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282 results for “data engineering”
Data from: Shrubs as ecosystem engineers across an environmental gradient: effects on species richness and exotic plant invasion
Ecosystem-engineering plants modify the physical environment and can increase species diversity and exotic species invasion. At the individual level, the effects of ecosystem engineers on other plants often become more positive in stressful environments. In this study, we investigated whether the community-level effects of ecosystem engineers also become stronger in more stressful environments. Using comparative and experimental approaches, we assessed the ability of a native shrub (Ericameria ericoides) to act as an ecosystem engineer across a stress gradient in a coastal dune in northern California, USA. We found increased coarse organic matter and lower wind speeds within shrub patches. Growth of a dominant invasive grass (Bromus diandrus) was facilitated both by aboveground shrub biomass and by growing in soil taken from shrub patches. Experimental removal of shrubs negatively affected species most associated with shrubs and positively affected species most often found outside of shrubs. Counter to the stress-gradient hypothesis, the effects of shrubs on the physical environment and individual plant growth did not increase across the established stress gradient at this site. At the community level, shrub patches increased beta diversity, and contained greater rarified richness and exotic plant cover than shrub-free patches. Shrub effects on rarified richness increased with environmental stress, but effects on exotic cover and beta diversity did not. Our study provides evidence for the community-level effects of shrubs as ecosystem engineers in this system, but shows that these effects do not necessarily become stronger in more stressful environments.
Data from: Engineering ER-stress dependent non-conventional mRNA splicing
The endoplasmic reticulum (ER) protein folding capacity is balanced with the protein folding burden to prevent accumulation of un- or misfolded proteins. The ER membrane-resident kinase/RNase Ire1 maintains ER protein homeostasis through two fundamentally distinct processes. First, Ire1 can initiate a transcriptional response through a non-conventional mRNA splicing reaction to increase the ER folding capacity. Second, Ire1 can decrease the ER folding burden through selective mRNA decay. In Saccharomyces cerevisiae and Schizosaccharomyces pombe, the two Ire1 functions have been evolutionarily separated. Here, we show that the respective Ire1 orthologs have become specialized for their functional outputs by divergence of their RNase specificities. In addition, RNA structural features separate the splicing substrates from the decay substrates. Using these insights, we engineered an S. pombe Ire1 cleavage substrate into a splicing substrate, which confers S. pombe with both Ire1 functional outputs.
Data from: Mammalian engineers drive soil microbial communities and ecosystem functions across a disturbance gradient
The effects of mammalian ecosystem engineers on soil microbial communities and ecosystem functions in terrestrial ecosystems are poorly known. Disturbance from livestock has been widely reported to reduce soil function, but disturbance by animals that forage in the soil may partially offset these negative effects of livestock, directly and/or indirectly by shifting the composition and diversity of soil microbial communities. Understanding the role of disturbance from livestock and ecosystem engineers in driving soil microbes and functions is essential for formulating sustainable ecosystem management and conservation policies. We compared soil bacterial community composition and enzyme concentrations within four microsites: foraging pits of two vertebrates, the indigenous short-beaked echidna (Tachyglossus aculeatus) and the exotic European rabbit (Oryctolagus cuniculus), and surface and subsurface soils along a gradient in grazing-induced disturbance in an arid woodland. Microbial community composition varied little across the disturbance gradient, but there were substantial differences among the four microsites. Echidna pits supported a lower relative abundance of Acidobacteria and Cyanobacteria, but a higher relative abundance of Proteobacteria than rabbit pits and surface microsites. Moreover, these microsite differences varied with disturbance. Rabbit pits had a similar profile to the subsoil or the surface soils under moderate and high, but not low disturbance. Overall, echidna foraging pits had the greatest positive effect on function, assessed as mean enzyme concentrations, but rabbits had the least. The positive effects of echidna foraging on function were indirectly driven via microbial community composition. In particular, increasing activity was positively associated with increasing relative abundance of Proteobacteria, but decreasing Acidobacteria. Our study suggests that soil disturbance by animals may offset, to some degree, the oft-reported negative effects of grazing-induced disturbance on soil function. Further, our results suggest that most of this effect will be derived from echidnas, with little positive effects due to rabbits. Activities that enhance the habitat for echidnas or reduce rabbit populations are likely to have a positive effect on soil function in these systems.
