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3,363 results for “Replication”
Replication Data for: "Ocean acidification increases susceptibility to sub-zero air temperatures in ecosystem engineers and limit poleward range shifts"
<p>These datasets contain all the raw data needed to replicate the results from our paper <em>Ocean acidification increases susceptibility to sub-zero air temperatures in ecosystem engineers and limit poleward range shifts</em> published in eLife - <a href="https://doi.org/10.7554/eLife.81080">https://doi.org/10.7554/eLife.81080</a></p>
Input data to replicate "The social cost of tropical cyclones"
<p>Input data for the <a href="https://dx.doi.org/10.5281/zenodo.8056520">scripts</a> that replicate the results of <a href="https://doi.org/10.1038/s41467-023-43114-4">Krichene et al. 2023</a>.</p> <p>To run the <a href="https://dx.doi.org/10.5281/zenodo.8056520">scripts</a>, the following files from this repository need to be placed in the <code>./data/input/</code> subdirectory of the project folder containing the <a href="https://dx.doi.org/10.5281/zenodo.8056520">scripts</a>:</p> <ul> <li><code>GMT.nc</code>: Global mean temperature time series as used by the <a href="https://gitlab.pik-potsdam.de/tovogt/tc_emulator">tropical cyclone emulator</a>.</li> <li><code>GrowthClimateDataset.dta</code>: The <a href="https://purl.stanford.edu/wb587wt4560">input data</a> of <a href="https://dx.doi.org/10.1038/nature15725">Burke et al. 2015</a>.</li> <li><code>IHME_GLOBAL_GDP_ESTIMATES_1950_2015.csv</code>: Historical GDP per capita data from <a href="https://doi.org/10.1186/1478-7954-10-12">James et al. 2012</a> (downloaded from <a href="https://ghdx.healthdata.org/record/ihme-data/gross-domestic-product-gdp-estimates-country-1950-2015">IHME</a>).</li> <li><code>mean_temperature_gswp3-w5e5.csv</code>: Population-weighted average national temperature time series for the historical period.</li> <li><code>pulse_response_ricke_caldeira_2014.csv</code>: The global mean temperature response of an additional emission pulse according to <a href="https://dx.doi.org/10.1088/1748-9326/9/12/124002">Ricke & Caldeira 2014</a>.</li> <li><code>tcdata/TCE-DAT_historic-exposure_1950-2015.csv</code> and <code>tcdata/TotalPopulation.csv</code>: Historical (national) numbers of people affected by tropical cyclones according to <a href="https://doi.org/10.5880/pik.2017.011">TCE-DAT</a> with the corresponding total population counts.</li> <li><code>tcdata/emulator/</code>: Projected (national) shares of people affected by tropical cyclones according to the <a href="https://gitlab.pik-potsdam.de/tc_cost/tc_emulator">tropical cyclone emulator</a> as computed by the scripts in the <a href="https://gitlab.pik-potsdam.de/tc_cost/tc_people_affected">corresponding repository</a>.</li> <li><code>wid_all_data.zip</code>: A bulk data set from the <a href="https://wid.world/bulk_download/wid_all_data.zip">World Inequality Database</a>.</li> </ul> <p>For more information, see <a href="https://doi.org/10.1038/s41467-023-43114-4">Krichene et al. 2023</a> and the README file provided with the <a href="https://dx.doi.org/10.5281/zenodo.8056520">scripts</a>.</p>
Bird Abundances at the Hubbard Brook Experimental Forest (1969-present) and on three replicate plots (1986-2000) in the White Mountain National Forest (Reformatted to the ecocomDP Design Pattern)
This data package is formatted as an ecocomDP (Ecological Community Data Pattern). For more information on ecocomDP see https://github.com/EDIorg/ecocomDP. This Level 1 data package was derived from the Level 0 data package found here: https://pasta.lternet.edu/package/metadata/eml/knb-lter-hbr/81/7. The abstract below was extracted from the Level 0 data package and is included for context: Bird abundances have been determined from timed censuses, territory maps and nest locations at the Hubbard Brook Experimental Forest from 1969 to the present. This data set includes counts of the number of adult birds (males and females) per 10 ha at HBEF (1969 - present) and on three additional plots within the White Mountain National Forest (1986 - 2000). These data were gathered as part of the Hubbard Brook Ecosystem Study (HBES). The HBES is a collaborative effort at the Hubbard Brook Experimental Forest, which is operated and maintained by the USDA Forest Service, Northern Research Station.
