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7,877 results for “supplementary material”
Usage and Attribution of Stack Overflow Code Snippets in GitHub Projects — Supplementary Material
<p><em>Background:</em> Stack Overflow (SO) is the largest Q&A website for software developers, providing a huge amount of copyable code snippets. Using those snippets raises various maintenance and legal issues. SO’s license (CC BY-SA 3.0) requires attribution, i.e., referencing the original question or answer, and requires derived work to adopt a compatible license. While there is a heated debate on SO’s license model for code snippets and the required attribution, little is known about the extent to which snippets are copied from SO without proper attribution.</p> <p><em>Aim:</em> Our main goal was to analyze how often code from SO posts is used in public GitHub projects, but not attributed as required by the license. Further, we wanted to investigate if developers are aware of SO’s license and its implications, and to what degree they adhere to the attribution requirements defined in SO’s terms of service.</p> <p><em>Method:</em> We present results of a large-scale empirical study analyzing the usage and attribution of non-trivial Java code snippets from SO answers in public GitHub projects. We followed three different approaches to triangulate an estimate for the ratio of unattributed usages and conducted two online surveys with software developers to complement our results.</p> <p><em>Results:</em> For the different sets of projects that we analyzed, the amount of projects containing files with a reference to SO varied between 3.3% and 11.9%. We found that at most 1.8% of all analyzed repositories containing code from SO used the code in a way compatible with CC BY-SA 3.0. Moreover, we estimate that at most a quarter of the copied code snippets from SO are attributed as required, i.e., using a link in a source code comment. About half of the surveyed developers admitted copying code from SO without attribution. Furthermore, about two thirds of them were not aware of the license of SO code snippets and its implications.</p>
Supplementary material for "Demographic assessment of reintroduced bearded vultures in the Alps: success in the core, challenges in the periphery"
<p><strong>Abstract</strong></p> <ol> <li> Regular assessment of reintroduced populations is essential to guide management and provide lessons for other reintroduction projects. Bearded vulture <em>Gypaetus barbatus</em> reintroduction in the Alps began in 1986 with the release of the first fledglings, the first successful reproduction was recorded in 1997, and the population has grown steadily since. A previous assessment suggested that no further releases would be required to establish a self-sustaining population from a demographic point of view. However, this conclusion was based on a small sample size and spatially homogeneous demographic rates of released individuals, which may differ from and be spatially variable among wild-hatched individuals.</li> <li>Using longitudinal data and breeding site survey data, we constructed an integrated population model to examine the demography of the entire Alpine population, spatially stratified into a core and a periphery. We performed retrospective population analyses to identify demographic reasons of spatial differences in population growth, and conducted population viability analyses to assess the impact of future threats and reintroduction options.</li> <li>In 2021, an estimated 173 (CRI: 149-199) females were present in the Alps, of which 65 (CRI: 63-67) were breeders. Adult survival and productivity were higher in the core than in the periphery, so the population grew more strongly in the core than in the periphery. Differences in adult survival contributed most to the differences in population growth between the two areas.</li> <li>The population viability analysis predicts that the Alpine population will double in 10 years but that an increase in the mortality hazard above 0.055 will lead to a population decline. Unlike the population in the core, the population in the periphery is dependent on further releases at this stage.</li> <li>Bearded vulture reintroductions in the Alps have succeeded in creating a self-sustaining population with higher reproductive success and similar survival probabilities to the autochthonous Pyrenean population. In general, management should focus on preventing further mortality risks. In the periphery, reducing current mortality and increasing reproductive success are essential to make the population independent of releases.