Data from: Are Cecropia trees ecosystem engineers? The effect of decomposing Cecropia leaves on arthropod communities
Ecosystem engineers structure species richness and the composition of biological communities. Although several studies have uncovered the importance of engineering environments, few studies have evaluated the effect of pioneering plants as ecosystem engineers, especially in tropical environments. When dead, Cecropia leaves become architecturally complex, acquiring a tridimensional shape due to desiccation, and may facilitate other organisms. Here we evaluate the role of these dead leaves in structuring species richness, abundance, biomass, and composition of macroinvertebrate communities on leaf litter in six protected areas of Brazilian Atlantic Rainforest. Predators were larger, more abundant, and presented higher standing stock in the presence of dead Cecropia leaves compared to soil debris (i.e., common leaf litter); however, detritivores had the opposite patterns. This resulted in shifts in body size structure of the assemblage, thus causing inversion of biomass pyramids to top-heavy in advanced stages of Cecropia leaves desiccation. Dead Cecropia leaves did not influence species richness and abundance of species, but they influenced the biomass of detritivores and predators in the communities. Our results demonstrated that pioneer trees can act as ecosystem engineers, by facilitating communities of invertebrate predators. In addition, our results suggest that the presence of Cecropia leaves can mediate trophic interactions and shape food web structure on the forest floor.
Structural Data for the Antibody Developability Manuscript: Cartography of Developability Landscapes in Native and Human-Engineered Antibodies
<p>Here is the additional structural data (predicted models and MD trajectories) for the "Cartography of the Developability Landscapes of Native and Human-Engineered Antibodies" manuscript. Please cite our paper when referring to and using this data. If you have any questions, please contact Eva Smorodina at ribes.ev@gmail.com. Thank you!</p>
Data for: Engineering A-type Dye-decolorizing Peroxidases by Modification of a Conserved Glutamate Residue
<p><span>Dye-decolorizing peroxidases (DyPs) are recently identified microbial enzymes that have been used in several Biotechnology applications from wastewater treatment to lignin valorization. However, their properties and mechanism of action still have many open questions. Their heme-containing active site is buried by three conserved flexible loops with a putative role in modulating substrate access and enzyme catalysis. Here, we investigated the role of a conserved glutamate residue in stabilizing interactions in loop 2 of A-type DyPs. First, we did site saturation mutagenesis of this residue, replacing it with all possible amino acids in bacterial DyPs from Bacillus subtilis (BsDyP) and from Kitasatospora aureofaciens (KaDyP1), the latter being characterized here for the first time. We screened the resulting libraries of variants for activity towards ABTS and identified variants with increased catalytic efficiency. The selected variants were purified and characterized for activity and stability. We furthermore used Molecular Dynamics simulations to rationalize the increased catalytic efficiency and found that the main reason is the electron channeling becoming easier from surface-exposed tryptophans. Based on our findings, we also propose that this glutamate could work as a pH switch in the wild-type enzyme, preventing intracellular damage. </span></p>
Open Data Package: Lessons Learned from Developing a Sustainability Awareness Framework for Software Engineering Using Design Science.