Measuring Software Testability Modulo Test Quality - Replication Package
<p>This repository represents the replication package for the paper <em>Measuring Software Testability Modulo Test Quality</em>.</p> <p>It includes the dataset and the Jupyter Notebook we used for the analysis in our paper.</p>
Benchmark and training data for replicating financial and insurance examples
<p>This dataset contains training, validation and out-of-sample test data for two European calls and two examples of portfolio of variable annuity guarantees.</p>
Synchronous transmissions on Bluetooth 5 and IEEE 802.15.4 - A replication study
<p>Archive of the following GitHub repository: <a href="https://github.com/romain-jacob/ST_data_and_viz">https://github.com/romain-jacob/ST_data_and_viz</a></p> <p>This repository contains the raw data and analysis scripts of a replication study of synchronous transmissions using the <a href="https://www.nordicsemi.com/en/Software%20and%20tools/Development%20Kits/nRF52840%20Dongle">nRF52840 Dongle</a> where we compare the success rate of synchronous transmission attempts using two transmitters while varying a number of parameters. The repository also contains the source code of a data visualization application, which you can either</p> <ul> <li>run locally or</li> <li><a href="https://github.com/romain-jacob/ST_data_and_viz/blob/master/URL">online in your web browser</a> at <a href="http://explore-st-data.ethz.ch/">http://explore-st-data.ethz.ch/</a></li> </ul> <p>The study is described in more details in the following publication.</p> <blockquote> <p><strong>Synchronous transmissions on Bluetooth 5 and IEEE 802.15.4 - A replication study</strong><br> Romain Jacob, Anna-Brit Schaper, Andreas Biri, Reto da Forno, Lothar Thiele<br> <a href="https://cpsbench20.ethz.ch/">CPS-IoTBench'20</a><br> [ <a href="https://openreview.net/forum?id=BSZPNEUHiS2">Direct link</a> ]</p> </blockquote> <p>The dataset has been collected during the <a href="https://doi.org/10.3929/ethz-b-000375332">Master thesis of Anna-Brit Schaper.</a></p>
Replication package of "Good Things Come In Threes: Improving Search-based Crash Reproduction With Helper Objectives"
<p>The replication package for the study about using new helper objectives (MOHO) for crash reproduction. This study has been accepted at ASE 2020.</p> <p> </p> <p>Abstract:</p> <p>Evolutionary intelligence approaches have been successfully applied to assist developers during debugging by generating a test case reproducing reported crashes. These approaches use a single fitness function called <em>Crash Distance</em> to guide the search process toward reproducing a target crash. Despite the reported achievements, these approaches do not always successfully reproduce some crashes due to a lack of test diversity (premature convergence). In this study, we introduce a new approach, called <em>MO-HO</em>, that addresses this issue via multi-objectivization. In particular, we introduce two new Helper-Objectives for crash reproduction, namely <em>test length</em> (to minimize) and <em>method sequence diversity</em> (to maximize), in addition to <em>Crash Distance</em>.</p> <p>We assessed <em>MO-HO</em> using five multi-objective evolutionary algorithms (NSGA-II, SPEA2, PESA-II, MOEA/D, FEMO) on 124 hard-to-reproduce crashes stemming from open-source projects. Our results indicate that SPEA2 is the best-performing multi-objective algorithm for <em>MO-HO</em>.</p> <p>We evaluated this best-performing algorithm for <em>MO-HO</em> against the state-of-the-art: single-objective approach (Single-Objective Search) and decomposition-based multi-objectivization approach (<em>De-MO</em>). Our results show that <em>MO-HO</em> reproduces five crashes that cannot be reproduced by the current state-of-the-art. Besides, <em>MO-HO</em> improves the effectiveness (+10% and +8% in reproduction ratio) and the efficiency in 34.6% and 36% of crashes (i.e., significantly lower running time) compared to Single-Objective Search and <em>De-MO</em>, respectively. For some crashes, the improvements are very large, being up to +93.3% for reproduction ratio and -92% for the required running time. </p>
The Daily Life of Software Engineers during the COVID-19 Pandemic -- Replication Package