</li> </ol> <p> </p> <p><strong>Readme</strong></p> <p>Data files and code for all analyses and figures presented in the paper. The two data files are provided in csv format (SightingData.csv, OccupancyData.csv). There are five code files written for R, but some the main analysis requires software JAGS. The main code (IPM_Code.txt) contains a description of the data, code for loading and managing the data, and for fitting the integrated population model. The other files contain custom written functions (Functions.txt), code for the density dependence test (DensityDependence_Code.txt), code for the retrospective analyses (tLTRE_Code.txt) and code for miscellaneous statistics and figure generation (Figure_Code.txt).</p>
Supplementary materials of <<Breaking the spiral of silence of Spanish centralist nationalism>>
<p>Supplementary materials of the paper <<Breaking the spiral of silence of Spanish centralist nationalism. An analysis of the impact of the electoral emergence of Vox in the pu-blic discussion on the territorial organisation>> includes the following documents:</p> <p>- Readme<br>- Appendices (ENG)<br>- Apéndices (ESP)<br>- Replication package</p>
Supplementary Material for "Invasive plants are associated with increased fire frequency but decreased burn severity in Southern California shrubland ecosystems"
<p>This Zenodo repository contains all data, scripts, and supplementary materials for the manuscript entitled, "Invasive plants are associated with increased fire frequency but decreased burn severity in Southern California shrubland ecosystems".</p>
Supplementary material: Negative valence in Obsessive-Compulsive Disorder: A worldwide mega-analysis of task-based functional neuroimaging data of the ENIGMA-OCD consortium
<p>The ridge plots attached here accompany the supplement to the manuscript <em>Negative valence in Obsessive-Compulsive Disorder: A worldwide mega-analysis of task-based functional neuroimaging data of the ENIGMA-OCD consortium</em> (Dzinalija et al., 2024)<em>. </em>These are full results of Figures 1, 2C, and 3C of the manuscript and Figures S3, S5, S7 and S9 of the supplement depicting whole-brain Bayesian multilevel models run using the Regional Bayesian Analysis toolbox (RBA; Chen et al., 2019). Whole-brain analyses were parcelated into the Schaefer-Yeo 7-network 200-parcel cortical atlas (Schaefer et al., 2018) and the Melbourne 32-region subcortical atlas (Tian et al., 2020). Results are presented according to contrast of interests: [Negative > Neutral], [OCD > Neutral], [Threat > Neutral], and [OCD > Threat], and effects of interest: [Diagnosis = OCD or HC], [MED = medication], [AO = age of onset], [YBOCS = OCD severity], and [Intercept = task effect]. </p> <p>P+ values denote the probability that there is increased brain activation in a given region of the Schaefer 200-parcel 7-network cortical atlas and Melbourne 32-region subcortical atlas. We used the guidelines proposed by Chen et al. (2019) to infer credibility of evidence, namely taking a positive posterior probability (P+) of <0.10 or >0.90 as indication of moderate evidence and, <0.05 or >0.95 or <0.025 or >0.975 as strong or very strong evidence, respectively. To interpret the pairwise comparisons presented as Group1-vs-Group2, posterior distributions to the right of the green no-effect line represent regions in which individuals in Group 1 show credible evidence for higher activation than individuals in Group 2. Regions with posterior distributions to the left of this line show credible evidence for higher activity in Group 2 than in Group 1. (Darker) red color represents regions in which individuals in Group 1 show moderate-to-very-strong evidence for higher activation than Group 2. (Darker) blue color represents regions in which Group 2 show moderate-to-very-strong evidence for higher activation than Group 1. Grey color represents regions in which there is no strong evidence of a difference between Group 1 and Group 2. Schaefer-Yeo 200-parcel atlas name abbreviations can be retrieved <a href="https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parcellation/Schaefer2018_LocalGlobal/Parcellations">via this link.</a></p>
Supplementary material for "Dynamics of a goshawk population across half a century is driven by the variation of first-year survival"
