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12,393 results for “materiality”
Material Efficiency Policy and Nationally Determined Contributions
<p>This is a table containing the data used to create Table 4, Number of G20 countries that include energy or material efficiency commitments in 2nd round of National Determined Contributions in the paper, Policy for material efficiency: Enabling new climate change mitigation strategies by Lifset et al.</p>
Supplementary material: High and hyper: is serotonin to blame for fentanyl-induced psychomotor side-effects in pigs?
<p>Supplementary material for article paper High and hyper: is serotonin to blame for fentanyl-induced psychomotor side-effects in pigs? </p>
Additional Material for Paper: IT Managers' Perspective on Technical Debt Management
<p>This is the additional material for the Paper "IT Managers’ Perspective on Technical Debt Management" submitted to the Journal of Systems and Software.</p> <p>The folder contains the following files:</p> <p> </p> <ul> <li>Consent form - blinded.pdf / Consent form.pdf:<br> The consent form was used to gather the participants' consent to participate in this study.</li> <li>PreliminarySurvey.pdf:<br> The survey was sent to all participants in advance to gather basic statistical data.</li> <li>ParticipantsOverview.pdf / ParticipantsOverview.xslx<br> The overview of all participants was extracted from the preliminary survey. For anonymity reasons, we can not provide the country/language of the participants.</li> <li>InterviewGuide.pdf<br> The interview guide was followed by the interviewers, including all questions and the rationale for questions added before the 2nd iteration.</li> <li>CodeSystem.xlsx<br> All Codes were gathered from the interviews with a short explanation (in Excel to use the grouping function for a better overview).</li> <li>AnalyticMemos_Themes.pdf<br> All free memos were created during the study, including all themes that led to the main concerns described in the paper.</li> <li>Focusgroup-discussion_Themes_slides.pdf<br> The slides were created for the focus group discussion. The participants were introduced to the "main concerns" and asked to comment on these findings.</li> <li>V4C_model.drawio<br> This is the original drawio file of our V4C model, including all diagrams from the paper. Additionally, we provide the complete version of the visibility diagram, which had to be reduced in the paper due to the page limitation. Also, the file contains one more diagram with another example of the model's usage.</li> <li>V4Cmodel.pdf, V4Cmodel_example.pdf, VisibilityOfCausesConsequences.pdf; VisibilityCycles.pdf<br> All diagrams of the paper are in single PDF files.</li> <li>V4CTDmodel+example.pptx<br> A short presentation of the model and an example of its usage in PowerPoint format to immediately use.</li> </ul>
Supplementary materials to: "SilicH2O: a graphical user interface for processing silicate glass Raman spectra and quantifying H2O"
<p>The dataset contains:</p> <ul> <li>supplementary text and figures as a single pdf</li> <li>Raman and compositional data in two separate excel files</li> </ul> <p> </p>
Supplementary material for 'The MAP metric in Information Retrieval Fault Localization'
<pre># map_bench4bl This is the supplementary material, data, and evaluation source code for the paper "The MAP metric in Information Retrieval Fault Localization" by Thomas Hirsch and Birgit Hofer. ## Preliminaries ### Python environment - Python 3.8 - pandas - numpy - matplotlib ## Datasets The [Bench4BL](<em>https://github.com/exatoa/Bench4BL</em>) dataset has been used in this evaluation, with the addition of intermediate files taken from the [SABL](<em>http://dx.doi.org/10.5281/zenodo.4681242</em>) experiment performed on this Bench4BL dataset. All data used in our evaluation is included in this repository. However, if the data is to be re-imported directly from these benchmark and datasets they have to be downloaded first and their local paths have to be set in [paths.py](<em>paths.py</em>). ### Bench4BL The Bench4BL dataset was published with the paper "Bench4BL: Reproducibility study on the performance of IR-based bug localization" by Lee, J., Kim, D., Bissyandé, T.F., Jung, W. and Le Traon, Y.. The dataset can be obtained [here](<em>https://github.com/exatoa/Bench4BL</em>). Follow the steps described in the corresponding [README](<em>https://github.com/exatoa/Bench4BL/blob/master/README.md</em>) to set up the dataset. The Bench4BL dataset contains the _old subjects_ subdataset, containing 558 bugs from AspectJ, JDT, PDE, SWT, and ZXing that have been widely used in older IRFL studies. This _old subjects_ subdataset was used in answering our RQ1, as