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4,694 results for “data analysis”
Data for: Raman microspectroscopy and laser-induced breakdown spectroscopy for the analysis of polyethylene microplastics in human soft tissues
<p>Data from Raman microspectrometry, LIBS, XRF, and particle sizer analysis supports the findings in the published article named Raman microspectroscopy and laser-induced breakdown spectroscopy to analyze polyethylene microplastics in human soft tissues. The aim of this research is to present the optimized protocol for the detection and analysis of microplastics in biological samples.</p> <p><strong> </strong></p> <p>The tonsil tissue is used for this experiment, and the workflow consists of a few steps: 1. digestion, 2. filtration, 3. analysis. </p> <p>The presented dataset includes the data for verifying the validity of this proposed protocol and the data from clinical experiments done on tonsils where the protocol is applied. We are focusing only on PE microplastics as they are one of the most frequent plastic types in the environment. </p> <p>Firstly, the data from the particle sizer show the size distribution before and after KOH treatment, which is necessary for digestion. We are testing if the particles are not affected by the KOH solution. The data are listed in an Excel sheet where the individual detected PE particle size [µm] and their frequencies [%] are annotated. The data are separated into 2 tables in one sheet - 1st represents data collected before KOH and the 2nd after KOH treatment. </p> <p>To test the limits of our selected systems for microplastic detection, we included the data from Raman and LIBS under the file ‘limitations.’ The different sizes of PE particles, from tens to 1 µm, were analyzed, and the spectra can be retrieved in the folders. The signal intensity can be observed to see the detection limits. For the Raman analysis, the particles were located on the filter. For LIBS, the particles were embedded in epoxy to enable the detection of PE particles in tens of microns. The Raman data are in .txt files and can be opened in any adequate software (Matlab, R, Python, etc.). LIBS data are in specific .libsdata format, which can be opened by LibsAnalyzer software by Lightigo. </p> <p><strong> </strong></p> <p>The clinical experiment was done on tonsil tissue. The tissue was disgusted and filtered. Then, the filters were analyzed. The dataset presents two sample groups: 1. control-native tissue and 2. test-spiked tissue with PE particles. The data from Raman analysis include both, with the aim to confirm the presence of PE particles in the test sample and to exclude the contamination in the control sample. The spectra are again in .txt files. In the case of control, spectra from unclassified particles are presented. For these reasons, the LIBS and XRF were run to exclude the possibility of the presence of polymeric material on the filter of the control sample. The analyzed chemical elements by LIBS for both samples are in the ASC file. Furthermore, individual PE particles were also analyzed on LIBS to obtain reference results for test samples with added PE microplastics. In the case of XRF, data from the empty filter, control, and test samples are included, each in a .txt file. Individual detected chemical elements and their intensities can be retrieved in the tables. </p> <p> </p>
Data and code for: Nonlinear life table response analysis: Decomposing nonlinear and nonadditive population growth responses to changes in environmental drivers
<p>Life table response experiments (LTREs) decompose differences in population growth rate between environments into separate contributions from each underlying demographic rate. However, most LTRE analyses make the unrealistic assumption that the relationships between demographic rates and environmental drivers are linear and independent, which may result in diminished accuracy when these assumptions are violated. In this study, we compare the relative efficacy of linear and second-order LTRE analyses in capturing changes in population growth rate caused by environmental driver changes. To explore this question, we analyze demographic data collected for three long-lived plant species: <em>Ardisia escallonioides</em> (Pascarella & Horvitz, 1998), <em>Silene acaulis</em>, and <em>Bistorta vivipara</em> (Doak & Morris, 2010). This repository includes data files containing vital rate (survival, growth, reproduction) observations or models for our three case studies, as well as an R script in which we use these demographic data to calculate linear and second-order LTRE approximations of changes in population growth rate for each system and generate the figures we present in our paper.</p>
Data from: Revised evolutionary and taxonomic synthesis for parrots (order: Psittaciformes) guided by phylogenomic analysis
