Find research datasets worth reusing

Dataset for "Spectroscopic investigation of faeces with surface-enhanced Raman scattering: a case study with coeliac patients on gluten-free diet"

This dataset contains all the spectra and OTU table data used in the paper "Spectroscopic investigation of faeces with surface-enhanced Raman scattering: a case study with coeliac patients on gluten-free diet", plus the R code to import the TXT (ASCII) files into a dataset, preprocess data, analzye data and generate the figures shown in the paper. Spectral data are available in 2 different format: - the original TXT files (as generated from the Raman instrument, 1 file = 1 spectrum) - as RData file (an hyperSpec object including metadata), directly to be opened in R The OTU table is available either as a single XLSX file or as a RData file to be opened in R. The R code used to generate the figures is available as a single file "Rcode.R".

opencc-by-4.0Sep 2021View details →

Seismic acquisition parameters to improve imaging beneath mafic igneous units: Case study from Australia's Northwest Shelf; supplementary material

This dataset comprises two supplementary materials. Supplementary Materials A includes seismic processing workflows conducted by industry on the seismic lines used in this study. The seismic processing workflows are not the property of the author but are publicly available on the NOPIMS and WAPIMS databases. Collating these workflows into supplementary materials provides a simple method for readers to access material important for this research paper. Supplementary Materials B is a collection of 2D seismic lines the author conducted stratigraphic horizon mapping on for this study as viewed in 3D. More details on this dataset can be found throughout the research paper "Seismic acquisition parameters to improve imaging beneath mafic igneous units: Case study from Australia’s Northwest Shelf".

opencc-zeroMar 2022View details →

Do ecological specialization and functional traits explain the abundance–frequency relationship? Arable weeds as a case study

Aim: The abundance-frequency relationship (AFR) is among the most-investigated pattern in biogeography, yet the relative contributions of niche-based processes related to ecological strategies, and of neutral processes related to spatial colonization-extinction dynamics, remains uncertain. Here, we tested the influences of ecological specialization and functional traits on local abundance and regional frequency, to determine the contribution of niche-based processes. Location: France and the UK. Taxon: Vascular plants. Methods: We used two arable weed surveys covering 1544 fields in Western Europe (France, UK), along with functional traits related to resource acquisition, flowering phenology and dispersal. We quantified specialization both to arable habitat and to individual crop types, and performed phylogenetic path analyses to test competing models accounting for direct and indirect relationships between traits, specialization, abundance and frequency. We performed the analyses for all species in each country, as well as for a subset of the most abundant species. Results: Local abundance of weeds increased with their regional frequency, but the relationship became negative or null when considering only the most abundant weeds. Specialization to arable habitat and to individual crop type either had a similar or opposite effect on regional frequency and local abundance explaining these positive and negative relationships, respectively. Regional frequency was not directly explained by any trait but indirectly by resource requirement traits conferring specialization to the arable habitat. Conversely, high local abundance was directly related to low seed mass, high SLA, early and short flowering. Main Conclusions: Direct/indirect effects of functional traits on local abundance/regional frequency, respectively, supports a significant role of niche-based processes in AFR. Neutral spillover dynamics could further explain a direct linkage of abundance and frequency. Similar causal paths and consistent influences of traits on specialization and abundance in the two studied regions suggest genericity of these findings.

Case study on an integrated interoperable metadata model for geoscience information resources

An integrated metadata schema was created to promote interoperability and to characterize historically collected geoscience data. The metadata standard describes the steps taken to develop a switching‐across methodology that allows geoscience metadata standards (ISO 19115, CSDGM, ANZLIC and INSPIRE) to communicate with one another. We also demonstrated a real example of one of the switching‐across that was created. A representative metadata schema was created using items from harmonization standards that might be optimally mapped. Semantic interoperability allows users to access equivalent classes across several metadata standards in a uniform and consistent rule. It also tries to provide fundamental aspects that might characterize acquisition information to enhance data reuse and current metadata standards for data preservation and distribution. This dataset contains 5 data and contains the content standard of each of the four metadata schema and the metadata information of integrated metadata schema. <ul> <li>data_ISO19115.xlsx: Core level of metadata elements for geographic resources of ISO 19115</li> <li>data_CSDGM.xlsx: Content Standard for Digital Geospatial Metadata of CSDGM</li> <li>data_INSPIRE.xlsx: Content Standard of INSPIRE metadata modeldata_ANZLIC.xlsx: Content Standard of ANZLIC Metadata Profile</li> <li>data_integrated model.xlsx: metadata class and their elements in the integrated interoperable metadata model</li> </ul>