<p>Following the onset of the COVID-19 pandemic and subsequent lockdowns, software engineers' daily life was disrupted and abruptly forced into remote working from home. This change deeply impacted typical working routines, affecting both well-being and productivity. Moreover, this pandemic will have long-lasting effects in the software industry, with several tech companies allowing their employees to work from home indefinitely if they wish to do so. Therefore, it is crucial to analyze and understand how a typical working day looks like when working from home and how individual activities affect software developers' well-being and productivity. We performed a two-wave longitudinal study involving almost 200 globally carefully selected software professionals, inferring daily activities with perceived well-being, productivity, and other relevant psychological and social variables. Results suggest that the time software engineers spent doing specific activities from home was similar when working in the office. (e.g., coding > emails > code review > networking). However, we also found some meaningful mean differences. The amount of time developers spent on each activity was unrelated to their well-being, perceived productivity, and other variables. We conclude that working remotely is not per se a challenge for organizations or developers.</p>
Gender Differences in Public Code Contributions: a 50-year Perspective - Replication Package
<p>This page details the steps needed to replicate the findings of the paper: <a href="https://upsilon.cc/~zack/">Stefano Zacchiroli</a>, <em>Gender Differences in Public Code Contributions: a 50-year Perspective</em>, <a href="https://www.computer.org/csdl/magazine/so">IEEE Software</a>, 2021.</p> <p>After retrieving the replication package, follow the instruction described in the README.html file.</p>
Replication package of https://doi.org/10.1088/1361-6595/abbae4
<p>This is the replication package of Plasma activation of N<sub>2</sub>, CH<sub>4</sub> and CO<sub>2</sub>: an assessment of the vibrational non-equilibrium time window, by A.W. van de Steeg et al.</p> <p>The zip file contains a general readme and all the required data on which the figures are based. </p> <p>Nearly all raw data is in .spe files, belonging to the Princeton Instruments camera used. The python library calibrate_fiber_pos can open the camera pictures.</p> <p> </p>
Today's cat is tomorrow's dog: accounting for time-based changes in the labels of ML vulnerability detection approaches (Replication Package Part 3: OpenSSL dataset)
<h1><strong>The Replication Package of</strong></h1> <h1><strong>"Today's cat is tomorrow's dog: accounting for time-based changes in the labels of ML vulnerability detection approaches"</strong></h1> <h3><strong>Part 3 (OPENSSL Dataset)</strong></h3> <div> <div>This repository includes:</div> <ol> <li><em><strong>Code.zip</strong></em> that contains the codes to replicate some parts of this study:<br>a. <em>1_generate_datasets</em> implements our methodology to generate the datasets.<br>b. <em>2_run_models</em> runs the ML models during the evaluation.<br>c. <em>3_result_replication </em>generates charts presented in the paper from the ML evaluation results.</li> <li><em><strong>Datasets.zip</strong></em> that contain 2 folders:<br>a. <em>original</em> datasets: 1 from <a href="https://github.com/CGCL-codes/VulDeePecker" target="_blank" rel="noopener">NVD Vuldeepecker</a> and 3 extracted from <a href="https://github.com/ZeoVan/MSR_20_Code_vulnerability_CSV_Dataset" target="_blank" rel="noopener">BigVul</a>.<br> <div> <div>b. <em>OPENSSL</em> datasets: train, validation, test sets for each time of observation extracted using our methodology from <a href="https://github.com/ZeoVan/MSR_20_Code_vulnerability_CSV_Dataset" target="_blank" rel="noopener">BigVul</a> dataset for project <em>openssl</em>.</div> </div> </li> <li><em><strong>Pretrained-models.zip</strong></em> that we generated during our evaluation (3 test results for each time point in the timeline [2013-2019]).</li> <li><em><strong>Results.zip</strong></em> of our evaluation, the folder <em>ALL</em> contains the overall results and other folders are results by model.