<p>Parrots (Order: Psittaciformes) are a diverse clade that are easily distinguishable from other birds. Despite the clear characters that define the Psittaciformes (hooked bills, zygodactylous feet, and plumage that is often predominantly green or red), relative morphological uniformity among parrots has made taxonomic classification a fraught endeavor for over a century. Parrot systematics were propelled forward when DNA sequencing data shed insights into higher- and species-level relationships. However, despite these significant advances, major gaps in taxon sampling and uncertainty in relationships remained due to inferring phylogenetic relationships with short fragments of DNA. Recent work using genome-wide molecular markers with nearly complete parrot species-level sampling has brought clarity to many of the remaining outstanding questions on taxonomic relationships. Here, we build on this work by including four additional species to present a taxonomic revision of Psittaciformes better aligned with its evolutionary tree. We infer maximum likelihood and time-calibrated phylogenies for parrots, present accounts for 106 genera, compare how our findings relate to previous work, and highlight future areas of research. The family-group nomenclature we propose reflects deep evolutionary divergences with diagnosable synapomorphies that are commensurate across comparable ranks in psittaciform clades. We erect three new family-group names at the rank of tribe (Brotogerini Smith, Thom and Joseph, 2024; Neophemini Schodde, Smith, Thom and Joseph, 2024; Bolbopsittacini Smith, Thom and Joseph, 2024). We elevate one tribe to subfamily rank for the cacatuid genus <em>Probosciger</em> and we restrict usage of the recently introduced tribe Touitini to its type-genus <em>Touit</em>. At shallower taxonomic scales, recognition of more rather than fewer genera addresses issues of paraphyly or high discordance in morphological and genomic characters at those levels. We support many reinstatements of older generic names advocated in recent decades and we further reinstate five valid, available generic names not widely used in recent literature if at all (<em>Licmetis</em>, <em>Gymnopsittacus</em>, <em>Clarkona</em>, <em>Suavipsitta</em>, <em>Cardeos</em>). We advocate the retention of <em>Vini</em> Lesson, 1833 over <em>Coriphilus</em> Wagler, 1832 based on preliminary examination showing substantially more frequent usage of the former. We redraw generic limits in some other cases (e.g., <em>Bolborhynchus</em> parrotlets and allies) and this includes recognizing fewer genera than recently proposed for the <em>Psittacula</em> <em>sensu lato</em> ringneck parakeets. Our revised classification of parrots addresses many longstanding taxonomic questions including those that have arisen through the acquisition of genetic data. It provides context for the temporal origins of psittaciform clades and the taxonomic and phenotypic diversification throughout their evolutionary history. We hope that it will be a benchmark guiding further taxonomic study as well as for downstream analyses in many other fields.</p>
Data from: Coral hypoxia response curve analysis
<p>Oxygen (O<sub>2</sub>) availability is essential for healthy coral reef functioning, yet how continued loss of dissolved O<sub>2</sub> via ocean deoxygenation impacts performance of reef building corals remains unclear. Here we examine how intra-colony spatial geometry of important Great Barrier Reef (GBR) coral species <em>Acropora</em> may influence variation in hypoxic thresholds for upregulation, to better understand capacity to tolerate future reductions in O<sub>2</sub> availability. We first evaluate application of more streamlined models used to parameterise Hypoxia Response Curve data, models that have been used historically to identify variable oxyregulatory capacity. Using closed-system respirometry to analyse O<sub>2</sub> drawdown rate, we show that a 2-parameter model returns similar outputs as previous 12<sup>th</sup> order models for descriptive statistics such as the average oxyregulation capacity (T<sub>pos</sub>) and the ambient O<sub>2</sub> level at which the coral exerts maximum regulation effort (P<sub>cmax</sub>), for diverse <em>Acropora</em> species<em>. </em>Following an experiment to evaluate whether stress induced by coral fragmentation for respirometry affected O<sub>2</sub> drawdown rate, we subsequently identify differences in hypoxic response for the interior and exterior colony locations for the species <em>Acropora abrotanoides</em>, <em>Acropora cf. microphthalma</em>, and <em>Acropora elseyi</em>. Average regulation capacity across species was greater (0.78 to 1.03 ± SE 0.08) at the colony interior compared to exterior (0.60 to 0.85 ± SE 0.08). Moreover, P<sub>cmax</sub> occurred at relatively low <em>p</em>O<sub>2</sub> of <30% (± 1.24; SE) air saturation for all species, across the colony. When compared against ambient O<sub>2</sub> availability, these factors corresponded to differences in mean intra-colony oxyregulation, suggesting that lower variation in dissolved O<sub>2</sub> corresponds with higher capacity for oxyregulation. Collectively our data shows that intra-colony spatial variation affects coral oxyregulation hypoxic thresholds, potentially driving differences in <em>Acropora </em>oxyregulatory capacity.</p>
Figure 4. Results from the phylogenetic analysis using discrete data only. A in Exploring phylogenetic relationships of Pteraspidiformes heterostracans (stem-gnathostomes) using continuous and discrete characters
Figure 4. Results from the phylogenetic analysis using discrete data only. A, strict consensus of 275 most parsimonious trees with equal character weights; length 276 steps, consistency index (CI) = 0.35, retention index (RI) = 0.59, and rescaled consistency index (RC) = 0.22. B, strict consensus of four most parsimonious trees with implied character weighting (k = 3) (tree length 23.11). Psammosteidae taxa in bold.