<p><strong><span>Abstract</span></strong></p> <p><span>Population dynamics are driven by stochastic and density-dependent processes acting on demographic rates. Individuals differ demographically, and to capture these differences, models of population dynamics are usually structured by age and stage, rarely by sex. An effect of sex on population dynamics is expected if the dynamics of males and females differ, requiring an unequal sex ratio at birth and/or sex-specific survival probabilities. Goshawks (<em>Accipiter gentilis</em>) show large sexual size dimorphism and differential survival, but it is unknown whether males and females contribute differently to population dynamics. We studied a goshawk population in northern Germany over 47 years using brood monitoring data, collected feathers and nestling ringing data. We jointly analyzed the data using a two-sex integrated population model and performed retrospective and prospective population analyses to understand whether the demographic drivers of population change differ between the sexes. The population showed large fluctuations, during which the number of breeding pairs doubled, but the long-term trend of the population was slightly negative. Female survival exceeded male survival during the first year of life. Females started to reproduce at a younger age than males, productivity increased with female age, the sex ratio of nestlings was male biased and there was moderate male immigration. Despite these differences, temporal variation in sex ratio did not contribute to population dynamics and the contribution of temporal variation in survival was similar for both sexes. Variation in first-year survival was the strongest driver in this population, regulated by a weak density-dependent feedback acting through female first-year survival. Overall, the contributions of the two sexes to population dynamics were similar in this monogamous species with strong sexual size dimorphism.</span></p> <p><strong><span>Read me</span></strong></p> <p><span>Data files and code for carrying out all analyses and generating all figures presented in the paper. The six data files are provided in csv format. There are five code files written for R, but some of the main analyses require the NIMBLE software. The main code (IPM_Code.txt) contains a description of the data, code for loading and managing the data, and for fitting the integrated population models. The other files contain custom written functions (Functions.txt), code for performing posterior predictive tests (PPT_Code.txt), code for reporting results and performing various other analyses (Output_analyses_Code.txt), and code for generating figures (Figures_Code.txt).</span></p>
Supplementary Material to "Partial melting of amphibole–clinozoisite eclogite at the pressure maximum (eclogite type locality, Eastern Alps, Austria)"
<p><span>Here we briefly describe the supplementary materials for the publication “Partial melting of amphibole–clinozoisite eclogite at the pressure maximum (eclogite type locality, Eastern Alps, Austria)” in the European Journal of Mineralogy, 35(5), 715-735 Schorn, S., Rogowitz, A., & Hauzenberger, C. A. (2023).</span></p>
SOTorrent: Reconstructing and Analyzing the Evolution of Stack Overflow Posts — Supplementary Material
<p>Stack Overflow is the most popular question-and-answer website for software developers, providing a large amount of code snippets and free-form text on a wide variety of topics. Like other software artifacts, questions and answers on Stack Overflow evolve over time, for example when bugs in code snippets are fixed, code is updated to work with a more recent library version, or text surrounding a code snippet is edited for clarity. To be able to analyze how content on Stack Overflow evolves, we built <em>SOTorrent</em>, an open dataset based on the official Stack Exchange data dump. <em>SOTorrent </em>provides access to the version history of Stack Overflow content at the level of whole posts and individual text or code blocks.</p> <p>This dataset has been retrieved from <em>SOTorrent </em>using the following scripts:</p> <p><a href="https://doi.org/10.5281/zenodo.1201679">https://doi.org/10.5281/zenodo.1201679</a></p> <p>For the MSR 2018 paper about SOTorrent, we used the following scripts to analyze the data:</p> <p><a href="https://doi.org/10.5281/zenodo.1201706">https://doi.org/10.5281/zenodo.1201706</a></p> <p>The files <em>sample_before_10.ods</em> and <em>sample_after_10.ods</em> contain our qualitative analysis of 50 comments that were made up to 10 minutes before/after an edit.</p>