discussed below, the corresponding scripts use _old subjects_ in their name to highlight this. #### SABL The SABL dataset is the online appendix of the paper "An Extensive Study of Smell-Aware Bug Localization" by TTakahashi, A., Sae-Lim, N., Hayashi, S. and Saeki, M.. The dataset can be downloaded [here](<em>http://dx.doi.org/10.5281/zenodo.4681242</em>). The experiments in this dataset build on top of Bench4BL and intermediate files are provided in the datapackage. #### Rankings Rankings for BLIA, BRTracer, and BugLocator were produced by running these tools on Bench4BL locally. Rankings for AmaLgam and BLUiR were taken from the SABL experiment dataset. ## Structure ### Folders Bench4BL ground truths: - bench4bl_old_subjects_summary - bench4bl_summary Localization results of the included tools in Bench4BL: - bench4bl_localization_results - bench4bl_localization_results_sabl Target projects size metrics: - cloc_results - cloc_results_old_subjects Utility functions: - utils Output folders containing results, generated figures and tables: - results - results_old_subjects ### Scripts Scripts for re-importing data from Bench4BL and SABL datasets: - data_preparation_step_1_cloc_bench4bl.py - data_preparation_step_1_cloc_old_subjects_bench4bl.py - data_preparation_step_2_import_ground_truth_from_bench4bl.py - data_preparation_step_2_import_ground_truth_from_old_subjects_bench4bl.py - data_preparation_step_3_import_bench4bl_ranking_results.py - data_preparation_step_3_import_sabl_ranking_results.py Utilities: - paths.py - utils/bench4bl_utils.py - utils/Logger.py ### Evaluation scripts for the corresponding research questions: **Dataset analysis:** - rq_0_dataset_analysis_bench4bl_issues.py **RQ1: How big is the average ground truth in Bench4BL datasets, and what proportion of bugs have a ground truth containing multiple files?** - rq_1_bench4bl_ground_truth_size.py - rq_1_old_subjects_bench4bl_ground_truth_size.py RQ2: Do the IRFL tools included in Bench4BL truncate their results? - rq_2_ranking_lengths.py **RQ3: How strong is $AP_{asrd}$ overestimating $AP_{mb}$ for truncated BugLocator retrieval results on the Bench4BL dataset? RQ3a: How strong is $AP_{asrd}$ overestimating $AP_{mb}$ for truncated BugLocator retrieval results when considering the bloated ground truth issue found in Bench4BL?** - rq_3_truncating_BugLocator_rankings_bench4bl.py **RQ3b: How strong is $AP_{asrd}$ overestimating $AP_{mb}$ for truncated BugLocator retrieval results when undefined $AP$ values are simply ignored?** - rq_3b_undefined_ap_BugLocator_rankings_bench4bl.py ## Licence All code and results are licensed under [CCA v4](<em>https://creativecommons.org/licenses/by/4.0/</em>), according to LICENSE file. Other licences may apply for some tools and datasets contained in this repo: [cloc-1.92.pl](<em>https://github.com/AlDanial/cloc</em>) under GPL v2, [Bench4BL](<em>https://github.com/exatoa/Bench4BL</em>) and [SABL](<em>http://dx.doi.org/10.5281/zenodo.4681242</em>) under CCA 4.0.</pre>
Soft skills required from software professionals in New Zealand (supplementary material)
<p>This repository contains supplementary material for the manuscript "Soft skills required from software professionals in New Zealand" published in Information and Software Technology (https://doi.org/10.1016/j.infsof.2023.107232):</p> <ul> <li>adverts.zip: PDF or HTML files of analyzed adverts.</li> <li>adverts_and_soft_skills.xlsx: Mapping of adverts to identified soft skills.</li> <li>hiring_companies_details.xlsx: Details about each hiring company that posted adverts, including their size (number of employees), core business (software/non-software), domain (standard sector), domain (non-standard sector [if applicable]), geographic distribution and target markets.</li> <li>recruitment_agencies.txt: Names of recruitment agencies that posted adverts.</li> </ul>
Host symbiont gene reconciliation supplementary material
<p>Cinara aphids dataset was obtained from the data of article by Manzano-Marin et al. ISME, 2019, and we chose a representative subset of the species present in the gene trees. We used an exterior source for the phylogeny for the enterobacteria present in the gene trees using Annotree (Mendler et al., Nucleic Acids Research, 2019) (for the one that are not associated to Cinara aphids, and are thus "free living" in this setting). </p> <p>Helicobacter pylori dataset was constructed by Alexia Nguyen Trung, gathering available whole genome sequences on NCBI with assigned geo populations on NCBI or pubMLST. <br> A phylogenetic tree was built based on the concatenation of universal-unicopy genes (322 genes), and a sample of 113 strains representing the diversity of H. pylori in the old world (excluding strains from the Americas) was obtained using Treemmer (Menardo et al, BMC Bioinformatics, 2018).