<p>Open Data Package for the paper: Stefanie Betz, Birgit Penzenstadler, Leticia Duboc, Ruzanna Chitchyan, Sedef Akinli Kocak, Ian Brooks, Shola Oyedeji, Jari Porras, Norbert Seyff, and Colin C. Venters. 2024. Lessons Learned from Developing a Sustainability Awareness Framework for Software Engineering Using Design Science. ACM Trans. Softw. Eng. Methodol. 24 00, JA, Article 00 (March 2024), 39 pages. https://doi.org/10.1145/3649597 25</p>
Linkage of hospital records and death certificates by a search engine and machine learning: training and test set data
<p>INTRODUCTION: Vital status is of central importance to hospital clinical research. However, hospital information systems record only in-hospital death information. Recently, the French government released a publicly available dataset containing death-certificate data for over 25 million individuals. The objective of this study was to link French death certificates to the Bordeaux University Hospital records to complete the vital status information.</p> <p>MATERIALS AND METHODS: Our linkage strategy was composed of a search engine to reduce the number of comparisons and machine-learning algorithms. The overall pipeline was evaluated by assembling a file containing 3,565 in-hospital deaths and 15,000 alive persons.</p> <p>RESULTS: The recall and precision of our linkage strategy were 97.5% and 99.97% for the upper threshold and 99.4% and 98.9% for the lower threshold, respectively.</p> <p>CONCLUSION: In this article, we demonstrated the feasibility of accurately linking hospital records with death certificates using a search engine and machine learning.</p>
[Research Data] Mining Relevant Solutions for Programming Tasks from Search Engine Results
<p>[Abstract]</p> <p>Software development is a knowledge-intensive activity. Official documentation for developers may not be sufficient for all developer needs. Searching for information on the Internet is a usual practice, but finding really useful information may be challenging, because the best solutions are not always among the first ranked pages. So, developers have to read and discard irrelevant pages, that is, pages that do not have code examples or that have content with little focus on the desired solution. This work aims at proposing an approach to mine relevant solutions for programming tasks from search engine results that remove irrelevant pages. The approach works as follows: a query related to the programming task is prepared, and given as an input to a search engine. The returned pages pass through an automatic filter to select relevant pages. We evaluated the top-20 pages returned by the Google search engine, for 10 different queries, and observed that only 31\% of the evaluated pages are relevant to developers. Then, we proposed and evaluated three different approaches to mine the relevant pages returned by the search engine. Google’s search engine has been used as a baseline, and our results have shown that Google’s search engine returns a reasonable number of irrelevant pages for developers, and we could find an effective approach to remove irrelevant pages, suggesting that developers could benefit from a customized web search filter for development content.</p> <p>[Contents of Research Data.rar file]</p> <p>The Research Data.rar file has a folder called Research Data that contains 3 folders internally, with the names: “01 – Source Code”, “02 - Data” and “03 – Preprocessing rules”. The folder “01 – Source Code” contains the JAVA source code of the implementations of the proposed approaches. The folder “02 - Data” contains the data of the evaluations carried out in the work, which are in the folders “01 - Evaluation results of pages returned by Google” and “02 - Results of approaches comparisons”. The folder “01 - Evaluation results of pages returned by Google” has the evaluations carried out on the first 20 pages returned by Google, following the criteria defined in the work, for the 10 queries considered in the evaluation. The folder “02 - Results of approaches comparisons” contains the results of the evaluation of the proposed approaches, for the 10 queries considered in the evaluation. In this evaluation, the number of pages given as input for the approaches was increased from 3 to 20 pages, for each number of pages a folder was generated with the results. In addition to the results of the Precision, Recall and F-Measure metrics that are in the file named Results Approaches.txt, other files were generated for analysis. For example, the Instances_without_outliers.txt file shows which pages were filtered out after applying the outlier page removal filter. The Selected Pages Approach 4.txt file, on the other hand, shows which pages were filtered after applying the filters of the GORCUO approach. The folder “03 - Preprocessing rules” has a file called Rules.java. In this file, there is the commented JAVA source code, from the implementation of the rules created in the pre-processing stage of the proposed approach.</p>
Raw and preprocessed data on the explosions of crankcases in marine main propulsion engines (1972-2018)
<table> <tbody> <tr> <td>Document title:</td> <td>Raw and preprocessed data on the explosions of crankcases in marine main propulsion engines (1972-2018)</td> </tr> <tr> <td>Author:</td> <td>Leszek Chybowski</td> </tr> <tr> <td>e-mail:</td> <td><a href="mailto:l.chybowski@am.szczecin.pl">l.chybowski@am.szczecin.pl</a></td> </tr> <tr> <td> </td> <td> </td> </tr> <tr> <td>Affiliation: </td> <td>Maritime University of Szczecin, Szczecin, Poland</td> </tr> <tr> <td>City:</td> <td>Szczecin, Poland</td> </tr> <tr> <td>Year:</td> <td>2022</td> </tr> <tr> <td> </td> <td> </td> </tr> <tr> <td>Grant:</td> <td>The research was prepared under Grant 1/S/KPBMIM/22 financed by the Ministry of Science and Higher Education of Poland.</td> </tr> <tr> <td> </td> <td> </td> </tr> <tr> <td>Licence:</td> <td>CC BY-NC 2.0</td> </tr> </tbody> </table>