</li> </ol> <p><strong>UPDATED version 5<br></strong>- added a GLOBAL_README.md which contains the 3 stages and how they are connected to each other<br>- updated LineVul.ipynb: import AdamW from torch.optim instead of transformers<br>- updated README.md in Code2Vec with the prerequisites of Java to run gradlew for astmine</p> <p><strong>UPDATED version 6<br></strong>- updated CodeBert.ipynb: import AdamW from torch.optim instead of transformers</p> <p>Documentations</p> <ol> <li><em><strong>INSTALL.pdf </strong></em>: how to install the codes</li> <li><em><strong>README.pdf</strong></em>: readme file</li> <li><em><strong>REQUIREMENTS.pdf</strong></em>: hardware and software requirements</li> <li><em><strong>STATUS.pdf</strong></em> : status for artifact submission</li> <li><em><strong>LICENSE.pdf</strong></em>: the license of this artifact</li> <li><em><strong>PAPER.pdf</strong></em>: the camera-ready version of the paper</li> </ol> </div> <div> <div>Please refer to the following repositories for the other datasets and pre-trained models:</div> <div>- Part 1 NVD Vuldeeepecker : <a href="https://doi.org/10.5281/zenodo.8207883" target="_blank" rel="noopener">https://doi.org/10.5281/zenodo.8207883</a></div> - Part 2 LINUX : <a href="https://doi.org/10.5281/zenodo.10960662" target="_blank" rel="noopener">https://doi.org/10.5281/zenodo.10960662</a><br> <div>- Part 4 POPPLER : <a href="https://doi.org/10.5281/zenodo.14713143">https://doi.org/10.5281/zenodo.14713143</a></div> <div> </div> <div>This work was partly funded by the EU under the H2020 Program AssureMOSS (Grant n. 952647) and the Horizon Europe Program Sec4AI4Sec (Grant n. 101120393), by the Italian Ministry of University and Research (MUR) under the P.N.R.R. – NextGenerationEU grant n.\ PE00000014 (SERICS subproject COVERT), and by the Dutch Research Council (NWO) under the grant NWA.1215.18.006 (Theseus) and grant KIC1.VE01.20.004 (HEWSTI). </div> </div>
Replication Data & Code - Large-scale land acquisitions exacerbate local land inequalities in Tanzania
<h3><strong>Reference</strong></h3><p>Sullivan J.A., Samii, C., Brown, D., Moyo, F., Agrawal, A. 2023. Large-scale land acquisitions exacerbate local farmland inequalities in Tanzania. Proceedings of the National Academy of Sciences 120, e2207398120. <a href="https://doi.org/10.1073/pnas.2207398120">https://doi.org/10.1073/pnas.2207398120</a> </p><h3><strong>Abstract</strong></h3><p>Land inequality stalls economic development, entrenches poverty, and is associated with environmental degradation. Yet, rigorous assessments of land-use interventions attend to inequality only rarely. A land inequality lens is especially important to understand how recent large-scale land acquisitions (LSLAs) affect smallholder and indigenous communities across as much as 100 million hectares around the world. This paper studies inequalities in land assets, specifically landholdings and farm size, to derive insights into the distributional outcomes of LSLAs. Using a household survey covering four pairs of land acquisition and control sites in Tanzania, we use a quasi-experimental design to characterize changes in land inequality and subsequent impacts on well-being. We find convincing evidence that LSLAs in Tanzania lead to both reduced landholdings and greater farmland inequality among smallholders. Households in proximity to LSLAs are associated with 21.1% (<i>P</i> = 0.02) smaller landholdings while evidence, although insignificant, is suggestive that farm sizes are also declining. Aggregate estimates, however, hide that households in the bottom quartiles of farm size suffer the brunt of landlessness and land loss induced by LSLAs that combine to generate greater farmland inequality. Additional analyses find that land inequality is not offset by improvements in other livelihood dimensions, rather farm size decreases among households near LSLAs are associated with no income improvements, lower wealth, increased poverty, and higher food insecurity. The results demonstrate that without explicit consideration of distributional outcomes, land-use policies can systematically reinforce existing inequalities.</p><h3><strong>Replication Data</strong></h3><p>We include anonymized household survey data from our analysis to support open and reproducible science. In particular, we provide i) an anoymized household dataset collected in 2018 (n=994) for households nearby (treatment) and far-away from (control) LSLAs and ii) a household dataset collected in 2019 (n=165) within the same sites. For the 2018 surveys, several anonymized extracts are provided including an imputed (n=10) dataset to fill in missing data that was used for the main analysis. This data can be found in the <i>hh_data</i> folder and includes:</p><ul><li><i>hh_imputed10_2018:</i> anonymized household dataset for 2018 with variables used for the main analysis where