<br> Then, 6 non pylori strains were added (H. hepaticus, H. acinonychis, H. canadensis, H felis, H. bizzozeronii, H. cetorum), as an external group. <br> In this study we considered the 1034 gene families, including 322 universal unicopy family, which displayed strains from the external group and from at least 3 continents.<br> The taleoutput repository contains the recphyloxml outputs of the methods used in the paper, am stands for the approach with amalgamation of the universal unicopy genes to construct a strain tree, while nc refers to the results with the tree constructed from the concatenate, and then the repositories refer to the putative population trees 1, 2, 3 and 4. 0u_0 is the strains genes reconciliation in recphyloxml format. 0upper is the host strains reconciliation in recphyloxml format.</p> <p>Finally, the last repository contains the simulated dataset. It was generated using Sagephy https://compbio.engr.uconn.edu/software/sagephy/ https://doi.org/10.1093/bioinformatics/btz081<br> For each instance, a host tree, a symbiont tree, and 5 gene trees were generated.</p> <p>We used the parameters proposed in https://doi.org/10.1145/3307339.3342168 \cite{kordi_inferring_2019}, as representative of small (D 0.133, T 0.266, L 0.266), medium (D 0.3, T 0.6, L 0.6) and high (D 0.6, T 1.2, L 1.2) transfer rates, without replacing transfers. The software enables to specify an inter transfer rate, corresponding to the probability for a gene transfer between different hosts. When a horizontal transfer is chosen during generation of the gene tree (inside a symbiont tree and knowing a host/symbiont reconciliation), the transfer is chosen to be an inter host one with the inter transfer rate. So an inter transfer rate of 0 corresponds to only intra transfer, and of 1 corresponds to a case where transfers are only between symbionts in separate hosts.</p> <p><br> We constructed two simulated datasets, one with a combination of the different rates for the DTL parameters (varrates), and one with only medium rates but with different rates of "inter" and "intra" transfers (coevol).<br> For the first dataset, we used all 9 combinations of small, medium and high rates for the symbiont generation and the gene generation, with only intra host gene transfer (i.e. an inter transfer rate of zero).<br> For the second dataset, we used only medium rates for both symbiont and genes generation, but we used 6 inter transfer rates going from 0 to 1. </p> <p>For both datasets, and for each set of rates, we generated 50 instances consisting of 1 host tree with 100 leaves, 1 symbiont tree and 5 gene trees, each generated in the pruned version of the other trees (branch that do not reach present are pruned before the generation of the next tree). We then kept each host leaves with a probability of 0.08 to simulate unexhaustive sampling, resulting in host trees with an average size of 8 leaves.<br> This ended up to 399 instances for the first dataset and 226 instances for the second one, and at least 29 instances of 5 genes for each set of parameters.</p> <p>Each repositiory is a simulation instance, varrates_k_l_i correspond to simulation number i with lower rate k and upper rate l. genes, symbiont, species are repositories containing the trees in newick of the genes, symbiont and host in newick. Gene trees are unrooted. Lower matching is a matching between gene and symbiont leaves, upper matching between symbiont and host leaves, gene_host_matching is a matching between gene and host leaves. Transfer list contains one file for each gene and with all transfers simulated, donor and receiver symbiont internal nodes.<br> Each instance also contains the output of tale used in the paper, with the three heuristic, the 2-level symbiont gene (_2l), the 3-level sequential heuristic (_dec) and the 3-level monte carlo approach (_mc) with 50 iterations. All the launch were with 5 rounds of parameters estimation (the default usage). The 0u_0 contain a sampled symbiont gene reconciliation in recphyloxml, and for the 3-level heuristics, 0upper a corresponding host symbiont reconciliation in recphyloxml (multiple ones for the montecarlo i_upper and iu_0 for i from 0 to 49). A known error in the recphyloxml transcription script, now corrected, has induced some errors in some of the recphyloxml files : for some transfers the indicated receiver species is the donor and not the receiver, however redundancy in the format makes it possible to retrieve the information by looking at the matching species in the next event of the gene, that will be the receiver species, we chose to leave it this way instead of relaunching all the computations, as it has no impact on the figures and results presented in our article (mostly constructed using the freq files). The files freq contains information on the frequencies of the different events summed up over gene symbionts reconciliation, lower_log_likelihood contains the log likelihood of the host and symbiont trees knowing the genes (the probability of the genes knowing the host and symbiont).</p>