Supplementary Material for "Formal methods in dependable systems engineering: a survey of professionals from Europe and North America"
<p>This report contains supplemental material for <a href="https://link.springer.com/article/10.1007%2Fs10664-020-09836-5">this paper</a>, including a detailed analysis of responses to certain questions, further visualizations of the collected data, details on our analysis of related work, and a copy of the whole questionnaire. This material was shared for the period of peer review and has been significantly updated, extended, and included in <a href="https://link.springer.com/article/10.1007%2Fs10664-020-09836-5">this journal publication</a>.</p>
Supplementary material for "Palaeo-demographic modelling supports a population bottleneck during the Pleistocene-Holocene transition in Iberia"
<p>This Supplementary material encompasses the archaeological radiocarbon dates for the Iberian Peninsula analyzed in the article “<em>Palaeo-demographic modelling supports a population bottleneck during the Pleistocene-Holocene transition in Iberia</em>". Specifically:</p> <ul> <li>‘<strong>PALEODEM_dataset.csv</strong>’ provides the dataset in comma-separated format. Contains the compiled raw data of each radiocarbon date used by every analytical procedure.</li> <li>‘<strong>PALEODEM_sites.xlsx</strong>’ is a spreadsheet containing the basic information of each archaeological site analyzed in this work. The columns include ID_site, name of Archaeological site, n<sup>o</sup> of <sup>14</sup>C dates, n<sup>o</sup> of assemblages, Regional Unit of correspondence, and bibliographical Reference.</li> <li>‘<strong>REFERENCES for PALEODEM_sites.docx</strong>’ is a text archive that collects the bibliographical references listed in the above mentioned ‘Reference’ column, that have been the main sources of archaeological information.</li> </ul>
Supplementary material to the manuscript: Regionalised Heat Demand and Power-To-Heat Capacities in Germany - An Open Data Set for Assessing Renewable Energy Integration
<p>This is the supplementary material for the manuscript:</p> <p>"Regionalised Heat Demand and Power-To-Heat Capacities in Germany - an Open Data Set for Assessing Renewable Energy Integration"</p> <p>Article DOI: <a href="https://doi.org/10.1016/j.apenergy.2019.114161">https://doi.org/10.1016/j.apenergy.2019.114161</a></p> <p>Open access preprint: <a href="https://arxiv.org/abs/1912.03763">https://arxiv.org/abs/1912.03763</a></p> <p> </p> <p><strong>DESCRIPTION OF THE DATASET AND LICENSES:</strong></p> <p>The subdirectory "04_results" contains the regionalised heat demand an power-to-heat capacity data on administrative district level (NUTS-3) for Germany. The subdirectories "01_census_special_evaluation_data" and "02_other_input_data" contain the utilised input data. The subdirectory "03_code" contains the developed and applied source code.</p> <p>The data in this repository are provided under open source licenses. For license information and other general information on the supplementary material, refer to the LICENSE files and README files in the respective subdirectories.</p> <p>For a detailed description of the approach developed by the author, the input data used and the generated results, refer to the manuscript "Regionalised Heat Demand and Power-To-Heat Capacities in Germany - an Open Data Set for Assessing Renewable Energy Integration".</p> <p><strong>METADATA:</strong></p> <p>Sector: Residential Buildings – Space Heating and Domestic Hot Water</p> <p>Geographical scope: Germany</p> <p>Geographical resolution: Administrative districts (NUTS-3)</p> <p>Temporal scope: 2011, three scenarios for 2030</p> <p>Temporal resolution: 15min</p> <p> </p> <p><strong>UNITS:</strong></p> <p>In the final results folders (04_results/01_installed_heating_p2h_capacity; 04_results/02_daily_time_series; 04_results/03_yearly_time_series) the units of the data are indicated in the file names or the column names, e.g. by "in_MW". In case of unit indication in the file name, the unit refers to all columns in the file.</p> <p>In the intermediate results folder (04_results/00_sql_tables_exported_to_csv) all units referring to power are "kW" and all units referring to energy are "kWh".</p> <p><strong>NEWS AND CONTACT:</strong></p> <p>This dataset will be used as part of the <a href="https://wiki.openmod-initiative.org/wiki/Region4FLEX">region4FLEX model</a>. We are currently enhancing the data by temporally and spatially resolved COP time series and determining load shifting potentials. If you wish to receive news or have general questions please contact: wilko.heitkoetter@dlr.de. </p>