missing data was imputed 10 times</li><li><i>hh_compensation_2018:</i> anonymized household extract for 2018 representing household benefits and compensation directly received from LSLAs</li><li><i>hh_migration_2018:</i> anonymized household extract for 2018 representing household migration behavior following LSLAs</li><li><i>hh_rsdata_2018:</i> extracted remote sensing data at the household geo-location for 2018</li><li><i>hh_land_<strong>2019</strong>:</i><strong> </strong> anonymized household extract for <strong>2019 </strong>of land variables</li></ul><p>Our analysis also incorporates data from the Living Standards Measurement Survey (LSMS) collected by the World Bank (found in <i>lsms_data</i> folder). We've provide sub-modules from the LSMS dataset relevant to our analysis but the full datasets can be access through the World Bank's Microdata Library (https://microdata.worldbank.org/index.php/home). </p><p>Across several analyses we use the LSLA boundaries for our four selected sites. We provide a shapefile for the LSLA boundaries in the <i>gis_data</i> folder.</p><p>Finally, our data replication includes several model outputs (found in <i>mod_outputs)</i>, particularly those that are lengthy to run in R. These datasets can optionally be loaded into R rather than re-running analysis using our <i>main_analysis.Rmd</i> script. </p><h3><strong>Replication Code</strong></h3><p>We provide replication code in the form of R Markdown (.Rmd) or R (.R) files. Alongside the replication data, this can be used to reproduce main figures, table, supplementary materials, and results reported in our article. Scripts include:</p><ul><li><i>main_analysis.Rmd:</i> main analysis supporting the finding, graphs, and tables reported in our main manuscript</li><li><i>compensation.R:</i> analysis of benefits and compensation received directly by households from LSLAs</li><li><i>landvalue.R:</i> analysis of household land values as a function of distance from LSLAs</li><li><i>migration.R:</i> analysis of migration behavior following LSLAs</li><li><i>selection_bias.R:</i> analysis of LSLA selection bias between control and treatment enumeration areas</li></ul>
Replication package and appendixes for Causal inference of server- and client-side code smells in web apps evolution
<p>-Analysis <br>--R scripts used to make the analisys, divided by folders<br>--Data folders used in the questions</p> <p>-Appendixes - used in the article to shwo extra tables and plots</p> <p>-data folders - Aggregation of data, each app has two files, CSV and xls</p> <p>-separated data folders - 5 files for each app, with lines corresponding to the each released official version<br>--serversmells<br>--clientsmells<br>--javascriptsmells<br>--Cloc(metrics)<br>--version (all oficial releases)</p> <p>-issues_bugs<br>--data -issues by app by release <br>--data_bugs_more - the same but only bugs, by app by release<br>--scripts - scrips used to aggregate issues (from daily issues to by release) anf the same for bugs</p> <p> </p>
Julia constitutive model integration replication files
<p>These files allow the user to check that their local version of Julia and the codes provided in the repository at <a href="https://github.com/nickcollins-craft/julia_constitutive_model_integration" target="_blank" rel="noopener">https://github.com/nickcollins-craft/julia_constitutive_model_integration</a> have successfully performed the integration and bifurcation analysis of a Cosserat Breakage Mechanics model. Each file is labelled with the integrator (h² or hyperplastic), the load condition (constant volume or constant confining stress) and whether it is an integration result (containing the mechanical information such as stresses and strains) or a localisation result (the wavelength corresponding to the largest value of the Lyapunov exponent, and a Boolean vector stating whether localisation has occurred or not). The files are in the jld2 format, which is read by Julia using the JLD2 and FileIO packages.</p>
Replication package for: "Is Secessionism Mostly About Income or Identity? A Global Analysis of 3,153 Subnational Regions"
