets are csv files (comma separated and . as decimal mark).  For each species group (moths, butterflies and grasshoppers), the following files are available: <ul> <li>a species list (files with 'species' in the name)</li> <li>an observations list (files with 'observations' in the name - for butterfly or moth species with two distinct flight periods, also a file with the data for the second generation is available)</li> </ul> For one species, Fabriciana adippe, separate files are available with corrected data. The species list files contain the following variables: <ul> <li>species_id (unique species id)</li> <li>scientific_name (accepted scientific name according to the GBIF taxonomic backbone)</li> <li>species_name_NL (Dutch species name)</li> <li>species_name_FR (French species name)</li> <li>season_start (n-th day of the year that marks the beginning of the first -and possibly only- generation)</li> <li>season_end (n-th day of the year that marks the end of the first -and possibly only- generation)</li> </ul> The observations files contain the following variables: <ul> <li>species_id (a unique identifier)</li> <li>year (year of observation)</li> <li>month (month of observation)</li> <li>day (day of observation)</li> <li>julian_day (n-th day of the year)</li> <li>site_id (unique identifier for the 1 km x 1km EEA 1 km x 1 km reference grid square <a href="https://www.eea.europa.eu/data-and-maps/data/eea-reference-grids-2">https://www.eea.europa.eu/data-and-maps/data/eea-reference-grids-2</a>)</li> <li>source (name of data provider)</li> <li>count (max number of sightings for the species for that day and site</li> </ul>

opencc-by-4.0Sep 2020View details →

Data from: How Bank Vole-PUUV Interactions Influence the Eco-Evolutionary Processes Driving Nephropathia Epidemica Epidemiology—An Experimental and Genomic Approach

Abstract: In Europe, Puumala virus (PUUV) is responsible for nephropathia epidemica (NE), a mild form of hemorrhagic fever with renal syndrome (HFRS). Despite the presence of its reservoir, the bank vole, on most of French territory, the geographic distribution of NE cases is heterogeneous and NE endemic and non-endemic areas have been reported. In this study we analyzed whether bank vole-PUUV interactions could partly shape these epidemiological differences. We performed crossed-experimental infections using wild bank voles from French endemic (Ardennes) and non-endemic (Loiret) areas and two French PUUV strains isolated from these areas. The serological response and dynamics of PUUV infection were compared between the four cross-infection combinations. Due to logistical constraints, this study was based on a small number of animals. Based on this experimental design, we saw a stronger serological response and presence of PUUV in excretory organs (bladder) in bank voles infected with the PUUV endemic strain. Moreover, the within-host viral diversity in excretory organs seemed to be higher than in other non-excretory organs for the NE endemic cross-infection but not for the NE non-endemic cross-infection. Despite the small number of rodents included, our results showed that genetically different PUUV strains and in a lesser extent their interaction with sympatric bank voles, could affect virus replication and diversity. This could impact PUUV excretion/transmission between rodents and to humans and in turn at least partly shape NE epidemiology in France.

opencc-zeroSep 2020View details →

Data and code from "A dimmer shade of pale: revealing the faint signature of local assembly processes on the structure of strongly filtered plant communities"

Trait-based ecology suggests that abiotic filtering is the main mechanism structuring the regional species pool in different subsets of habitat-specific species. At more local spatial scales, other ecological processes may add on giving rise to complex patterns of functional diversity (FD). Understanding how assembly processes operating on the habitat-specific species pools produce the locally observed plant assemblages is an ongoing challenge. Here, we evaluated the importance of different processes to community assembly in an alpine fellfield, assessing its effects on local plant trait FD. Using classical randomization tests and linear mixed models, we compared the observed FD with expectations from three null models that hierarchically incorporate additional assembly constraints: stochastic null models (random assembly), independence null models (each species responding individual and independently to abiotic environment), and co-occurrence null models (species responding to environmental variation and to the presence of other species). We sampled species composition in 115 quadrats across 24 locations in the central Pyrenees (Spain) that differed in soil conditions, solar radiation and elevation. Overall, the classical randomization tests were unable to find differences between the observed and expected functional patterns, suggesting that the strong abiotic filters that sort out the flora of extreme regional environments blur any signal of other local processes. However, our approach based on linear mixed models revealed the signature of different ecological processes. In the case of seed mass and leaf thickness, observed FD significantly deviated from the expectations of the stochastic model, suggesting that fine-scale abiotic filtering and facilitation can be behind these patterns. Our study highlights how the hierarchical incorporation of ecological additional constraints may shed light on the dim signal left by local assembly processes in alpine environments.

Data from: Solute Production and Transport Processes in Chinese Monsoonal Rivers: Implications for Global Climate Change

Concentration-discharge (C-Q) relationships provide new insights into solute production processes. Temporal sampling and analyses are needed to investigate the chemical weathering behaviors and reduce the estimation errors of fluxes. But few studies have been done in Asian monsoonal rivers, which play an important role in global carbon cycle. We analyzed the dissolved solutes of Three largest rivers in China. Datong and Qingxi in Changjiang River were selected to represent the midterm and outlet of the Changjiang River. Lijin was selected as the outlet of the Yellow River. We analyzed the major ions, which can represent the chemical weathering index. Our study may help deepen the understanding of chemical weathering and solutes fluxes.

opencc-zeroSep 2020View details →

Data from: Tropical forest type influences community assembly processes in arbuscular mycorrhizal fungi

Aim: Plant community assembly in tropical rainforest has been shown to be largely governed by stochastic processes, but as arbuscular mycorrhizal (AM) fungi display limited host preference, they may not follow the same stochastic assembly pattern. Here, we determined the relative importance of environmental and spatial drivers responsible for the community assembly process of AM fungi in two types of tropical rainforest (semideciduous rainforest and dense ombrophilous forests). Location: Atlantic rainforest in northeastern Brazil, South America. Taxon: Arbuscular mycorrhizal fungi (Glomeromycota). Methods: We collected root samples from eight protected areas of Atlantic forest along a 700 km transect in northeastern Brazil. We measured the relative importance of deterministic and stochastic processes by redundancy analysis (RDA) and variation partitioning in comparison with null expectations using ad hoc generated neutral communities. Furthermore, we accessed species associations from co-occurrence data, at different scales using a Bayesian approach of Hierarchical Modelling of Species Communities (HMSC). Results: Overall, the extent to which stochastic and deterministic processes affected community assembly depended on the forest type and the spatial scale. Specifically, we found that abiotic and biotic predictors of AM fungal community assemblages are related to environmental homogeneity in tropical rainforests. Main conclusions: The results of the study show that dynamics in community assembly was clearly different between the two forest types, and that the difference most likely is due to differences in responses to environmental variables.

opencc-by-4.0Oct 2020View details →

cTaG processed data

Pre-processed dataset generated from COSMIC somatic mutation data (v9). This data was used for constructing the pan-cancer feature matrix used for building models. The same data is used for generating tissue specific feature matrices for identification of driver genes in various tissues.