Redox paradox of vanadium in Tavorite LiVPO4F1-yOy : supplementary materials
<p>Vanadyl-type defects in vanadium oxy-fluoride phosphates confer interesting properties to these materials as positive electrodes in Li-ion or Na-ion batteries... <strong>List figures :</strong></p> <p><strong>2019-122-SM-FIGS1 :</strong> <strong>(a)</strong> Comparison of the SXRPD patterns obtained for the pristine LiVPO<sub>4</sub>F<sub>0.45</sub>O<sub>0.55</sub> material <em>in situ</em>, in the electrochemical cell, (blue) and in a sealed capillary (black). The symbols mark peaks not belonging to the LiVPO<sub>4</sub>F<sub>0.45</sub>O<sub>0.55</sub> phase (originating from lithium metal, beryllium, aluminum, PTFE, separator and Li<sub>3</sub>V<sub>2</sub>(PO<sub>4</sub>)<sub>3</sub> impurity). The grey areas represent the excluded 2θ regions for Rietveld refinement. <strong>(b)</strong> Comparison between voltage profiles obtained <em>in situ </em>in electrochemical cells during the XRD and XAS experiments and in coin cells. The small features seen at 3.7 and 4.1V originate from the Li<sub>3</sub>V<sub>2</sub>(PO<sub>4</sub>)<sub>3</sub> impurity.</p> <p><strong>2019-122-SM-FIGS2 :</strong> Rietveld refinement of (a) LiVPO<sub>4</sub>F<sub>0.45</sub>O<sub>0.55</sub> and (b) Li<sub>0.45</sub>VPO<sub>4</sub>F<sub>0.45</sub>O<sub>0.55</sub>, the PTFE contribution is represented by *. For (b) two phases are required to fit the pattern: LiVPO<sub>4</sub>F<sub>0.45</sub>O<sub>0.55</sub> (91(1) w%, blue markers) and Li<sub>0.25</sub>VPO<sub>4</sub>F<sub>0.45</sub>O<sub>0.55</sub> (9(1) w% brown markers).</p> <p><strong>2019-122-SM-FIGS3 :</strong> Rietveld refinement of the last pattern obtained <em>operando</em> after Lithium deintercalation from LiVPO<sub>4</sub>F<sub>0.45</sub>O<sub>0.55</sub> (#126, corresponding to an overall composition of Li<sub>0.2</sub>VPO<sub>4</sub>F<sub>0.45</sub>O<sub>0.55</sub>): the refinement was performed considering a mixture of 3 phases, Li<sub>0.45</sub>VPO<sub>4</sub>F<sub>0.45</sub>O<sub>0.55</sub> (orange), Li<sub>0.25</sub>VPO<sub>4</sub>F<sub>0.45</sub>O<sub>0.55</sub> (brown) and VPO<sub>4</sub>F<sub>0.45</sub>O<sub>0.55</sub> (red), with their contributions being of 17(1), 58(1) and 25(1) wt.%, respectively. The peak highlighted by # corresponds to the LiV<sub>2</sub>(PO<sub>4</sub>)<sub>3</sub> impurity (<em>i.e.</em> delithiated form of Li<sub>3</sub>V<sub>2</sub>(PO<sub>4</sub>)<sub>3</sub>). For the refinement, the profile and the atomic position of the secondary phases (i.e. LiVPO<sub>4</sub>F<sub>0.45</sub>O<sub>0.55 </sub>and VPO<sub>4</sub>F<sub>0.45</sub>O<sub>0.55</sub>) have been fixed based on their individual refinements (i.e. pattern #86 and <em>ex situ fully charged </em>pattern) whereas the cell parameters, profile and atomic positions of Li<sub>0.25</sub>VPO<sub>4</sub>F<sub>0.45</sub>O<sub>0.55 </sub>have been refined independently.</p> <p><strong>2019-122-SM-FIGS4 : (a)</strong> SXRPD patterns obtained <em>operando</em> during lithium extraction from LiVPO<sub>4</sub>F<sub>0.25</sub>O<sub>0.75</sub>, <strong>(b)</strong> Selected SXRPD patterns at specific compositions.</p> <p><strong>2019-122-SM-FIGS5 : </strong>Evolution of the volume changes for each Li<sub>x</sub>VPO<sub>4</sub>F<sub>1-y</sub>O<sub>y</sub> sample as function of x during the first step of the charge (i.e. until Δx = y).</p> <p><strong>2019-122-SM-FIGS6 : (a)</strong> The evolution of the pre-edge intensity (obtained by integration of the signal from 5464 to 5474 eV) and the edge position (taken at half jump) upon cycling.<strong> (b)</strong> The variance plot justifying the use of three components.</p> <p><strong>2019-122-SM-FIGS7 : (a)</strong> V K-edge XANES spectra of several Tavorite-type references: LiV<sup>III</sup>PO<sub>4</sub>F (black line), LiV<sup>IV</sup>PO<sub>4</sub>O (grey line), V<sup>IV</sup>PO<sub>4</sub>F (orange line) and V<sup>V</sup>PO<sub>4</sub>O (red line) and LiVPO<sub>4</sub>F<sub>0.45</sub>O<sub>0.55</sub> (purple line). <strong>(b)</strong> The enlargement of the pre-edge region with the typical energy position of each pre-edge contributions (<em>i.e.</em> F-V<sup>3+</sup>O<sub>4</sub>-F, O=V<sup>4+</sup>O<sub>4</sub>—O and O=V<sup>5+</sup>O<sub>4</sub>—O)</p> <p><strong>2019-122-SM-FIGS8 : </strong>Magnitude of the Fourier transforms of the reconstructed components obtained by MCR-ALS (k-range: 2.7-12.7 Å<sup>-1</sup>, sine window). Li<sub>x</sub>VPO<sub>4</sub>F<sub>0.45</sub>O<sub>0.55</sub> with x = 1, 0.45 and 0 respectively for components #1, #2 and #3. The black lines represent the fit done in the R space (R range: 1.0 – 2.05 Å, dR = 0.1 Å, sine window).</p> <p> </p> <p> </p> <p> </p> <p> </p> <p> </p> <p> </p>