Data from: "Rare earth elements sediment analysis tracing anthropogenic activities in the stratigraphic sequence of Alagankulam (India)"
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Data from: Metabarcoding analysis provides insight into the link between prey and plant intake in a large alpine cat carnivore, the snow leopard
<p>Species of the family Felidae (a group represented by cats) are thought to be obligate carnivores, specialized for hunting and consuming other animals. However, the detection of plants in the feces of felids raises questions about the role of plants in their diet. This is particularly true for the snow leopard (Panthera uncia), a big cat native to central and South Asia's high mountains. Our study aimed to comprehensively identify the prey and plants consumed by snow leopards as well as six other sympatric mammals. We applied DNA metabarcoding methods on 126 fecal samples collected from the Sarychat-Ertash Nature Reserve in Kyrgyzstan. We found that among the three most common plant families in snow leopard feces, Tamaricaceae (genus Myricaraia) was consumed often by snow leopards. The genus Myricaria frequently appeared in samples lacking any animal prey DNA, indicating that snow leopards might have consumed this plant especially when their digestive tracts were empty. We also observed a significant difference in plant composition between male and female snow leopards, and potentially between sampling seasons. We provide a comprehensive overview of the prey and plants detected in the feces of snow leopards and sympatric mammals. We believe our findings will help in formulating hypotheses and guiding future research to understand the adaptive significance of plant-eating behavior in felids and animal-plant relationships in the ecosystem.</p>
Data from: Transcriptome analysis of apical meristem enriched bud samples for size dependent flowering commitment in Crocus sativus reveal role of sugar and auxin signalling
<p><strong>Background</strong></p> <p>Cultivation of <em>Crocus sativus</em> (saffron) faces challenges due to inconsistent flowering patterns and variations in yield. Flowering takes place in a graded way with smaller corms unable to produce flowers. Enhancing the productivity requires a comprehensive understanding of the underlying genetic mechanisms that govern this size based flowering initiation and commitment. Therefore, samples enriched with non-flowering and flowering apical buds from small (<6g) and large (>14g) corms were sequenced. </p> <p><strong>Methods and Results</strong></p> <p>Apical bud enriched samples from small and large corms were collected immediately after break of dormancy in July. RNA sequencing was performed using Illumina Novaseq 6000. <em>De-novo</em> transcriptome assembly and analysis using flowering committed buds from large corms at post-dormancy and their comparison with vegetative shoot primordia from small corms pointed out the major role of Auxin and ABA hormonal regulation. Many genes with known dual responses in flowering development and circadian rhythm like Flowering locus T and Cryptochrome 1 along with a transcript showing homology with small auxin upregulated RNA (SAUR) exhibited induced expression in flowering buds. Thorough prediction of <em>Crocus sativus</em> non-coding RNA repertoire has been carried out for the first time. Enolase was found to be acting as a major hub with protein-protein interaction analysis using Arabidopsis counterparts.</p> <p><strong>Conclusion</strong></p> <p>Transcripts belong to key pathways including phenylpropanoid biosynthesis, hormone signaling and carbon metabolism were found significantly modulated. KEGG assessment and protein-protein interaction analysis confirm the expression data. Findings unravel the genetic determinants driving the size-dependent flowering in <em>Crocus sativus</em>.</p>
Post‐processed data and analysis codes for the research "Significant reduction of potential exposure to extreme marine heatwaves by achieving carbon neutrality"
<p>[Earth's Future] Oh et al. "Significant reduction of potential exposure to extreme marine heatwaves by achieving carbon neutrality"</p> <p>1. Information for Raw datasets<br>- The data of eight global climate models from the Coupled Model Intercomparison Project Phase 6 (CMIP6) can be accessed at https://esgf-node.llnl.gov/search/cmip6/, <br> and can also be accessed in Eyring et al. (2016). <br>- The NOAA OISST high resolution dataset can be obtained in Reynolds et al. (2007) or via https://psl.noaa.gov/data/gridded/data.noaa.oisst.v2.highres.html. <br>- The five ocean mask dataset can be obtained from https://reccap2-ocean.github.io/regions/. </p> <p>2. Information for Software<br>- The raw data in this study were analyzed using Fortran 90, R version 4.0.3, and Grads version 2.2.1.<br>- The Fortran 90 can be accessed at https://www.intel.com/content/www/us/en/developer/articles/tool/oneapi-standalone-components.html#fortran. <br>- The R version 4.0.3 is available from https://cran.r-project.org/bin/windows/base/old/4.0.3/. <br>- The Grads version 2.2.1 can be downloaded from http://cola.gmu.edu/grads/downloads.php.</p> <p>3. Information for Post-Processed data and Codes used in this work.<br>Please find each folder and the relevant post-processed dataset and codes.</p>