Comparison of the Birth Weights of Infants with Esophageal Atresia and Tracheoesophageal Fistula and Infants with Inguinal Hernia: A Retrospective Case–Control Study

Esophageal atresia with tracheoesophageal fistula is the most common tracheoesophageal malformation. Amniotic fluid swallowing into the upper blind sack and aspiration were observed during fetal life. Tracheoesophageal fistula serves as a sideway passage of amniotic fluid into the gastrointestinal tract. Compared with inguinal hernia, gestational age adjusted birth weights were lower for infants with esophageal atresia. In esophageal atresia with tracheoesophageal fistula nutrition by aspirated amniotic fluid did not fully compensate the intrauterine growth deficit.

Flight milestones extraction and analysis: a case study for Stockholm Arlanda airport

State vector data for movements (arrivals and departures) at <a href="https://en.wikipedia.org/wiki/Stockholm_Arlanda_Airport">Stockholm Arlanda</a> (IATA: ARN, ICAO: ESSA) for the month of September 2021 as extracted from The OpenSky Network historical database.

opencc-by-4.0Jul 2021View details →

Data and script for binomial GLMs in "Lithic Analysis of Andean Sedentary Societies, a Case Study from the Chachapoyas Region, Peru, and Potential Applications." (Pratt & Guengerich)

This submission contains data and R-script that enable to reproduce the binomial generalized linear models in the paper “Lithic Analysis of Andean Sedentary Societies, a Case Study from the Chachapoyas Region, Peru, and Potential Applications” by Lauren V. Pratt & Anna Guengerich. Please cite the above paper if you use the files included in this Zenodo record in your work.

opencc-zeroApr 2022View details →

Case study data of the paper: A methodological guide to observe local-scale geodiversity for biodiversity research and management

Current global environmental change calls for comprehensive and complementing approaches for biodiversity conservation. According to recent research, consideration of the diversity of Earth's abiotic features (i.e., geodiversity) could provide new insights and applications into the investigation and management of biodiversity. However, methods to map and quantify geodiversity at local scale have not been developed although this scale is important for conservation planning. Here, we introduce a field methodology for observing plot-scale geodiversity, pilot the method in an Arctic-alpine tundra environment, provide empirical evidence on the plot-scale biodiversity-geodiversity relationship and give guidance for practitioners on the implementation of the method. The field method is based on observation of geofeatures, i.e., elements of geology, geomorphology, and hydrology, from a given area surrounding a location of species observations. As a result, the method provides novel information on the variation of abiotic nature for biodiversity research and management. The method was piloted in northern Norway and Finland by observing geofeatures from 76 sites at three scales (5, 10 and 25 m radii). To explore the relationship between measures of biodiversity and geodiversity, the occurrence of vascular plant species was recorded from 2 m x 2 m plots at the same sites. According to the results, vascular plant species richness was positively correlated with the richness of geofeatures (Rs = 0.18–0.59). The connection was strongest in habitats characterized by deciduous shrubs. The method has a high potential for observing geofeatures without extensive geological or geomorphological training or field survey experience and could be applied by conservation practitioners. Consideration of geodiversity in understanding, analysing and conserving biodiversity could facilitate environmental management and ensure the long-term sustainability of ecosystem functions. With the developed method, it is possible to cost-efficiently observe the elements of geodiversity that are useful in ecology and biodiversity conservation. Our approach can be adapted in different ecosystems and biodiversity investigations. The method can be adjusted depending on the abiotic conditions, expertise of the observer(s), and the equipment available.