Supplementary material: Efficient in vivo screening method for the identification of C4 photosynthesis inhibitors based on cell suspensions of the single-cell C4 plant Bienertia sinuspersici
<p>Data described in Minges et al. (2019) Efficient <em>in vivo</em> screening method for the identification of C<sub>4</sub> photosynthesis inhibitors based on cell suspensions of the single-cell C<sub>4</sub> plant <em>Bienertia sinuspersici</em>. doi: <a href="https://doi.org/10.3389/fpls.2019.01350">10.3389/fpls.2019.01350</a></p> <p> </p>
Cretaceous-scope supplementary material to "The Cretaceous World: Plate Tectonics, Paleogeography, and Paleoclimate"
<p>Cretaceous Supplemental Materials for the study ‘<em>The Cretaceous World: Plate Tectonics, Paleogeography and Paleoclimate</em>’ by C.R. Scotese C. Vérard, L. Burgener, R. P. Elling and A.T. Kocsis (<a href="https://doi.org/10.1144/sp544-2024-28">https://doi.org/10.1144/sp544-2024-28</a>). Please cite this article if you use any material here in your publication.</p> <p>Please see the included '<em>Cretaceous Supplemental Materials Explanation.docx</em>' document for description of supplementary items and table of contents. </p>
Phanerozoic-scope supplementary material to "The Cretaceous World: Plate Tectonics, Paleogeography, and Paleoclimate" from the PALEOMAP project
<p>Phanerozoic Supplemental Materials for the study ‘<em>The Cretaceous World: Plate Tectonics, Paleogeography and Paleoclimate</em>’ by C.R. Scotese C. Vérard, L. Burgener, R. P. Elling and A.T. Kocsis (<a href="https://doi.org/10.1144/sp544-2024-28">https://doi.org/10.1144/sp544-2024-28</a>). Please cite this article if you use any material here in your publication.</p> <p>Please see the included '<em>Phanerozoic Supplemental Materials Explanation.docx</em>' document for description of supplementary items and table of contents. </p>
Evaluating Open Science Practices in Indoor Positioning and Indoor Navigation Research (Supplementary Material: Full Paper Listing and Analysis)
<p>Supplementary material of the paper:</p> <p>Title: "Evaluating Open Science Practices in Indoor Positioning and Indoor Navigation Research"<br>Subtitle: "A Survey of the IPIN's Reference Papers of 2022 and 2023 Editions"</p> <p>The paper is accepted to the "14th International Conference on Indoor Positioning and Indoor Navigation, IPIN 2024, Hong Kong, October 14-17, 2024, IEEE, 2024.</p> <p>An Author's accepted version of the manuscript is available here: <a href="../records/13684170" target="_blank" rel="noopener">https://zenodo.org/records/13684170</a> </p> <p>If you want to refer to this work, please cite this Zenodo entry as well as the published conference version.</p> <p> </p> <p>---------------------------------------</p> <p>This entry contains two files:</p> <ul> <li>"Paper Characterization Spreadsheet.xlsx": <strong>The spreadsheet of the full analysis of this work</strong>, as described in the paper. It characterizes various features of the analyzed papers and forms the raw data on which the analyses of our work were based.</li> <li>"Main features of the manuscripts analysed in Zenodo Record #12088175.pdf": A document summarizing the main features of the IPIN's Reference Papers of the 2022 and 2023 Editions, that contain some form of open resources (Open Data, Code, or Material).</li> </ul> <p> </p> <p> </p> <p> </p>
Supplementary Material: Knobs and dials of retrieving JWST transmission spectra. I. The importance of p-T profile complexity