IMDb Film & Series Data Analysis
<p><span>El conjunto de datos para este proyecto contendrá los siguientes descriptivos sobre películas y series de IMDb, lo que permitirá analizar las distintas tendencias en la industria: <em>Title, Year, Genres, Directors, Actors, Rating, Reviews, Duration, Type, Episode, Season, Budget, Revenue</em>. Estos campos creo que son lo suficientemente descriptivos como para permitirnos un análisis en profundidad de las películas, series, actores, directores, etc. a lo largo del tiempo.</span></p> <p><span><span>·<span> </span></span></span><strong><em><span>Title:</span></em></strong><span> El título de la película o serie.</span></p> <p><span><span>·<span> </span></span></span><strong><em><span>Year:</span></em></strong><span> El año en que se lanzó la película o serie.</span></p> <p><span><span>·<span> </span></span></span><strong><em><span>Genres:</span></em></strong><span> El género de la película o serie (por ejemplo, drama, comedia, acción, etc.).</span></p> <p><span><span>·<span> </span></span></span><strong><em><span>Directors:</span></em></strong><span> El director de la película o serie.</span></p> <p><span><span>·<span> </span></span></span><strong><em><span>Actors:</span></em></strong><span> Los actores principales de la película o serie.</span></p> <p><span><span>·<span> </span></span></span><strong><em><span>Rating:</span></em></strong><span> La calificación de la película o serie en IMDb.</span></p> <p><span><span>·<span> </span></span></span><strong><em><span>Reviews:</span></em></strong><span> El número de reseñas de usuarios para la película o serie.</span></p> <p><span><span>·<span> </span></span></span><strong><em><span>Duration:</span></em></strong><span> La duración de la película o serie en minutos.</span></p> <p><span><span>·<span> </span></span></span><strong><em><span>Type:</span></em></strong><span> Si es una película o serie.</span></p> <p><span><span>·<span> </span></span></span><strong><em><span>Episode:</span></em></strong><span> El número de episodios si es una serie.</span></p> <p><span><span>·<span> </span></span></span><strong><em><span>Season:</span></em></strong><span> El número de temporadas si es una serie.</span></p> <p><span><span>·<span> </span></span></span><strong><em><span>Budget:</span></em></strong><span> El presupuesto de la película o serie.</span></p> <p><span><span>·<span> </span></span></span><strong><em><span>Revenue:</span></em></strong><span> La recaudación de la película o serie.</span></p> <p><span>Los datos del conjunto abarcan un periodo de tiempo que se extiende desde el lanzamiento de IMDb en octubre de 1990 hasta el presente mes de abril de 2024.</span></p>
Forest gap dynamics with repeat lidar in Berchtesgaden National Park - Data and analysis scripts
<p>This repository holds data and code for the paper: Krüger, K., Senf, C., Jucker, T., Pflugmacher, D., Seidl, R. (2024). Gap expansion is the dominant driver of canopy openings in a temperate mountain forest landscape. Journal of Ecology. <span><a href="http://doi.org/10.1111/1365-2745.14320">http://doi.org/10.1111/1365-2745.14320</a> </span></p> <p><strong>NOTE:</strong> This is a static repository, but the project might evolve. See the connected GitHub repository for latest updates!</p> <p>All data to reproduce the results are available, all other layers can be generated with the code provided in this repository. The Canopy Height Models underlying the analysis and respective processing scripts for the lidar data, are available from the corresponding author upon reasonable request. Gap layers derived from the Canopy Height Models are available in this repository.</p> <p>Empty folders are set up to follow the directory structure of the scripts. </p>
Data Sources for Bottom-Up Archetype-based Modelling of Nigerian Residential Dwellings for Scenario Analysis
<p><strong>Dataset Name:</strong><br><em>Literature Data, Archetype Parameter Sheets, and Schedules for the publication, named Bottom-Up Archetype-based Modelling of Nigerian Residential Dwellings for Scenario Analysis</em>.</p> <p><strong>Description:</strong><br>This dataset includes Excel sheets containing literature sources, archetypal data, and schedules for Nigerian residential dwelling typologies.</p> <p><strong>Files:</strong><br>The following files are included in the dataset:</p> <ul> <li> Nigeria<em>_LiteratureSources.xlsx:</em> Excel sheet containing literature sources and references,</li> <li> Nigeria<em>_ArchetypeParameters.xlsx</em>: Archetype models' semantic, geometric, and technical data used in the generation of energy models,</li> <li> Nigeria<em>_Schedules.xlsx:</em> Excel sheet containing the operation schedules compiled from literature sources and reorganized by expert consensus and given in Designbuilder input format.</li> </ul> <p><strong>Usage:</strong><br>The dataset is intended for researching and analyzing the Nigerian residential buildings. The literature sources included in the Nigeria_LiteratureSources.xlsx and Nigeria_ArchetypeParameters.xlsx files can be used to verify, support, or reproduce the research findings.</p> <p><strong>License:</strong><br>The dataset is licensed under Creative Commons Attribution 4.0 International.</p> <p><strong>Citation:</strong><br>If you use this dataset in your research, please cite it as follows and contact the corresponding author:</p> <p>Chibuikem Chrysogonus Nwagwu, Sahin Akin, and Edgar G. Hertwich. 2024. “Data Sources for Bottom-Up Archetype-based Modelling of Nigerian Residential Dwellings for Scenario Analysis” https://doi.org/10.5281/zenodo.10995123</p> <p><strong>Contact:</strong><br>The archetypes' energy models (DesignBuilder or IDF files) as well as full material and energy use result sheets can be provided on request. If you have any questions or comments about the dataset, please contact <strong>chibuikem.nwagwu@sintef.no, the corresponding author.</strong></p>
