Find research datasets worth reusing

opencc-by-4.0Jan 2019View details →

SparkWiki: Wikipedia graph dataset and pagecounts pre-processing tools

SparkWiki toolkit can be used in various scenarios where you are interested in researching Wikipedia graph and pageview statistics. Graph and pageviews can be used and studied separately. The code used to process Wikipedia SQL dumps, along with deployment instructions, are located on <a href="https://github.com/epfl-lts2/sparkwiki">GitHub</a>. To test an example of a pre-processed graph, you can download a dump of the English Wikipedia graph (see attached wikipedia_nrc.dump), which you can directly import into a Neo4J instance. The dump is intended for neo4j version 3.x and can be imported using the following command (make sure you do not have an existing wikipedia.db database as the command below will overwrite its content): <code>sudo -u neo4j neo4j-admin load --force --from=wikipedia_nrc.dump --database=wikipedia.db</code> If you try to import it into Neo4J version 4.x, you need to set the property  <code>dbms.allow_upgrade=true</code> in <code>/etc/neo4j/neo4j.conf</code>  before importing. When you start the neo4j server it will upgrade the database s.t. it is compatible with version 4.x.

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-by-4.0Sep 2020View details →

MONITORING AND MODELING OF HYDROLOGICAL PROCESSES IN THE SEMIARID REGION OF BRAZIL: THE CARIRI EXPERIMENTAL BASINS

DATASET DESCRIPTION - Two experimental basins – the Cariri basins – were installed in a typically semiarid region in the State of Paraíba, Brazil, for obtaining reliable estimates of runoff and soil erosion in different scales to evaluate the influence of the human activities and other factors over the processes of runoff and erosion. In the first basin, located in the municipality of Sumé, the field studies were carried out at three different scales: four micro-basins with an area of around 0.5 ha; nine standard Wischmeier-type erosion plots of 100 m2 and seven sample plots of 1 m2. The experimental units had varied vegetal cover and management and, except the sample plots, were subjected to natural rainfall events only, and were monitored from 1982 to 1991. The total runoff and total sediment yield were determined for each of the events of precipitation. The installations of the second basin, in the near municipality of São João do Cariri, were planned for the continuation of the studies initiated at Sumé, and include erosion plots (100 m2), micro-basins, and sub-basins, which are being monitored for runoff and sediment production up to now. Among them, two nested micro-basins were monitored to detect any scale effect at the micro-basin level. Nearly 600 events of natural precipitation, that produced runoff in at least one of the experimental units, have been registered. This bulk of data was utilised to evaluate the influence of various factors, including cultivation practices. The data collected so far has been successfully used to calibrate hydrological models for plots and micro-basins. Parameters have been tested by means of cross validations among micro-basins and sub-basins. FILENAMES – The data files are divided into three categories: Description of the equipment utilized for collecting data and their locations, the data collected from the monitored experimental basins and another with maps, figures and pictures. The file names are designated with the basin name and the content. The files describing the equipment comprise: BASINNAME_DATADESCRIPTION, where BASINNAME could be EBS or EBSJC. The files with the data collected in the experimental basins are denominated like: BASINNAME_DATANAME. The DATANAME will be one of the three that may be, precipitation, runoff and sediment yield, or climatologic data. The file with maps and other information are identified as: BASINNAME_GEOPHYSICDATANAME, and BASINNAME_PICTURES. The geophysical data refer to topographic data, soil data, land cover and the drainage network. Graphs, pictures, etc., are included in the PICTURES file. DATAFORMAT – The data file about equipment and localization as well as the data collected in experimental units are of the type “. csv”, the geophysical data are of either “.dwg” or “.shp”. The figures and picture are in the format: .jpeg, .png or .tif. ACKNOWLEDGEMENTS – SUDENE – the Superintendency for the Development of the Northeast of Brazil with the cooperation of ORSTOM – the French Government Agency for Technical Cooperation Overseas was responsible for implementing the program of Representative and Experimental Basins in the region beginning in the decade of 1970. Pierre Audry, Eric Cadier, Jean Leprun and Michel Molinier, hydrologists and soil scientists from France played key roles in the selection of site, installation of experimental units and beginning the operation of the EBS. Beronildo Freitas was the engineer from SUDENE responsible for technical coordination and administration. The contributions of other researchers and technical people have been listed by Srinivasan and Galvão (2003). The installation of the research catchment at São João de Cariri had the valuable collaboration of GTZ, the cooperation Agency of the Government of Germany. Dr. Ing Ubald Koch was responsible for getting all the equipment, installing them and conducting research work along with the members of the Hydrology Research Group of the Federal Universities of Paraiba and Campina Grande. Late prof. Manoel Gilberto de Barros efficiently coordinated the field work. Eduardo Figueiredo, Celso Santos and Ricardo Aragão have made note worthy contributions. The Ministry of Science and Technology of Brazil has provided the bulk of the financial support needed for the operation of the basins, through its main funding agencies of CNPq (National Council for Development of Science and Technology) and FINEP (Agency for Financing research Studies and Projects).

