Find research datasets worth reusing

Aerosol indirect-effect-derived PM2.5 contributions during the development of convective clouds over the Yellow Sea in July of 2017

Meteorological processes are investigated during the development of deep convective clouds over the Yellow Sea inside a quasi-stationary rainy front in the East Asian region. WRF-Chem simulations were conducted to assess the aerosol-indirect-effect (AIE)-derived PM2.5 contributions to the cloud microphysical process in deep convective clouds and the associated precipitation. In our dataset, you can find output of WRF-Chem baseline simulations (BASE) and other sensitivity simulated outputs (CONTROL). Furthermore, model variables of precipitations, cloud top temperature (CTT), surface-level pressure (SLP), convective available potential energy (CAPE), and hydrometer mixing ratios of cloud water (qcloud), raindrops (qrain), and ice (qice) can be found in these zip files. If you have any difficulty downloading these datasets, please feel free to contact the first author, kimhsung@gmail.com. All references and acknowledgments can be found in our paper

Supplementary material of the study "Help! I need somebody. A Mapping Study about Expert Identification in Software Development"

Supplementary Material Context: Software development is a knowledge-intensive activity, and its success in an organization relies deeply on knowledge sharing. Knowledge management challenges are often increased in agile environments, which involve a lot of tacit knowledge, commonly acquired through experiences and hard to be made explicit. Therefore, knowledge sharing among practitioners is crucial. However, identifying suitable experts to share specific knowledge is not trivial. It involves not only discovering the individuals with the desired knowledge but also considering other factors that may improve the expert responsiveness, such as social connections and availability. Objective: Considering the important role experts play in knowledge sharing, we decided to investigate approaches that help identify experts that can share knowledge in software development. Our goal is to provide a panorama of the existing approaches and shine a light on research opportunities. Method: We carried out a systematic literature mapping and analyzed 17 publications. Results: The results show that most approaches have relied on code repositories as a source of evidence for identifying experts and, consequently, focus on supporting developers and aiding in the codification activity. Additionally, expert identification has been mostly automated, and factors beyond possessing the desired knowledge have often been disregarded. Conclusion: Although there are several expert identification approaches, there has been a lack of concern with factors that influence reaching the most suitable expert for a specific situation (e.g., considering the characteristics of the person seeking knowledge). Moreover, there is a need for deeper reflection on how to better explore different artifacts as sources of expert evidence and how to combine them to improve expert identification. This package contains supplementary material of the study performed to investigate approaches that help identify experts that can share knowledge in software development. It contains: <ul> <li>A spreadsheet containing raw data (research protocol, considered and selected publications, and research questions answers).</li> </ul>

Evolution of Teamwork Quality Instruments in Agile Software Development: A Systematic Literature Review

Suplemmentary Material of the article: Evolution of Teamwork Quality Instruments in Agile Software Development: A Systematic Literature Review

Phenotype images of the developing heart from wild type and Sox7 mutant mouse embryo

The cardiac endothelium influences ventricular chamber development by coordinating trabeculation and compaction. However, the endothelial-specific molecular mechanisms mediating this coordination are not fully understood. Here, we identified the Sox7 transcription factor as a critical cue instructing cardiac endothelium identity during ventricular chamber development. Endothelial-specific loss of Sox7 function in mice results in cardiac ventricular defects similar to non-compaction cardiomyopathy, with a change in the proportions of trabecular and compact cardiomyocytes in the mutant hearts. This phenotype is paralleled by abnormal coronary artery formation. Loss of Sox7 function disrupts the transcriptional regulation of the Notch pathway and connexins 37 and 40, which govern coronary arterial specification. Upon Sox7 endothelial-specific deletion, single-nuclei transcriptomics analysis identified the depletion of a subset of Sox9/Gpc3 positive endocardial progenitor cells and an increase in erythro-myeloid cell lineages. Fate mapping analysis revealed that a subset of Sox7-null endothelial cells transdifferentiate into hematopoietic but not cardiomyocyte lineages. Our findings determine that Sox7 maintains cardiac endothelial cell identity, which is crucial to the cellular cross-talk that drives ventricular compaction and coronary artery development.