Dead Sea Scrolls data collection (images, labels, prediction plots) for dating ancient manuscripts using radiocarbon and AI-based writing style analysis
<p>The dataset is associated with the following article:<br>Title: <strong>Dating ancient manuscripts using radiocarbon and AI-based writing style analysis</strong><br>Authors: Mladen Popović, Maruf A. Dhali, Lambert Schomaker, Johannes van der Plicht, Kaare Lund Rasmussen, Jacopo La Nasa, Ilaria Degano, Maria Perla Colombini, and Eibert Tigchelaar<br><em>(Under review)</em></p> <p>This data set is collected for the ERC project:<br>The Hands that Wrote the Bible: Digital Palaeography and Scribal Culture of the Dead Sea Scrolls<br>PI: Mladen Popović<br>Grant agreement ID: 640497<br>Project website: <a href="https://cordis.europa.eu/project/id/640497">https://cordis.europa.eu/project/id/640497</a></p> <p> </p> <p><strong>Copyright (c) </strong> University of Groningen, 2024. All rights reserved.<br><strong>Disclaimer and copyright notice for all data contained on the *.tar.gz files:</strong></p> <p><strong>1)</strong> permission is hereby granted to use the data for research purposes. It is not allowed to distribute this data for commercial purposes.</p> <p><strong>2) </strong>provider gives no express or implied warranty of any kind, and any implied warranties of merchantability and fitness for purpose are disclaimed.</p> <p><strong>3) </strong>provider shall not be liable for any direct, indirect, special, incidental, or consequential damages arising out of any use of this data.</p> <p><strong>4) </strong>the user should refer to the first public article mentioned above on this data set.</p> <p><strong>5) </strong>the recipient should refrain from proliferating the data set to third parties external to his/her local research group. Please refer interested researchers to this site to obtain their own copy.</p> <p> </p> <p><strong>Organization of the data:<br></strong><em>(Update on 19 April 2024: OxCal data for accepted 2-sigma ranges are updated with the incusion and exclusion of minor peaks. New prediction plots are added after the model is trained with accepted 2-sigma ranges, including minor peaks. The old plots are also kept. <br><br><OLD Updates below; disregard><br>updated on 07-Feb-2024: OxCal data for selected ranges added in a new directory in addition to previously available original OxCal data. Enoch's prediction plots and test images are reorganized for easy access to the users.<br><OLD Updates above; disregard><br><br>Please use the files from this version and disregard the previous two versions: 10.5281/zenodo.10629480 and 10.5281/zenodo.8168210)</em></p> <p>There are four *.tar.gz files:</p> <p><em><strong>C14-Oxcal-data-updated.tar.gz</strong></em> contains one directory with radiocarbon data (OxCal [1] raw data) for all 30 manuscripts. Three additional directories contain name-corrected files for original OxCal data, files with accepted ranges, and files with accepted ranges including minor peaks. Please refer to the original article for details about OxCal data and the manuscripts. 25 out of 30 raw OxCal data are used (accepted ranges only) as the training labels during the training of Enoch, the date prediction model.</p> <p><em><strong>train-images-c14.tar.gz</strong></em> contains the clean and preprocessed (binarized, aligned, and arrangement corrected) training images for the 25 radiocarbon-dated training manuscripts (including 4Q52; 64 images in total). </p> <p><em><strong>test-images-all.tar.gz</strong></em> contains the clean and preprocessed test images for 135 previously undated manuscripts. The images are organized in three different directories: the first one with all 359 images for the 135 manuscripts, the second one with the selected 135 images, and the final one with 25 images to illustrate the poor quality of images. </p> <p><em><strong>Enoch-prediction-new-with-minor-peaks.tar.gz</strong></em> contains the new date prediction plots for each of the 135 test images, where Enoch was trained with the inclusion of minor peaks for the 2-sigma accepted ranges and with a data balancing threshold of 0.05. These plots are used by expert palaeographers' evaluation of Enoch's style-based date predictions of 135 previously undated manuscripts.</p> <p><em><strong>Enoch-predictions.tar.gz</strong></em> contains the date prediction plots for each of the 135 test images. There are two directories inside the *.tar.gz file:<br><br>- <em>prediction-plots-for-selected-135:</em> Prediction plots with data balancing threshold of 0.05. <br>- <em>extra-plots:</em> contains four additional directories:<br> - <em>Enoch-predictions-c14wo4Q52-balanced05:</em> Prediction plots with data balancing threshold of 0.05. <br> - <em>Enoch-predictions-c14wo4Q52-balanced10:</em> Prediction plots with data balancing threshold of 0.1.