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.

opencc-zeroAug 2020View details →

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.

opencc-by-4.0Sep 2020View details →

Optimizing the Geometric Configuration and Manufacturing Process of High Mast Illumination Poles

This work presents the development of a high-fidelity model that accounts for the cumulative effect of welding and hot- dip galvanizing on the determining the resulting residual stresses and deformations induced during the manufacturing process of high mast illumination poles (HMIPs). This model is meant to elucidate the root causes of weld toe cracks in HMIPs. A TxDOT pole-to-base plate connection detail was used as the reference model in the analysis. Welding was modeled using the plug-in Abaqus Welding Interface (AWI), which automatically implements a series of sequential thermal and mechanical analyses. Then, the welding stress results were used as initial input to the galvanizing analysis. The cumulative stress results were compared against simulations that only considered the galvanizing process. A parametric study was then conducted to quantify the variation in the residual stresses and equivalent plastic strain magnitudes induced during the welding and galvanizing of HMIPs due to changes in welding and galvanizing practices. The results revealed that the cumulative effects of the different processes involved in the manufacturing of HMIPs contribute to the formation of galvanizing cracks in HMIPs. Also, increasing the dipping submersion speed during galvanizing and lowering the torch temperature magnitude during welding results in fewer zones prone to cracking. Altering the angle of inclination effect did not have a significant impact on the results. Performing variations in the manufacturing practices used for the fabrication of HMIPs can contribute to reducing the extensive inspection procedures conducted post-galvanizing to identify cracks.

opencc-by-4.0Dec 2019View details →

Processed SpectrumDocuments from AllPositive (case study for MS2Query)

Processed SpectrumDocuments of the "AllPositive" dataset created from GNPS positive ionmode mass spectra. They are used in a case study for MS2Query: https://github.com/iomega/ms2query. Reading this pickle file in python will give a tuple of two lists of spec2vec.SpectrumDocument. The first list contains 2,000 spectra and the second list contains 93,320 spectra that are used as query and library spectra in the case study.

opencc-by-4.0Nov 2020View details →

Adaptation to hand-tapping affects sensory processing of numerosity directly: evidence from reaction times and confidence

Each file contains a matrix called “MatriceRisultati”. Each row of the matrix “MatriceRisultati” is a trial.  The columns contain the following information: <ul> <li>1st: Number of trial</li> <li>2nd: Test numerosity</li> <li>3rd: Subject response on numerosity </li> <li>4th: Subject response on their confidence level</li> <li>5th: Response time</li> <li>6th: 0 if the test numerosity< 16; 1 if the test numerosity> 16</li> </ul>

opencc-by-4.0Nov 2020View details →

GUITAR-FX-DIST: A Dataset of Processed Guitar Recordings for Music Research - (Mono Continuous)