opencc-zeroMay 2022View details →

Data from: Encoding laboratory testing data: case studies of the national implementation of HHS requirements and related standards in five laboratories

Objective: Assess the effectiveness of providing Logical Observation Identifiers Names and Codes (LOINC®)-to-In Vitro Diagnostic (LIVD) coding specification, required by the United States Department of Health and Human Services for SARS-CoV-2 reporting, in medical center laboratories and utilize findings to inform future United States Food and Drug Administration policy on the use of real-world evidence in regulatory decisions. Materials and Methods: We compared gaps and similarities between diagnostic test manufacturers' recommended LOINC® codes and the LOINC® codes used in medical center laboratories for the same tests. Results: Five medical centers and three test manufacturers extracted data from laboratory information systems (LIS) for prioritized tests of interest. The data submission ranged from 74 to 532 LOINC® codes per site. Three test manufacturers submitted 15 LIVD catalogs representing 26 distinct devices, 6956 tests, and 686 LOINC® codes. We identified mismatches in how medical centers use LOINC® to encode laboratory tests compared to how test manufacturers encode the same laboratory tests. Of 331 tests available in the LIVD files, 136 (41%) were represented by a mismatched LOINC® code by the medical centers (chi-square 45.0, 4 df, P &lt; .0001). Discussion: The five medical centers and three test manufacturers vary in how they organize, categorize, and store LIS catalog information. This variation impacts data quality and interoperability. Conclusion: The results of the study indicate that providing the LIVD mappings was not sufficient to support laboratory data interoperability. National implementation of LIVD and further efforts to promote laboratory interoperability will require a more comprehensive effort and continuing evaluation and quality control.

opencc-by-4.0Apr 2022View details →

Case Study - Performance Changes of Apache Tomcat at Code Level

This dataset provides the data of the case study on <a href="https://github.com/apache/tomcat">Apache Tomcat</a> that was conducted as part of the bachelor thesis "Extending Peass to Detect Performance Changes of Apache Tomcat". The data was generated by <a href="https://github.com/DaGeRe/peass">Peass</a> and the <a href="https://github.com/stro18/peass-ant">Peass-Ant plugin</a>. Contents The dataset is divided into case_study_1v-100v.tar.xz and case_study_100v-200v.tar.xz. Both parts contain the following data: <ul> <li>select/ - Results of regression test selection, especially: <ul> <li>results/traceTestSelection_tomcat.json - Tests selected based on static code analysis and trace analysis</li> </ul> </li> <li>3 x measure_p*_100vm_400iter/ - Results of performance measurements, especially: <ul> <li>clean/ - Mean of measurements per VM</li> <li>results/changes.json - Tests containing performance changes, computed with t-test</li> </ul> </li> <li>rca_p3_100vm_400iter/ - Results of root cause analysis, especially: <ul> <li>rca/tree/ - Measurements results per called method</li> <li>results/*/*.html - Visualization of root cause analysis</li> </ul> </li> </ul> Additionally, f1_score.tar.xz is included in this dataset, It contains heatmaps visualizing the F1-score that were used to compare different measurement configurations. Extraction of Data Move all .tar.xz files to an empty directory and execute for each file: <pre><code class="language-bash">tar -Jxf <file></code></pre>

Code of "Inclusion of flood diversion canal operation in the H08 hydrological model with a case study from the Chao Phraya River basin: model development and validation"

Code used to prepare a paper entitled "Inclusion of flood diversion canal operation in the H08 hydrological model with a case study from the Chao Phraya River basin: model development and validation" which was submitted to Hydrology and Earth System Sciences.

Objective identification of high-wind features within extratropical cyclones using a probabilistic random forest (RAMEFI). Part I: Method and illustrative case studies - Video Supplement

These videos provide examples of application of RAMEFI (RAndom-forest based MEsoscale wind Feature Identification), a new objective identification of high-wind features within extratropical cyclones, for twelve selected case studies.