Impressive pan-genomic diversity of E. coli from a wild animal community near urban development reflects human impacts

Data provided here support the findings of this study and code will allow the replication of analyses therein. To do so, first download and unzip the associated data files. For each analysis, the following files are required: PCAs: PCA.R, prokka_annotations.zip (and VirulenceFinder_results.csv for virulence factor PCA) Sankey diagram: Plasmid_AMR_Sankey.R, mlplasmids_results.zip, MOBsuite_results.zip, ResFinder_results.csv Pathotype assignment: VF_data_analysis.R, VirulenceFinder_results.csv TableS1_Ecoli_metadata.csv contains the isolate metadata (n=143) for all above analyses.

Dataset for the paper "Trends in studies developed in Europe about inclusion and diversity in schools: A systematic research projects review"

Resources for the Systematic Research Projects Review (SRPR) about European research projects on school inclusion and diversity. The SRPR is related to the project "Gamified Values Education For Fostering Migrant Integration at Schools (GAMIGRATION)" funded by Erasmus+ programme of the European Union (ref. 2021-1-ES01-KA220-SCH-000032607). Search conducted on CORDIS and Erasmus+ platform.

Supporting Data Set for Paper "Can Videos as a By-Product of GUI Testing Help Developers Understand GUI Tests?"

This data set is a supporting material for an accepted paper "Can Videos as a By-Product of GUI Testing Help Developers Understand GUI Tests?" on 2023 IEEE 31st International Requirements Engineering Conference Workshops (REW 2023). This dataset consists of <ul> <li>a consent form of the study in English;</li> <li>a tutorial video for TakeNote App (see TakeNote Tutorial-v02);</li> <li>a questionnaire in HTML format;</li> <li>used videos (in HTML Video Player with Videos and VTT files) and screenshots;</li> <li>the source code of the HTML Video Player (in HTML Video Player with Videos and VTT files);</li> <li>obtained and coded results from the questionnaire (see Study-Data-4EmpiRE-v22);</li> <li>calculation steps of the Mann-Whitney U Test;</li> <li>the source code of the TakeNote App.</li> </ul>

A Benchmark Analytical Solution for Variable Viscosity Flow in Fractured Media: Development and Comparative Analysis with Numerical Simulations

This data is associated with (a) Figure 3. Comparison between the velocities obtained through analytical calculations and those estimated numerically, and (b) Figure 4. Comparison of the BTCs obtained through analytical calculations and those estimated numerically.

Results on temperature development for 1xco2, 2xco2, and 2xch4 for Arctic and Antarctica

Results on temperature development for 1xco2, 2xco2, and 2xch4 for Arctic and Antarctica calculated by our line-by-line code, as described: Justus Notholt. (2023). Line-by-line code ILBL from 26 Aug 2022 (2022.08). Zenodo. https://doi.org/10.5281/zenodo.8168114

Reversing the great degradation of nature through economic development

We analyze past and anticipated future trends in crop yields, per capita consumption, and population to estimate agricultural land requirements globally by 2050 and 2100. Assuming "business as usual," higher-income countries are expected to show little or no net growth in cropland by the end of the century, even in the face of moderate climate change. In contrast, in lower-income countries, we project that land requirements will grow dramatically, and climate change will likely double this expansion. Although economic growth is often considered to work in opposition to conservation, accelerating economic development in lower-income countries, which would help alleviate poverty and increase standards of living, would also greatly reduce potential cropland expansion in lower-income countries, even with climate change, owing to slower population growth and improved crop yields that more than offset increased per capita consumption. Combining economic development in low-income countries with reduced consumption in high-income countries could dramatically shrink global cropland requirements by the year 2100 even with moderate climate change. Such a remarkable reduction in cropland area would have enormous benefits for both biodiversity and global climate change.

opencc-by-4.0Dec 2023View details →

Developing Kalanchoë blossfeldiana as a resource for comparatively studying C3 and crassulacean acid metabolism

Reviewer Link

Data for: Photoperiod effects in a freshwater community: amphibian larvae develop faster and zooplankton abundance increases under an early-season photoperiod