<br> - <em>Enoch-predictions-c14wo4Q52-unbalanced:</em> Unbalanced raw predictions.<br> - <em>Enoch-predictions-c14wo4Q52-combined:</em> Combined plots with all three prediction plots (unbalanced, 0.05, 0.1).<br>Please refer to the original article for more details.</p> <p>The updated code to run the plot is available here: <a href="https://doi.org/10.5281/zenodo.10998860">https://doi.org/10.5281/zenodo.10998860</a></p> <p><strong>If you have any questions, please get in touch with us:</strong><br>Mladen Popović <m.popovic(at)rug.nl><br>Maruf A. Dhali <m.a.dhali(at)rug.nl><br>Lambert Schomaker <l.r.b.schomaker(at)rug.nl></p> <p> </p> <p><strong>References:</strong><br>1. Bronk Ramsey, C. (2001). Development of the radiocarbon calibration program. <em>Radiocarbon</em>, <em>43</em>(2A), 355-363.</p>
Codes and Data for "Vertically resolved analysis of the Madden-Julian Oscillation highlights the role of convective transport of moist static energy"
<p>This file contains the analysis code and a condensed version of data to reproduce figures in the paper "Vertically resolved analysis of the Madden-Julian Oscillation highlights the role of convective transport of moist static energy". </p>
Chemical analysis dataset for contaminants of emerging concern and bioanalytical data for samples from a low mountain stream in Central Germany
<p>In 2022, river-water samples were collected at six sampling sites along the Holtemme River in Central Germany using large-volume solid phase extraction. The extracts were analysed by target chemical analysis for contaminants of emerging concern. In addition, the extracts were analysed in a bioanalytical test battery using effect-based tools. The battery included assays for cytotoxicity (neutral red retention assay), oxidative stress (Nrf2-CALUX®), endocrine disruption (ER-, AR-, anti-ER-, anti-AR-, GR- and PR-CALUX®) and the fish embryotoxicity test with zebrafish (<em>Danio rerio</em>). The data obtained are included in the .csv files in this repository.</p>
Spreadsheet with reverse analysis routine for STC assessment in electrolyzers with CO2RR example data
<p>Supplementary material to manuscript "Unfolding electrolyzer characteristics to reveal solar-to-chemical efficiency potential: rapid analysis method bridging electrochemistry and photovoltaics " accepted for publication to ChemSusChem journal in November 2024<br>Authors: Oleksandr Astakhov, Therese Cibaka, Lars Wieprecht, Uwe Rau, Tsvetelina Merdzhanova IMD-3 Photovoltaics Forschungszentrum Jülich GmbH, Jülich, Germany<br>Version 5 14.11.2024<br>Contact: Oleksandr Astakhov email: o.astakhov@fz-juelich.de<br>Calculation of maximum STC (solar to chemical efficiency, same as STF - solar to fuel efficiency) in photovoltaic-driven electrolyzers (PV-EC) <br>The analysis addresses any type of PV-EC systems with direct and indirect coupling<br>Coupling efficiency ηC is treated as a constant explicitly. Set ηC to be 100% to evaluate the limit of STC the electrolyzer can achieve<br>The analysis is performed towards individual products. If EC produces several products each of them must be analysed in a separate table<br>STC dependencies for three major parameters PV-efficiency, Irradiance G and PV-to-EC area ratio AR are calculated<br>Example dataset is for EC cell for CO2 reduction with data presented for CO as a product</p>
Data for Analysis for "A Framework for Adapting Conversational Intelligent Tutoring Systems to enable Collaborative Learning"
<p>This dataset includes, the data files for validating the statistical analysis from "A Framework for Adapting Conversational Intelligent Tutoring Systems to enable Collaborative Learning"</p> <p> </p> <p>The dataset is composed of 1500 files named following the pattern `Test-R-N-User-C-P.csv` where</p> <ul> <li>R is the n-th repetition. From 0 to 50</li> <li>N is the number of concurrent users. From 100 to 1000</li> <li>C is the treatment. chat for the framework version. chat-session for the legacy version.</li> <li>P is the problem number. 16 or 352.</li> </ul> <p>The data files corresponding to chat and problem 16 are those that in the paper are identified as Framework. The files por problem 352 are the collaborative version with students grouped.</p> <p>Each csv, is composed following the standard formate by Apache JMeter, and contains XX columns:</p> <ul> <li>timeStamp - UNIX timestamp of the request</li> <li>elapsed - Time taken to finish the request</li> <li>label - which step</li> <li>responseCode - HTTP response code</li> <li>responseMessage</li> <li>threadName</li> <li>dataType</li> <li>success - true|false</li> <li>failureMessage</li> <li>sentBytes</li> <li>grpThreads</li> <li>allThreads - Threads running</li> <li>URL - Endpoint URL</li> <li>Latency</li> <li>SampleCount</li> <li>ErrorCount - Cumulative amount of errors</li> <li>IdleTime </li> <li>Connect - Connection time</li> </ul> <p> </p>
Data analysis Protocol for a Joint Study into the Impacts of AI on professional Competencies of IT Professionals and Implications for Computing Students. ITiCSE 2024 Working Group 02.