<p>This is supplementary material to <a title="Schleich et al. (2024)" href="https://www.aanda.org/articles/aa/abs/2024/10/aa51845-24/aa51845-24.html" target="_blank" rel="noopener">Schleich et al. (2024)</a>. The content of the provided data repository (also described in the file "content.txt") is as follows:</p> <p> </p> <h2>ADDITIONAL ANALYSIS</h2> <p>This folder contains a collection of ancillary data products for the evaluation of the retrievals performed in this work.</p> <ul> <li>'bayes-factor' contains the data tables for evaluating the Bayes' factor for each separate collection of models(*)</li> <li>'corner-plots' contains a collection of all corner plots associated with the individual input cases</li> <li>'fit-residuals' contains all fit residuals for the individual atmospheric retrievals performed in this work (used to make Fig. C.1)</li> <li>'resampled-pt-profiles' contains resampled p-T profiles to generate Figs. 6 and F.1</li> <li>'retrieval-accuracy' contains additional plots related to the accuracy of each retrieval (used to make Fig. 5, as well as Figs. E.1 - E.5)</li> </ul> <p><br>(*) SIDE NOTE:<br>Table headers in the "bayes-factor" data tables reference evidence reported from MultiNest (variable "Z"), and calculated Bayes factor (variable R). The case with log(R) = 0 is necessarily the reference case, and outliers are marked in a binary table with 1 (|log(R)| > 5) or 0 (|log(R)| < 5). In all cases, "log" refers to the natural logarithm.</p> <ul> <li>If someone actually reads this, I'm sorry. I also spent way too much time trying to track down if the values reported in MultiNest are natural or base-10 logarithm. I have now been convinced that it is worth it, always, to either specify "ln" for the base-e logarithm, or give the base of your logarithm if your write it down (i.e. log_10(X)) -Simon.</li> </ul> <h1> </h1> <h2>RETRIEVAL RESULTS</h2> <p>This folder contains the data products associated with the retrieval runs for each synthetic spectrum. The sub-directories are aranged by the following keys:</p> <ul> <li>'drs' and 'pandexo' refere to the two noise cases considered</li> <li>'inv-t' and 'norm-t' refere to the two underlying p-T profiles used to make the synthetic spectra</li> <li>'hpc', 'mpc', and 'lpc' refere two the three cloud-top pressure cases considerd</li> </ul> <p>Each individual folder contains (1) the TauREx parameter files for running retrievals using the selection of p-T profiles, (2) a folder called 'results', which containts the associated data products, and (3) a folder called 'chains', which stores the ancillary data products associated with the MultiNest sampling runs of each retrieval.</p> <p> We note that for the "drs_inv-t_mpc" case, the chains for the isothermal, 2-point, and 4-point runs have been lost</p> <p> </p> <h2>SYNTHETIC SPECTRA</h2> <p>This folder contains data products associated with the sample of synthetic transmission spectra.</p> <ul> <li>'pt-profile_*.csv' are csv-files containing the p-T points used to make Figure 1 , and to generate the synthetic transmissions spectra</li> <li>'forward-models' contains TauREx parameter files and forward models for the sample of synthetic transmission spectra. Each of the sub-directories also contains a faux-spectrum representing the wavelength-map of NIRSpec PRISM <ul> <li>'no-clouds' contains contains the above for generating Figure 3.</li> <li>'inv-t' contains forward models using the "inverse" p-T profile</li> <li>'norm-t' contains forwrad models using the "monotonic" p-T profile</li> </ul> </li> </ul>
Infrared Video of Bone Drilling - Supplementary material for article "Thermal Evaluation of Bone Drilling: Assessing Drill Bits and Sequential Drilling"
<p>Video 1 shows sequential bone drilling with 5 drill bits (⌀2.0 mm, ⌀2.5 mm, ⌀3.2 mm, ⌀3.7 mm, and ⌀4.1 mm) used in series following the manufacturer's recommended spindle speeds.</p> <p>Video 2 shows bone drilling with a single drill bit (⌀2.0 mm) with a spindle speed of 1500 rpm.</p> <p>These videos are supplementary to the article, "Thermal Evaluation of Bone Drilling: Assessing Drill Bits and Sequential Drilling" published in the journal <em>Bioengineering. </em></p>
Supplementary material for journal article "Challenge dose titration in a Mycobacterium bovis infection model in goats"
<p>Supplementary Figure and Table to Journal article. Figure shows daily rectal temperature of each animal after inoculation. Table 1 shows number and volume of pulmonary lesions for each animal as detected by computed tomography imaging. Table 2 gives details about scoring used at clinical examination.</p>
Supplementary material (part 2): "Evaluation of AROME Model Valley Wind Simulations in the Inn Valley, Austria"