Research data: "Effects of Network Structures on the Production Planning in Closed-loop Supply Chains – A Case Study based Analysis for Lithium-ion Batteries in Europe"

This data set belongs to the paper Effects of Network Structures on the Production Planning in Closed-loop Supply Chains – A Case Study based Analysis for Lithium-ion Batteries in Europe in the International Journal of Production Economics (DOI). The BatPac model, as well as, the model for the economic assessment of the recycling route are not included. The needed data can be found in the file (name). Further, the BatPaC model can be gather from the website of Argonne National Laboratory and the assessment tool for the recycling routes via this DOI: 10.5281/zenodo.6500946.   This work is part of the research project Recycling 4.0 (EFRE | ZW 6-85018080), which is funded by the European Regional Development Fund and managed by the development bank for the German federal state of Lower Saxony (NBank).

Elevational patterns in tropical bryophyte diversity differ among substrates: a case study on Baru volcano, Panama

Questions. Bryophytes attain their highest diversity in tropical mountain forests. Although distribution patterns have been described, little emphasis has been placed on comparing patterns among substrates (e.g., terrestrial, epiphytic). Understanding these patterns is important, because they determine not only the pool of genetic resources, but also the functioning of these forest ecosystems. Therefore, we studied how bryophyte species diversity changes with elevation, how elevational patterns differ between substrate types, and how elevational trends relate to environmental drivers. Location. Baru Volcano, Panama. Methods. At each of eight elevations, between 1900 and 3300 m, bryophytes were collected in 600-cm2 plots from six substrate types with four replicates. Species cover was registered as a measure of relative abundance. Species richness and community structure were determined and related to elevation, substrate types, and environmental drivers at three scales (plots, sets of four replicate plots per substrate per elevation, and all plots at each elevation). Results. Bryophyte species richness decreased towards higher elevations, at all three scales and on all substrates except bryophytes on soil, for which, at the plot scale, richness peaked at higher elevations than on the other substrates. Relative humidity explained richness slightly better than elevation. Communities at the lowest elevations had the most uneven compositions, due to the presence of many small species with low abundance. Conclusions. In studies on the spatial distribution of bryophyte diversity, it is essential to consider different substrates and spatial scales separately. If substrates differ in their elevational species-richness patterns, climate and land-use change may affect bryophyte diversity patterns not only directly, but also indirectly via changes in substrate availability. Therefore, a better understanding of the spatial variation in bryophyte diversity in mountains is essential to elucidate the effects of environmental change on this important group of plants and their implications for ecosystem functioning. FILE: Main data base_JVC.xlsx Sheet=TaxonomicInformation Our database contains taxonomic information on bryophyte species collected along an elevation gradient on the Baru volcano, Panama. Sheet=data The relative abundance of each species or morpho-species is included per 600-cm2 plot in each of the six considered substrates (soil = terricolous, rock = saxicolous, decomposing downed log (i.e. lying on the ground) = lignicolous, tree base = epiphytic on tree base, tree trunk = epiphytic on tree trunk, and understorey branch = epiphytic on branch). Sheet: climatic info In addition, we present the information on the climate recorded between April and December 2017. Acronyms: elev: elevation, tempmean: mean temperature over the measurement period (°C), tempmin: minimum temperature over the measurement period (°C), tempmax: maximum temperature over the measurement period (°C), rhmean: mean relative humidity over the measurement period (%), rhmin: minimum relative humidity over the measurement period (%), rhmax: maximum relative humidity over the measurement period (%), cancov: canopy-cover (%), heican: height of the canopy ( m).