<p>This repository contains the data and code to replicate the analyses performed in <a href="https://academic.oup.com/ej/article/135/668/1261/7918442?utm_source=authortollfreelink&utm_campaign=ej&utm_medium=email&guestAccessKey=d6c8adb1-257c-47ad-827c-79b94cf86664" target="_blank" rel="noopener">"Is Secessionism Mostly About Income or Identity? A Global Analysis of 3,153 Subnational Regions"</a> by <a href="https://people.smu.edu/kdesmet/">Klaus </a><a href="https://people.smu.edu/kdesmet/" target="_blank" rel="noopener">Desmet</a>, <a href="https://sites.google.com/view/ignacioortuno" target="_blank" rel="noopener">Ignacio Ortuño-Ortín</a>, and <a href="http://omerozak.com">Ömer </a><a href="http://omerozak.com" target="_blank" rel="noopener">Özak</a>. If you use the code or data in this repository, please cite both the original paper and the dataset.<br><br>Citation:</p> <p>Desmet, Klaus, Ortuño-Ortín, Ignacio, and Özak, Ömer. (2024) "<a href="https://academic.oup.com/ej/article/135/668/1261/7918442?utm_source=authortollfreelink&utm_campaign=ej&utm_medium=email&guestAccessKey=d6c8adb1-257c-47ad-827c-79b94cf86664" target="_blank" rel="noopener">Is Secessionism Mostly About Income or Identity? A Global Analysis of 3,153 Subnational Regions</a>", Economic Journal, Volume 135, Issue 668, May 2025, Pages 1261–1299.</p>
Replication Data for Lead-Free Semiconductors, Phase-Evolution and Superior Stability of Multinary Tin Chalcohalides
<p>Tin-based semiconductors are highly desirable materials for energy applications due to their low toxicity and biocompatibility relative to analogous lead-based semiconductors. In particular, tin-based<br>chalcohalides possess optoelectronic properties that are ideal for photovoltaic and photocatalytic applications. In addition, they are believed to benefit from increased stability compared with halide perovskites.<br>However, to fully realize their potential, it is first necessary to better understand and predict the synthesis and phase evolution of these complex materials. Here, we describe a versatile solution-phase method for the<br>preparation of the multinary tin chalcohalide semiconductors Sn2SbS2I3, Sn2BiS2I3, Sn2BiSI5, and Sn2SI2. We demonstrate how certain thiocyanate precursors are selective toward the synthesis of chalcohalides, thus<br>preventing the formation of binary and other lower order impurities rather than the preferred multinary compositions. Critically, we utilized 119Sn ssNMR spectroscopy to further assess the phase purity of these materials. Further, we validate that the tin chalcohalides exhibit excellent water stability under ambient conditions, as well as remarkable resistance to heat over time compared to halide perovskites. Together, this work enables the isolation of lead-free, stable, direct band gap chalcohalide compositions that will help engineer more stable and biocompatible semiconductors and devices.</p>
Replication data for "The uncertain future of protected lands and waters" - protected area base layer for Amazonia
<p>We created a database of terrestrial and coastal protected areas (PAs) for all nine Amazonian countries following the IUCN definition for PAs and including only state-designated and state-managed PAs. We used the best available sources of archival data, including original legal documents, to confirm information about PAs. We included PAs that currently exist, as well as those that existed previously but have been degazetted. We note that this database differs from the World Database of Protected Areas (WDPA) for several reasons:</p> <p>• we focus on nationally-designated PAs and omit international or local designations</p> <p>• we include previously protected areas</p> <p>• we exclude other area-based conservation interventions other than state-designated and state-managed PAs (such as indigenous lands, privately protected areas, recreational sites, and community based natural resource management areas) which are included in the WDPA in certain countries</p> <p>• We use the establishment date as provided in each PA’s gazettement legal document, rather than the Status Year field in the WDPA, which lists the year that the PA’s current designation was established (46)</p> <p>• We use the spatial extent as provided in each PA’s gazettement legal document, rather than the spatial extent provided in the WDPA. The spatial extent in the WDPA (Rep_Area) is reported by nations and may represent the area as measured in GIS or paper maps, rather than the legally gazetted area.</p> <p>See Table S16 for detailed information by country describing the sources of PA data used for the nine Amazonian countries. </p> <p>Citation of original paper: Golden Kroner, R. E., Qin, S., Cook, C. N., Krithivasan, R., Pack, S. M., Bonilla, O. D., Cort-Kansinally, K. A., Coutinho, B., Feng, M., Martínez Garcia, M. I., He, Y., Kennedy, C. J., Lebreton, C., Ledezma, J. C., Lovejoy, T. E., Luther, D. A., Parmanand, Y., Ruíz-Agudelo, C. A., Yerena, E., … Mascia, M. B. (2019). The uncertain future of protected lands and waters. <em>Science</em>, <em>364</em>(6443), 881–886. <a href="https://doi.org/10.1126/science.aau5525">https://doi.org/10.1126/science.aau5525</a></p>