Organisms that shift their phenologies in response to global warming will experience novel photic environments, as photoperiod (daylength) continues to follow the same annual cycle. How different organisms respond to novel photoperiods could result in phenological mismatches and altered interspecific interactions. We conducted an outdoor mesocosm experiment exposing green frog (Rana clamitans) larvae, gray treefrog (Hyla versicolor) larvae, phytoplankton, periphyton, and zooplankton to a three-month shift in photoperiod: an early-season photoperiod (simulating April) and a late-season photoperiod (simulating July). We manipulated photoperiod by covering and uncovering tanks with clear or light-blocking lids to mimic realistic changes in daylength. We assessed amphibian life history traits and measured phytoplankton, periphyton, and zooplankton abundances. Green frog larvae and gray treefrog metamorphs were more developed under the early-season photoperiod. Gray treefrog total length was also reduced, but photoperiod did not affect green frog total length. Although phytoplankton and periphyton abundances were not affected by photoperiod, copepod nauplii were in greater abundance under the early-season photoperiod. Overall, this simplified aquatic community did not exhibit significant changes to structure when exposed to a three-month shift in photoperiod. Temperate amphibians that breed earlier in the year may develop faster, which may have long-term costs to post-metamorphic growth and performance. Asynchronous shifts in zooplankton abundances in response to altered photoperiods could subsequently affect freshwater community structure. While photoperiod has been shown to individually affect freshwater organisms, our study using replicated outdoor wetland communities shows that the comprehensive effects of photoperiod may be less important than other cues such as temperature and precipitation.

opencc-by-4.0May 2022View details →

Dataset underlying the paper Generating variability from motor primitives during infant locomotor development

EMG data after basic preprocessing Each file is a matrix of M colomns and S*T raws with : M = number of muscles (from m1 to m10: right Rectus Femoris, left Rectus Femoris, right Tibialis Anterior, left Tibialis Anterior, right Biceps Femoris, left Biceps Femoris, right Soleus, left Soleus, right Gluteus Medius, left Gluteus Medius). S = number of steps (specific to each file) T = number of time points per step (always equals to 200)   File names are ordered as follows: inputMat_S{subjectnumber}_C{conditionnumber}_a{agenumber}_200bins_10muscles subject number car take values between 1 and 18 condition number can take the following values: 1 for stepping on a treadmill, 2 for stepping overground, 4 for kicking and 5 for walking  age number can take the following values: 1 for around birth, 2 for around three months, 4 for around walking onset

Data for the publication: "Development and In-Vivo Validation of a Portable Phosphorescence Lifetime-Based Fiber-Optic Oxygen Sensor"

This data set contains all raw data for the publication “Development and In-Vivo Validation of a Portable Phosphorescence Lifetime-Based Fiber-Optic Oxygen Sensor”: - Raw sensor data - Python scripts - particle photon scripts - CAD Drawings - PCB Designs

opencc-by-4.0Dec 2022View details →

Assessing and managing environmental hazards of polymers: historical development, science advances and policy options

Supporting information (open data) from Assessing and managing environmental hazards of polymers: historical development, science advances and policy options

Data from: Sorghum bicolor TX08001 nodal root tissue development gene expression profiling