GRASS GIS Location for South-East US urban growth case study

GRASS GIS Location containing data prepared for a FUTURES urban growth modeling case study for the South East United States (NC, SC, TN, GA, AL, FL). Contains NLCD 2001-2019 (land cover for all years; 2001 and 2019 impervious descriptor), county boundaries, USGS DEM, PAD-US protected areas.

opencc-zeroJun 2022View details →

Supplementary data for: From genomics to integrative taxonomy? The case study of Pocillopora corals

With the advent of genomics, sequencing thousands of loci from hundreds of individuals now appears feasible at reasonable costs, allowing complex phylogenies to be resolved. This is particularly relevant for cnidarians, for which insufficient data due to the small number of currently available markers, coupled with difficulties in inferring gene trees and morphological incongruences, encrypts species boundaries, thereby blurring the study and conservation of these organisms. Yet, can genomics alone be used to delimit species in an integrative taxonomic context? Here, focusing on the coral genus Pocillopora, which plays key roles in Indo-Pacific reef ecosystems but has challenged taxonomists for decades, we explored and discussed the usefulness of multiple criteria (genetics, morphology, biogeography and symbiosis ecology) to delimit species of this genus. Phylogenetic inferences, clustering approaches and species delimitation methods based on genome-wide single-nucleotide polymorphisms (SNPs) were first used to resolve Pocillopora phylogeny and propose genomic species hypotheses from 356 colonies sampled across the Indo-Pacific (western Indian Ocean, tropical southwestern Pacific and south-east Polynesia). These species hypotheses were then compared to previous genetic evidences, as well as to evidences based on morphology, biogeography and symbiosis. Genomics allowed to delimit 21 species hypotheses where only seven are currently recognised based on current taxonomy. Moreover, 13 species were strongly supported by all approaches, either confirming their currently recognised species status, or supporting the presence of new species that need to be formally described. Some of the other genomic species hypotheses were supported by biogeographic or symbiosis evidences, but additional investigations are needed to state on their species status. Altogether, our results support (1) the obsolescence of macromorphology (i.e., overall colony and branches shape) but the relevance of micromorphology (i.e., corallite structures) to refine Pocillopora species limits, (2) the need to identify molecularly species prior to their study, as morphology can blur species identification on the field, (3) the relevance of the mtORF (coupled with other markers in some cases) as a diagnostic marker of most species, and (4) the need for a taxonomical revision in the Pocillopora genus. These results give new insights into the usefulness of multiple criteria for resolving Pocillopora species limits and will ultimately provide helpful insights for the conservation of the species from this scleractinian genus.

Applying an Inconsistency Repair Mechanism for clone-and-own Code Smell Analysis: the Apo-games Case Study (Evaluation Data)

This is a repository containing the artifacts and the results of the evaluation of the solution paper "Applying an Inconsistency Repair Mechanism for clone-and-own Code Smell Analysis: the Apo-games Case Study"

Disentangling the impact of event- and annual-scale precipitation extremes on critical-zone hydrology in semiarid loess: A case study in apple tree plantation

The dataset is the basic data of the author's paper ' Disentangling the impact of event-and annual-scale precipitation extremes on critical-zone hydrology in semiarid loess - a case study in apple tree plantation '. The main content of this paper is to study the hydrological effect of extreme precipitation on the critical area of semi-arid loess. Taking apple plantation as an example, the data set includes the soil moisture and soil temperature data monitored in the field and the apple tree transpiration data. The measured data are used to calibrate and verify the model used in this paper. The water vapor flux, apple tree evapotranspiration and soil leakage data of the simulated soil profile are also included to analyze the hydrological effect of extreme precipitation on the critical area of loess.

Quantifying research interests in 7,521 mammalian species with h-index: a case study (model output)

Model results for Quantifying research interests in 7,521 mammalian species with h-index: a case study

Dataset of paper "Solar water disinfection in high-volume containers: From the laboratory to the field. A case study in Tigray, Ethiopia"

Dataset of paper "Solar water disinfection in high-volume containers: From the laboratory to the field. A case study in Tigray, Ethiopia" <ul> <li>Data of the global daily dose and average, maximum, and minimum temperatures during the year in Tigray (Ethiopia) and Almería (Spain).</li> <li>: Data of the experimental E. coli inactivation profiles under different conditions of UV radiation, water temperature, water composition and container’s volume.</li> </ul>