<p><em>Part 2</em> of supplementary material for the Master's Thesis: "Evaluation of AROME Model Valley Wind Simulations in the Inn Valley, Austria" (Wibmer 2024, available <a href="https://resolver.obvsg.at/urn:nbn:at:at-ubi:1-151801">here</a>).</p> <p>Due to memory constraints, the supplementary material consists of two parts:</p> <ul> <li><em><strong>Part 1: </strong></em>(available <a href="https://doi.org/10.5281/zenodo.10849397" target="_blank" rel="noopener">here</a>) Includes Python scripts and model setup files, along with the first part of the datasets, including ERA-reanalysis data, observational data, and the preprocessed AROME model output (NetCDF files) of the <em>0.5-km</em> simulation.</li> <li><em><strong>Part 2: </strong></em>Includes the preprocessed AROME model output (NetCDF files) of the <em>1.0-km </em>and <em>2.5-km</em> simulations (see description below).</li> </ul> <p>To reproduce part of the figures, users must download the Python scripts and the preprocessed AROME model datasets (NetCDF files). <br>The Python scripts should be placed in the same parent folder because some of them depend on each other <strong>(!! Important !!).</strong><br>Original AROME model output files (GRIB2 format) are not published due to their large size.</p> <p>The naming convention for the AROME simulations uses OP* (where * represents the grid spacing in meters) to differentiate the model runs based on their horizontal<br>grid spacing:</p> <ul> <li><strong><em>OP2500:</em></strong> for 2.5 km</li> <li><em><strong>OP1000: </strong></em>for 1.0 km</li> <li><em><strong>OP500:</strong></em> for 0.5 km</li> </ul> <h3><strong>Datasets Part 2</strong></h3> <p>Due to memory constraints, the datasets needed for the analyses are split up into two parts. The second part of the supplementary material contains:</p> <ul> <li><strong>datasets_OP1000.tar.xz</strong>: Contains the preprocessed AROME-Aut model output data (NetCDF files) of the <em>1.0-km</em> simulation. </li> <li><strong>datasets_OP2500.tar.xz</strong>: Contains the preprocessed AROME-Aut model output data (NetCDF files) of the <em>2.5-km</em> simulation. </li> </ul> <p>The datasets of the<em> 0.5-km</em> simulation (<strong>datasets_OP500.tar.xz</strong>)<strong> </strong>can be found in Part 1 of the supplementary material (available <a href="https://doi.org/10.5281/zenodo.10849397" target="_blank" rel="noopener">here</a>).<br>The NetCDF datasets of the performed AROME-Aut simulations are packaged and compressed into <code><em><strong>.tar.xz</strong></em></code> files.<br>The Python scripts, available <a href="https://doi.org/10.5281/zenodo.10849397" target="_blank" rel="noopener">here</a>, require these NetCDF datasets for plotting and analyses routines.<br>The provided NetCDF datasets are preprocessed from the <em>GRIB2</em> output of the AROME-Aut simulations. <br>For the scripts to function properly, you need to adjust the path to the datasets within <code><strong>path_handling.py</strong></code><strong>.</strong></p> <p>Each <strong><code>datasets_OP*.tar.xz</code></strong> file contains NetCDF files for different type of levels: <em>surface, hybridPressure </em>(model levels)<em>, isobaricInhPa </em>(pressure levels),<em> meanSea </em>(mean sea level)<em>, heightAboveGround </em>(constant height levels)<em>. </em> The following naming convention for the datasets is used:</p> <ul> <li><strong>ds_OP*_<em>var</em>_hybridPressure_<em>[lon1, lon2, lat1, lat2]</em>.nc</strong>: Contains data on <em>hybrid pressure model levels</em> for a specific variable (<em>var</em>; e.g., <em>u, v, z, pres, q, t</em>) for the geographical extent defined in the brackets. </li> <li><strong>ds_OP*_interp_hybridPressure_<em>(lon,lat)</em>.nc</strong>: Combined dataset on <em>hybrid pressure model levels.</em> The data is bilinearly interpolated to the specified location <em>(lon, lat)</em>.</li> <li><strong>ds_OP*_<em>var</em>_surface_<em>whole</em>.nc</strong>: Contains data on <em>model surface </em>for a specified variable (<em>var</em>; e.g., <em>z, sp, t, tcc</em>) for the <em>whole </em>available domain extent.</li> <li><strong>ds_OP*_heightAboveGround_instant_<em>whole</em>.nc</strong>: Combined dataset on <em>height levels </em>(e.g., <em>2-m and 10-m</em>) for the <em>whole </em>available domain extent.</li> <li><strong>ds_OP*_<em>var</em>_meanSea_<em>whole</em>.nc</strong>: Contains data on <em>mean sea level</em> for specified variable (<em>var;</em> e.g., <em>prmsl</em>) for the <em>whole</em> available domain extent. </li> </ul> <p>The original GRIB2 files are not provided due to their large size. For further information about the GRIB2 files or the NetCDF datasets, please feel free to contact me.</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.