<h1><a name="_Toc169648661"></a><span>Overview</span></h1> <p><strong><span> </span></strong></p> <p><span>The purpose of this protocol is to help us define a common protocol for sharing and analysing data for the ITiCSE 2024 working group: “<em>WG02: A Multi-Institutional-Multi-National Study into the Impacts of AI on Work Practices of IT Professionals and Implications for Computing Students</em>”. <span> </span>Excerpts from the working group plan to place the protocol in context (Clear et al., 2024) are given below.</span></p> <p><strong><em><span> </span></em></strong></p> <p><strong><em><span>Background and Related Work</span></em></strong></p> <p><em><span>As Artificial Intelligence (AI) continues to make its presence felt in transforming workplaces around the world [1,10], and the Information Technology industry in particular, it is essential to understand its impact on the work practices of IT professionals, and the implications for computing students and curricula. This research project builds on work initiated jointly, in Sweden, New Zealand and Scotland, investigating concerns about the increasing impacts of Artificial Intelligence in IT Sector workplaces for employee work engagement [11,13,1] and the implications for tertiary study, assessment and curricula in computing [4, 8, 10, 9].<span> </span></span></em></p> <p><em><span>“Work engagement”, has been defined as the positive inner state where employees are fully present and engaged in their work, and is closely linked to motivation, learning, productivity, and accountability [11, 13]. Within the context of (Generative) AI at work, IT professionals have been noted as early adopters of AI [10, 1]. Their involvement in implementing and utilising AI technologies can provide valuable insights into the interplay between AI and work engagement.<span> </span>The implications for students are significant as future IT professionals, who must acquire and enhance competencies to adapt and thrive in digital workplaces. </span></em></p> <p><em><span> </span></em></p> <p><strong><em><span>2</span></em></strong><em><span><span> </span><strong>Goals of the Working Group</strong></span></em></p> <p><em><span>By exploring the relationship between work engagement and learning, this study aims to shed light on the dynamics that drive employee engagement and its connection to the professional development of competencies. The previous study has interviewed IT professionals with the following research questions (RQ):</span></em></p> <p><em><span> </span></em></p> <p><em><span>RQ1: How does AI influence work engagement for IT professionals?</span></em></p> <p><em><span>RQ2: How does AI affect the socio-technical work dynamics for IT professionals?</span></em></p> <p><em><span>RQ3: What are the implications of integrating AI on the acquisition and enhancement of professional competencies and the learning processes of IT professionals?</span></em></p> <p><em><span> </span></em></p> <p><strong><em><span>3</span></em></strong><em><span><span> </span><strong>Methodology</strong></span></em></p> <p><em><span>This working group aims to analyse the corpus of interview data collected from multiple countries to better understand the implications for computing students, tertiary computing education curricula and assessment of the new professional competencies emerging from this work. This study informed by the literature on work engagement, automation and motivation for IT professionals [11, 13], will use a combination of multi-vocal literature review [7] and qualitative research methods [2, 5], including thematic analysis of the interviews, to investigate the state of the practice in and challenges IT Professionals face within their local/global work contexts. The literature on professional competencies in computing [4, 3, 6] will be drawn upon to characterise the new needs identified in this analysis.<span> </span>Further implications for computing curricula design and assessment will be developed from this analysis. </span></em></p> <p><span>REFERENCES</span></p> <p><span>[1]<span> </span>ACM Technology Policy Council. 2023. Principles for the development, deployment, and use of generative AI technologies, ACM New York.</span></p> <p><span>[2]<span> </span>Braun, V. and Clarke, V. 2021. One size fits all? What counts as quality practice in (reflexive) thematic analysis? <em>Qualitative research in psychology</em>, <em>18</em> (3). 328-352.</span></p> <p><span>[3]<span> </span>Clear, A., Clear, T., Vichare, A., Charles, T., Frezza, S., Gutica, M., Lunt, B., Maiorana, F., Pears, A. and Pitt, F. 2020. Designing Computer Science<span> </span>Competency Statements: A Process and Curriculum Model for the 21st Century in <em>Proceedings of the 2020 ACM Conference on Innovation and Technology in Computer Science Education</em>, ACM, New York.</span></p> <p><span>[4]<span> </span>Clear, A., Parrish, A. and CC2020 Task Force. 2020. Computing Curricula 2020 - CC2020 - Paradigms for Future Computing Curricula ACM and IEEE-CS eds. <em>A Computing Curricula Series Report </em>ACM, New York.</span></p> <p><span>[5]<span> </span>Cruzes, D.S. and Dyba, T. 2011. Recommended steps for thematic synthesis in software engineering. in <em>2011 international symposium on empirical software engineering and measurement</em>, IEEE, 2011, 275-284.</span></p> <p><span>[6]<span> </span>Frezza, S., Clear, T. and Clear, A. 2020. Unpacking Dispositions in the CC2020 Computing Curriculum Overview Report in <em>2020 IEEE Frontiers in Education Conference (FIE)</em>, IEEE, Uppsala, Sweden. </span></p> <p><span>[7]<span> </span>Garousi, V., Felderer, M., & Mäntylä, M. V. 2019. Guidelines for including grey literature and conducting multivocal literature reviews in software engineering. <em>Information and Software Technology</em>, <em>106.