GUITAR-FX-DIST is a dataset of electric guitar recordings processed with overdrive, distortion and fuzz audio effects. It was developed for research in guitar effects detection, classification and parameters estimation. The dataset is also useful for research on automatic music transcription, intelligent music production, signal processing or effects modelling. It contains both unprocessed and processed recordings. The dataset is split into 4 sub-datasets: Mono Continuous, Mono Discrete, Poly Continuous, Poly Discrete   Authors: Marco Comunità - <a href="http://c4dm.eecs.qmul.ac.uk/">Centre for Digital Music</a>, Queen Mary University of London   Reference: If you make use of GUITAR-FX-DIST, please cite the following publication: <pre><code>@article{comunità2021guitar, title={Guitar Effects Recognition and Parameter Estimation with Convolutional Neural Networks}, author={Comunità, Marco and Stowell, Dan and Reiss, Joshua D.}, journal={Journal of the Audio Engineering Society}, year={2021}, volume={69}, number={7/8}, pages={594-604}, doi={}, month={July} }</code></pre>   Dataset Snapshot: <ul> <li>Size: ~550k samples (~305 hours) + 550k mel spectrograms</li> <li>Audio Format: WAV - 44.1kHz, 16bit, mono, -6dBFS</li> <li>Mel-Spectrogram Format: NPY - 128 frequency bands, sample rate 22050Hz, window length 1024, hop size 512,</li> <li>Effects: 14 between overdrive, distortion and fuzz</li> <li>Unprocessed recordings <ul> <li>624 monophonic notes</li> <li>420 polyphonic (2, 3 and 4 notes intervals and chords)</li> <li>2 guitars, with up to 2 pick-up settings and up to 3 plucking styles (finger pluck - hard, finger pluck - soft, pick) <ul> <li>Schecter Diamond C-1 Classic</li> <li>Chester Stratocaster</li> </ul> </li> </ul> </li> <li>Samples length: 2 sec</li> </ul>   Unprocessed Recordings: The original (unprocessed) recordings are from the <a href="https://www.idmt.fraunhofer.de/en/business_units/m2d/smt/audio_effects.html">IDMT-SMT-Audio-Effects</a> dataset. For details please refer to the website and the accompagning publication: Stein, Michael; Abeßer, Jakob; Dittmar, Christian; Schuller, Gerald: Automatic Detection of Audio Effects in Guitar and Bass Recordings. Proceedings of the AES 128th Convention, 2010.   Processed Recordings: The processed recordings are divided into 4 sub-datasets which are named depending on the unprocessed recordings used (monophonic or polyphonic) and on the settings' values (discrete or continuous). The sub-datasets are called: Mono Discrete, Poly Discrete, Mono Continuous, Poly Continuous Mono Discrete and Poly Discrete use a discrete set of combinations selected as the most common and representative settings a person might use (see README file for details). For Mono Continuous and Poly Continuous both unprocessed samples as well as settings’ values are drawn from a uniform distribution (10000 samples for each effect). Samples: <ul> <li>Mono Discrete: ~160k</li> <li>Poly Discrete: ~110k</li> <li>Mono Continuous: 140k</li> <li>Poly Continuous: 140k</li> </ul>   Scripts: The dataset includes the MATLAB scripts used to generate the samples

opencc-zeroDec 2020View details →

Central processing of leg proprioception in Drosophila: Physiology and behavior data

Proprioception, the sense of self-movement and position, is mediated by mechanosensory neurons that detect diverse features of body kinematics. Although proprioceptive feedback is crucial for accurate motor control, little is known about how downstream circuits transform limb sensory information to guide motor output. Here, we investigate neural circuits in Drosophila that process proprioceptive information from the fly leg. We identify three cell-types from distinct developmental lineages that are positioned to receive input from proprioceptor subtypes encoding tibia position, movement, and vibration. 13Bα neurons encode femur-tibia joint angle and mediate postural changes in tibia position. 9Aα neurons also drive changes in leg posture, but encode a combination of directional movement, high-frequency vibration, and joint angle. Activating 10Bα neurons, which encode tibia vibration at specific joint angles, elicits pausing in walking flies. Altogether, our results reveal that central circuits integrate information across proprioceptor subtypes to construct complex sensorimotor representations that mediate diverse behaviors, including reflexive control of limb posture and detection of leg vibration.

Simulating δ15N of atmospheric NOx with the impacts from atmospheric processes

A new emission dataset of NOx, which incorporates the 15N isotope, was used to simulate the δ15N values in CAMQ (the Community Multiscale Air Quality Modeling System), in order to qualitatively analyze the changes in δ15N values, due to the disperse, mixing, and transport of the atmospheric NOx emitted from different sources, driven by atmospheric processes.

Amyloid burden quantification depends on PET and MR image processing methodology

The enclosed datasets refer to the work developed at the University Medical Center Groningen and consist of the minimally required PET image data to replicate the results of the study entitled "Amyloid burden quantification depends on PET and MR image processing methodology" which abstract can be found below: <blockquote> Quantification of amyloid load with positron emission tomography can be useful to assess Alzheimer’s Disease in-vivo. However, quantification can be affected by the image processing methodology applied. This study’s goal was to address how amyloid quantification is influenced by different semi-automatic image processing pipelines. Images were analysed in their Native Space and Standard Space; non-rigid spatial transformation methods based on maximum a posteriori approaches and tissue probability maps (TPM) for regularisation were explored. Furthermore, grey matter tissue segmentations were defined before and after spatial normalisation, and also using a population-based template. Five quantification metrics were analysed: two intensity-based, two volumetric-based, and one multi-parametric feature. Intensity-related metrics were not meaningfully affected by spatial normalisation and did not significantly depend on the grey matter segmentation method, with an impact similar to that expected from test-retest studies (≤10%). Yet, volumetric and multi-parametric features were sensitive to the image processing methodology, with an overall variability up to 45%. Therefore, the analysis should be carried out in Native Space avoiding non-rigid spatial transformations. For analyses in Standard Space, spatial normalisation regularised by TPM is preferred. Volumetric-based measurements should be done in Native Space, while intensity-based metrics are more robust against differences in image processing pipelines. </blockquote>