Raw Data of the Survey on the Practitioners' Perspectives towards Requirements Engineering
<p>Here, we present the necessary files for our survey conducted among practitioners from diverse profiles with the purpose of understanding practitioners' perspectives towards the requirements engineering.</p>
Data set to Remote sensing-supported mapping of the activity of a subterranean landscape engineer across an afro-alpine ecosystem
<p>This data set is part of the article Wraase et al. (2022): Remote sensing -supported mapping of the activity of a subterranean landscape engineer across an afro-alpine ecosystem. Remote sensing in Ecology and Conservation. (https://doi.org/10.1002/RSE2.303)</p> <p>The repository contains a Readme file ("readme.txt") and two additional folders labeled: “input data” and “script”.<br> <br> The first folder contains 13 data files further divided into three subfolders “cca_analysis”, “main_modelling_prc_texture_idx” and “vectors”. Data formats are .csv format for all tables, .rds files for model objects from R and .shp format for all vector data.</p> <p>The second folder contains all 31 R-scripts necessary to do the analysis, as described in the article. Additionally, the folder is further categorized into five subfolders equivalent to the main analysis operations: “cca_analysis”, “landsat_temp_modelling”, “main_modelling_prc”, “maxent” and “texture_idx”.</p>
A flexible operation-based infrastructure for collaborative model-driven engineering (Evaluation Data)
<p>Repository containing the UML models used in the evaluation of the paper entitled: "A flexible operation-based infrastructure for collaborative model-driven engineering" submitted to ECMFA 2023.</p>
Fulfilling Industrial Needs for Consistency Among Engineering Artifacts - Evaluation Data
<p>This is a dataset with the evaluation data from the paper entitled "Fulfilling Industrial Needs for Consistency Among Engineering Artifacts". The dataset also contains two demo videos showing the approach being used in practice.</p>
A translation-independent directed evolution strategy to engineer aminoacyl-tRNA synthetases_NGS data analysis
<p>These data files are associated with the NGS analysis done in the publication :"A translation-independent directed evolution strategy to engineer aminoacyl-tRNA synthetases". This compressed file contains the raw file as well as the processed files to arrive at the conclusions published. The python scripts used for processing the data are available on github (link provided in the manuscript).</p>
Data from: Ecosystem engineers shape ecological network structure and stability: a framework and literature review
<p>Ecosystem engineering is a ubiquitous process where species influence the physical environment and thereby structure ecological communities. However, there has been little effort to synthesise or predict how ecosystem engineering may impact the structure and stability of interaction networks. To assess the current scientific understanding of ecosystem engineering impacts via habitat forming, habitat modification, and bioturbation on interaction networks/food webs, we reviewed the literature covering marine, freshwater, and terrestrial food webs, plant-pollinator networks, and theory. We provide a conceptual framework and identify three major pathways of engineering impact on networks through changes in resource availability and energy flow, habitat heterogeneity, and environmental filtering. These three processes often work in concert and most studies report that engineering increases species richness. This is particularly marked for engineers that increase habitat heterogeneity and thereby the number of available niches. The response of network structure to ecosystem engineering varies, however some patterns emerge from this review. Engineered habitat heterogeneity leads to a higher number of links between species in the networks and increases link density. Connectance can be negatively or positively affected by ecosystem engineer impact, depending on the engineering pathway and the engineer impact of species richness. We discuss how ecosystem engineers can stabilize or destabilize communities through the changes in niche space, diversity, network structure, and the dependency on the engineering impact. Theory and empirical evidence need to inform each other to better integrate ecosystem engineering and ecological networks. A mechanistic understanding how ecosystem engineering traits shape interactions networks and their stability will be important to predict species extinctions and can provide crucial information for conservation and ecosystem restoration.</p>
Nanoscale engineering and dynamical stabilization of mesoscopic spin textures - Experimental Data
<p>Experimental data for "Nanoscale engineering and dynamical stabilization of mesoscopic spin textures".</p> <p>Data is organized by figure in which it is discussed. Filenames are organized by date/timestamp collected. Figures composed of multiple, separately taken datasets have been uploaded into separate folders, organized by subfigure or other identifier.</p> <p>All datasets are matlab (.m) filetype. Each contains three column vectors; the signal and phase of the FFT of readout, and the time at which the readout was performed.</p>
The input data of the multi-patch geometries used in: M. Kapl, A. Kosmač, V. Vitrih, Isogeometric collocation for solving the biharmonic equation over planar multi-patch domains, Computer Methods in Applied Mechanics and Engineering 424 (2024) 116882; DOI: 10.1016/j.cma.2024.116882
Open the record for dataset details and reuse information.