</em> 101-121</span></p> <p><span>[8]<span> </span>Jacques, L. 2023. Teaching CS-101 at the Dawn of ChatGPT. <em>ACM Inroads</em>, <em>14</em> (2). 40-46.</span></p> <p><span>[9]<span> </span>Liffiton, M., Sheese, B., Savelka, J. and Denny, P. 2023. CodeHelp: Using Large Language Models with Guardrails for Scalable Support in Programming Classes. <em>arXiv preprint arXiv:2308.06921</em>.</span></p> <p><span>[10]<span> </span>Prather, J., Denny, P., Leinonen, J., Becker, B.A., Albluwi, I., Craig, M., Keuning, H., Kiesler, N., Kohn, T. and Luxton-Reilly, A. 2023. The robots are here: Navigating the generative ai revolution in computing education. <em>arXiv preprint arXiv:2310.00658</em>.</span></p> <p><span>[11]<span> </span>Roto, V., Palanque, P. and Karvonen, H., 2019. Engaging automation at work–a literature review. in <em>Human Work Interaction Design. Designing Engaging Automation: 5th IFIP WG 13.6 Working Conference, HWID 2018, Espoo, Finland, August 20-21, 2018, Revised Selected Papers 5</em>, Springer, 158-172.</span></p> <p><span>[12]<span> </span>SFIA Foundation. 2023. SFIA skills aligned to EU ICT Profiles, SFIA Institute, London.</span></p> <p><span>[13]<span> </span>Sharp, H., Baddoo, N., Beecham, S., Hall, T. and Robinson, H. 2009. Models of motivation in software engineering. <em>Information and software technology</em>, <em>51</em> (1). 219-233.</span></p> <p><em><span> </span></em></p>
Unique composition and evolution histories of low velocity mantle domains: Data and analysis
<p>Dataset and Jupyter notebook accompanying 'Unique composition and evolution histories of low velocity mantle domains'. </p> <p>Dataset includes:</p> <ul> <li>Present day properties of simulated mantle for simulations RCY, B=0.22, B=0.44, visc2, visc3, CMB2600, CMB2800, COMP, PRM, MER.</li> <li>Present day predicted seismic properties for simulations RCY, B=0.22, B=0.44, visc2, visc3, CMB2600, CMB2800, COMP, MER.</li> <li>Present day predicted seismic properties for simulation PRM assuming 'primordial' material to be i) basaltic oceanic crust ii) chondrite enriched basalt (CEB).</li> <li>Present day delta Vs for simulations RCY, B=0.22, B=0.44, visc2, visc3, CMB2600, CMB2800, COMP, PRM, MER, filtered using the resolution of seismic tomography model S40RTS.</li> <li>Properties of simulated mantle at 100 Myr intervals from 900 Ma - 100 Ma inclusive for simulation RCY. </li> <li>P-T tables with predicted abundance of post-perovskite for different mantle lithologies (harzburgite, lherzolite and basalt - as defined in the paper).</li> </ul> <p>Jupyter notebook `s-llvps.ipynb` contains code for identifying simulated large low-velocity provinces (S-LLVPs), extracting assoicated model properties and plotting results. Python module files terra_utils.py and ppv.py are also included and required by the code in the notebook. </p> <p>There are a number of pre-requisite packages that will need to be installed in order to run the Jupyter notebook, including <a title="terratools" href="https://github.com/mantle-convection-constrained/terratools" target="_blank" rel="noopener">terratools</a>, a software package written specifically for reading and postprocessing outputs from TERRA simulations. Installation instructions can be found on the GitHub repository. </p> <p>Due to the TERRA code pre-dating open source licensing, we do not currently have permission to publicly share all aspects of the code. In code_pieces.F90 we include code snippets which were implemented for this study. </p> <p>Simulations were conducted using ARCHER2, the UK's national super-computing service. </p> <p>RCY.mp4 is a movie produced for simualtion RCY, visualising the evolution of temperature (right panels) and bulk composition (left panels). Hot iso-surface (red) drawn at +500 K and cold iso-surface (blue) drawn at -400 K, composition iso-surface drawn at C=0.6. Red and blue lines indicate overlying ridges / subduction zones taken from the plate motion reconstructions of Müller et al (2022). </p>
Supplementary data frames, AlphaFold models, Normal Mode Analysis (NMA) Data, and NMA of Corresponding NMR Ensembles in the S2RCI, MD, and S2 Datasets for "Gradations in protein dynamics captured by experimental NMR are not well represented by AlphaFold2 models and other computational metrics"
<h1><strong>Changes applied to V2</strong></h1> <p>In addition to the supplementary dataframes and AlphaFold models from each dataset in V1, V2 includes the additional data outlined below.</p> <p>The <strong>S2RCI</strong> and <strong>MD</strong> datasets include comprehensive analyses of AlphaFold2 models (both before and after truncation). These datasets feature: </p> <ul> <li><strong>AlphaFold2 Models</strong>: Both original and truncated structures. </li> <li><strong>WEBnma Modes</strong>: `modes.txt` files generated from WEBnma analysis, available for both non-truncated and truncated AF2 models. </li> <li><strong>Root-Mean-Square-Fluctuations (RMSF)</strong>: Profiles calculated before and after truncation of AF2 models. </li> <li><strong>NMR Data: Normal Mode Analysis (NMA)</strong>: Performed on corresponding NMR ensembles (see below). </li> </ul> <p> </p> <p>The <strong>NMR Data</strong> of NMA in these datasets includes: </p> <ul> <li>NMR ensembles </li> <li>Individual NMR models extracted from each ensemble </li> <li>STRIDE secondary structure calculations per-individual NMR models</li> <li>RMSF profiles per-individual NMR models</li> </ul> <p>For detailed information, please refer to the `Readme.txt` file within each corresponding folder. </p> <p>The <strong>S2 dataset</strong> includes all the features listed above, except for the NMR analysis.</p>
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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)
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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.