Highly parallel genomic selection response in replicated Drosophila melanogaster populations with reduced genetic variation
<p>Many adaptive traits are polygenic and frequently more loci contributing to the phenotype are segregating than needed to express the phenotypic optimum. Experimental evolution with replicated populations adapting to a new controlled environment provides a powerful approach to study polygenic adaptation. Since genetic redundancy often results in non-parallel selection responses among replicates, we propose a modified Evolve and Resequence (E&R) design that maximizes the similarity among replicates. Rather than starting from many founders, we only use two inbred <em>Drosophila melanogaster</em>strains and expose them to a very extreme, hot temperature environment (29°C). After 20 generations, we detect many genomic regions with a strong, highly parallel selection response in 10 evolved replicates. The X chromosome has a more pronounced selection response than the autosomes, which may be attributed to dominance effects. Furthermore, we find that the median selection coefficient for all chromosomes is higher in our two-genotype experiment than in classic E&R studies. Since two random genomes harbor sufficient variation for adaptive responses, we propose that this approach is particularly well-suited for the analysis of polygenic adaptation.</p> <p>See the README.txt file to get a description of the uploaded files. Scripts.zip contains annotated command lines and scripts for the project (see internal README.txt file).</p>
Relative abundance of the CHC extracts of each population replicate's of I. uriae ticks from Iceland after log centered ratio transformation
<p>Relative abundance of the CHC extracts of each population replicate’s of I. uriae ticks from Iceland after log centered ratio transformation.</p>
Replication data for: Energy flow analysis of an industrial ammonia refrigeration system
<p>This dataset includes energy data acquired from a pelagic fish processing plant, including data from an industrial ammonia refrigeration system that provides cooling and freezing. In addition, production data is included. Data from the system was analysed within the KSP project PCM-STORE (308847) supported by the Research Council of Norway and industry partners. PCM-STORE aims at building knowledge on novel PCM technologies for low-temperature thermal energy storage. Collecting and analysing data is an important part of evaluating the potential for reduction of CO2 emissions and increasing energy efficiency. Many processing plants measure and log data, but it is not often published. This dataset includes specific energy demand, peak power demand, power demand for different sections of the plant, ambient temperatures, and production volumes. The data was collected in 2021. The included graphics show the refrigeration system and some resulting tables and graphs. Production follows a seasonal cycle throughout the year, with no (or very low) production in the spring (Mar-May), and peak production in the autumn (Sep-Nov). The cycle is linked to the seasonal availability of fish. Annual SEC numbers (200-247 kWh/tonnes) were found to be in line with other Norwegian pelagic plants. A strong dependency between SEC and volume throughput were also found, where months of low production resulted in high SEC values and vice versa. Knowledge about the processes indicates that a fillet production is more energy intensive compared to round production, due to more energy demand from the fillet sections, higher mass (fish and brine) in each box and higher requirement of hot water for cleaning. This dataset is related to the conference paper "Energy flow analysis of an industrial ammonia refrigeration system and potential for a cold thermal energy storage" presented at the 15th IIR Gustav Lorentzen Conference on Natural Refrigerants, Trondheim, Norway 13-15 June 2022.</p>
ScienceDex guides
Understand access before you commit
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.