<div class="page"> <div class="section"> <div class="layoutArea"> <div class="column"> Bioenergy sorghum's large nodal root system enables deposition of soil organic carbon deep in soil profiles aiding production of low carbon intensity biofuels from this crop. During bioenergy sorghum's long growing season, plants produce ~175 nodal roots In review bearing lateral roots that take up water and nutrients from >2 m deep in soil profiles, and aerial roots that support a complex phyllosphere. In the current study, nodal root bud development, a slow process spanning ~40 days, was characterized using microscopy and transcriptome analysis. A first ring of 10-15 nodal root buds was initiated in the stem pulvinus of phytomer 7 near sub-epidermal vascular bundles. A second ring of buds formed above the first ring much later in phytomer development. Nascent nodal root buds from phytomer 7 exhibited relatively high expression of pericycle marker genes (PFA) and genes involved in auxin transport (ABCB19, PIN4, LAX2), cytokinin signaling (TSO, MYB3R1), and cell proliferation (CYCB2;4, CDKB2;1, REM1). Following initiation, expression of genes involved in cell proliferation and cytokinin-signaling decreased while expression of genes involved in proliferative arrest, ABA-signaling, dormancy and stress tolerance increased. Further bud development was correlated with increased expression of WOX11 and PLT5 followed by PLT2, PLT4 and genes encoding RGF peptides that regulate PLT-expression and bud development. Expression of the ARF7-regulated LBD29, a gene required for nodal root formation, increased in parallel with increasing bud size to a maximum late in NRB development. Appearance of the nodal root bud cap late in development coincided with expression of SMB and FEZ, whereas genes such as WOX5 and two MYB36 family members were expressed at higher levels in outgrowing aerial roots. Genes involved in gibberellin, brassinosteroid, strigolactone, ethylene, jasmonate, salicyclic acid, and eATP signaling showed complex patterns of expression during nodal root bud formation. Overall, this study provides a detailed description of bioenergy sorghum nodal root bud development and transcriptome information useful for molecular analysis of networks that regulate nodal root development. </div> </div> </div> </div>

opencc-zeroAug 2023View details →

Early onset of urea synthesis and ammonia detoxification pathways in three terrestrially developing frogs

Frogs evolved terrestrial development multiple times, necessitating mechanisms to avoid ammonia toxicity at early stages. Urea synthesis from ammonia is a key adaptation that reduces water dependence after metamorphosis. We tested for early expression and plasticity of enzymatic mechanisms of ammonia detoxification in three terrestrial-breeding frogs: foam-nest-dwelling larvae of Leptodactylus fragilis (Lf) and arboreal embryos of Hyalinobatrachium fleischmanni (Hf) and Agalychnis callidryas (Ac). Activity of two ornithine-urea cycle (OUC) enzymes, arginase and CPSase 1, and levels of their products urea and CP in tissues were high in Lf regardless of nest hydration but reduced in experimental low- vs. high-ammonia environments. High OUC activity in wet and dry nests, comparable to that under experimental high ammonia, suggests terrestrial Lf larvae maintain high capacity for urea excretion regardless of their immediate risk of ammonia toxicity. This may aid survival through unpredictably long waiting periods before rain enables their transition to water. Moderate levels of urea and CP were present in Hf and Ac tissues and enzymatic activities were lower than in Lf. In both species, embryos in drying clutches can hatch and enter the water early, behaviorally avoiding ammonia toxicity. Moreover, glutamine synthetase is active in early stages of all three species, condensing ammonia and glutamate to glutamine as another mechanism of detoxification. Enzyme activity appeared highest in Lf, although substrate and product levels were higher in Ac and Lf. Our results reveal that multiple biochemical mechanisms of ammonia detoxification occur in early life stages of anuran lineages that evolved terrestrial development.

opencc-by-4.0Jan 2023View details →

Development of a pipeline for analyzing the gene expression profile of transcripts

<pre>Data corresponding to the scientific initiation project in bioinformatics. </pre> <pre>The data in the parcial_report_input folder are equivalent to raw counts, metadata and data of FPKM values of genes from the analysis performed during the first six months of the project. They correspond the counts and metadata from a previous study from renal cell carcinoma. As for the Final_report_input, it also contains counts and metadata, but from a previous study of ostesarcoma. The metadata and raw data files can be found under the accesion number hs000699.v1.p1 in dbGAP. The scripts wrote to perform pre-processing of samples, differential expression analysis, network analysis and functional annotation can be found in <a href="https://github.com/meidanis-lab/trans-pipeline">GitHub repository</a>. </pre>

opencc-by-4.0Aug 2023View details →

GERDAT021-Dataset for "Development and testing of the Outcome Prioritization Tool adjusted to older patients with cancer: A pilot study"

This dataset shows the data underlying the publication "Development and testing of the Outcome Prioritization Tool adjusted to older patients with cancer: A pilot study published in JGO on 21 July 2023, which can be found at <a href="https://doi.org/10.1016/j.jgo.2023.101590">10.1016/j.jgo.2023.101590</a>."