FASTQ Data for: A Primordial DNA Store and Compute Engine
<p>Raw FASTQ data generated for the evaluation of the publication "A Primordial DNA Store and Compute Engine" to appear in Nature Nanotechnology.</p> <p> </p> <p>Please contact ajkeung@ncsu.edu regarding queries on the data set.</p>
Data from: Contextualizing the 2019–2020 Kangaroo Island Bushfires: Quantifying Landscape-Level Influences on Past Severity and Recovery with Landsat and Google Earth Engine
<p><strong>Paper Abstract:</strong></p> <p>The 2019–2020 Kangaroo Island bushfires in South Australia burned almost half of the island. To understand how to avoid future severe ‘mega-fires’ and how vegetation may recover from 2019–2020, we can utilize information from the bulk of historical fires in an area. Landsat time-series of vegetation change provide this opportunity, but there has been little analysis of large numbers of fires to build a landscape-level understanding and quantify drivers in an Australian context. In this study, we built a yearly cloud-free surface reflectance normalized burn ratio (NBR) time-series (1988–2020) using all available summer Landsat images over Kangaroo Island. Data were collected in Google Earth Engine and fitted with LandTrendr. Burn severity and post-fire recovery were quantified for 47 fires, with a new recovery metric facilitating comparison where fire frequency is high. Variables representing the current burn, fire history, vegetation structure, and topography were related to severity and yearly recovery with random forest and bivariate analysis. Results show that the 2019–2020 bushfires were the most widespread and severe, followed by 2007–2008. Vegetation recovers quickly, with NBR stabilizing ten years post-fire on average. Severity is most influenced by fire frequency, vegetation capacity and land use with more severe burns in nature conservation areas with dense vegetation and a history of frequent fires. Influence on recovery varied with time since fire, with initial (year 1–3) faster recovery observed in areas with less surviving vegetation. Later (year 6–10) recovery was most influenced by a variable representing burn year and further investigation indicates that precipitation increases in later post-fire years likely facilitated faster recovery. The relative abundance of eucalypt woodlands also has a positive influence on recovery in middle and later years. These results provide valuable information to land managers on Kangaroo Island and in similar environments, who should consider adjusting practices to limit future mega-fire risk and potential ecosystem shifts if severe fires become more frequent with climate change.</p> <p> </p> <p><strong>Data details:</strong></p> <p>See paper: <a href="https://www.mdpi.com/2072-4292/12/23/3942">Remote Sensing | Free Full-Text | Contextualizing the 2019–2020 Kangaroo Island Bushfires: Quantifying Landscape-Level Influences on Past Severity and Recovery with Landsat and Google Earth Engine (mdpi.com)</a></p> <p>See code on GitHub: <a href="https://github.com/ZZMitch/KangarooIslandFireHistory_1988to2020">ZZMitch/KangarooIslandFireHistory_1988to2020: Code from "Contextualizing the 2019–2020 Kangaroo Island Bushfires: Quantifying Landscape-Level Influences on Past Severity and Recovery with Landsat and Google Earth Engine" (RS, 2020) (github.com)</a></p> <p> </p> <p><strong>If you use these data, please reference: </strong></p> <p>Bonney, M.T., He, Y., Myint, S.W., 2020. Contextualizing the 2019–2020 Kangaroo Island bushfires: Quantifying landscape-level influences on past severity and recovery with Landsat and Google Earth Engine. Remote Sensing 12(23), <a href="https://doi.org/10.3390/rs12233942" rel="nofollow">https://doi.org/10.3390/rs12233942</a>.</p>
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.