A quantitative method to calibrate the SWAN wave model - pre-processed model outputs

The pre-processed MAT files for the paper 'A quantitative method to calibrate the SWAN wave model'

Dataset of alternative process plan networks for dynamic integrated process planning and scheduling

This dataset includes 3D models of representative manufacturing parts (jobs) as well as their features. For each of the manufacturing part, alternative process plan networks are given containing alternative machine tools, cutting tools, Tool Access Directions (TADs) and manufacturing times. The dataset also includes a detailed technical specification for all parts and calculated manufacturing times for all operations based on given alternative manufacturing resources.

opencc-by-4.0Jan 2021View details →

Dataset for the decay process of PM2.5 pollution episodes around Beijing

PM2.5 concentrations in the 28 cities around Beijing (Apm);  Time series of the decay phase days (LocaDate); Time series of the dry-day decay phase days (LocaDateNoPre)

opencc-zeroJan 2021View details →

Weak genetic signal for phenotypic integration implicates developmental processes as major regulators of trait covariation

Phenotypic integration is an important metric that describes the degree of covariation among traits in a population, and is hypothesized to arise due to selection for shared functional processes. Our ability to identify the genetic and/or developmental underpinnings of integration is marred by temporally overlapping cell-, tissue-, and structure-level processes that serve to continually 'overwrite' the structure of covariation among traits through ontogeny. Here we examine whether traits that are integrated at the phenotypic level, also exhibit a shared genetic basis (e.g., pleiotropy). We micro-CT scanned two hard tissue traits, and two soft tissue traits (mandible, pectoral girdle, atrium, and ventricle respectively) from an F5 hybrid population of Lake Malawi cichlids, and used geometric morphometrics to extract 3D shape information from each trait. Given the large degree of asymmetric variation that may reflect developmental instability, we separated symmetric- from asymmetric-components of shape variation. We then performed quantitative trait loci (QTL) analysis to determine the degree of genetic overlap between shapes. While we found ubiquitous associations among traits at the phenotypic level, except for a handful of notable exceptions, our QTL analysis revealed few overlapping genetic regions. Taken together, this indicates developmental interactions can play a large role in determining the degree of phenotypic integration among traits, and likely obfuscate the genotype to phenotype map, limiting our ability to gain a comprehensive picture of the genetic contributors responsible for phenotypic divergence.

opencc-zeroJan 2021View details →

Species richness in North Atlantic fish: process concealed by pattern

Aim Previous analyses of marine fish species richness based on presence-absence data have shown changes with latitude and average species size, but little is known about the underlying processes. To elucidate these processes we use metabolic, neutral, and descriptive statistical models to analyse how richness responds to maximum species length, fish abundance, temperature, primary production, depth, latitude, and longitude, while accounting for differences in species catchability, sampling effort, and mesh size. Data Results from 53,382 bottom trawl hauls representing 50 fish assemblages. Location The northern Atlantic from Nova Scotia to Guinea, the Mediterranean, the Arctic Sea. Time period 1977-2013 Methods A descriptive Generalised Additive Model was used to identify functional relationships between species richness and potential drivers, after which non-linear estimation techniques were used to parameterize: 1) a 'best' fitting model of species richness built on the functional relationships, 2) an environmental model based on latitude, longitude and depth, and mechanistic models based on 3) metabolic and 4) neutral theory. Results In the 'best' model the number of species observed is a lognormal function of maximum species length. It increases significantly with temperature, primary production, sampling effort, and abundance, and declines with depth and, for small species, with the mesh size in the trawl. The 'best' model explains close to 90% of the deviance and the neutral, metabolic, and environmental models 89%. In all four models, maximum species length and either temperature or latitude account for more than half of the deviance explained. Main conclusion The two mechanistic models explain the patterns in demersal fish species richness in the northern Atlantic almost equally well. A better understanding of the underlying drivers is likely to require development of dynamic mechanistic models of richness and size evolution, fit not only to extant distributions, but also to historical environmental conditions and to past speciation and extinction rates.