Formica exsecta comparison of the bacterial and fungal microbiomes of nest material and the ants
<p>This study explores the microbiome of the ant <em>Formica exsecta,</em> and compares this to the microbiome found in the nest material. We found fundamental differences in both the bacterial and the fungal communities between ants and their nest material, but no significant differences in the bacterial and fungal communities among colonies. Species diversity, species richness, and evenness were all significantly lower for bacteria in ants than in nest material, whereas for fungi only species richness was lower in ants, than in nest material. No such differences were found among ants from diffrent colonies.</p>
Supplementary material to 'Gamma Cascades in Gadolinium Isotopes'
<p>The two data files contain a list of 10^7 gamma cascades in Gd-156 and Gd-158 each.</p> <p>The gamma cascades are calculated within the framework of the statistical Hauser-Feshbach model for neutron capture on Gd-155 and Gd-157. The neutron energy was set to 5 keV. The data set relate to Figs.6</p> <p>and 14 of the publication.</p>
Data and Supplemental Materials for "Unraveling the Geologic History of Miranda's Inverness Corona"
<p>This set of materials contains:</p> <p>(1) Topographic Profiles 1-8 (or A-H) with associated codes for FFT analysis</p> <p>(2) Modulated Transfer Function (MTF) filter applied to Voyager 2 images for processing</p> <p>(3) ArcPro Map Package containing the geologic map of Inverness Corona and basemap images</p> <p> </p>
Supplementary materials for Education and Information Technologies
<p>Anonymized supplementary materials for publication 'Using Data Clustering to Reveal Trainees’ Behavior \\in Cybersecurity Education' in the journal Education and Information Technologies</p> <p> </p>
Comparison of Root End Sealing Ability of three Retrograde Filling Materials in Teeth with Root Apices Resected at 900 using dye penetration method under fluorescent microscope.
<p>Checking the depth of dye penetration and thereby evaluating the sealing ability of retrograde materials</p>
Supplementary Materials: Three years of wastewater surveillance for new psychoactive substances from 16 countries
<p>Supplementary Materials</p>
Dataset from Nature Materials paper: Amorphous nickel hydroxide shell tailors local chemical environment on platinum surface for alkaline hydrogen evolution reaction
<p>Dataset of the paper "Amorphous nickel hydroxide shell tailors local chemical environment on platinum surface for alkaline hydrogen evolution reaction" accepted in Nature Materials.</p> <p>- GCGA_inputs.zip: A zip file containing all needed input files to run a grand canonical genetic algorithm (GCGA) global optimization structure search. Note that the script would need modifications to be compatible with later version of the GOCIA package, please following the most updated instructions at https://github.com/zishengz/gocia</p> <p>- GCGA_Ni12OxHy_all_samples.db: An ASE database file containing all unique structures from the GCGA search of Ni12OxHy on a Pt(111) surface. </p> <p>- GM_Ni12O25H13.vasp: The structure of the global minimum structure from GCGA search, which is also the surface structure we focused on in this study, in VASP structure format.</p> <p>- rxn_structures.zip: A zip file containing the structures of reaction intermediates investigated in this work, in VASP structure format</p> <p> </p>
Supplementary materials for: Exploring the impact of read clustering thresholds on RADseq-based systematics: an empirical example from European amphibians
<p><span>Restriction site-Associated DNA sequencing (RADseq) has great potential for genome-wide systematics studies of non-model organisms. However, accurately assembling RADseq reads into orthologous loci remains a major challenge in the absence of a reference genome. Traditional assembly pipelines cluster putative orthologous sequences based on a user-defined clustering threshold. Because improper clustering of orthologs is expected to affect results in downstream analyses, it is crucial to design pipelines for empirically optimizing the clustering threshold. While this issue has been largely discussed from a population genomics perspective, it remains understudied in the context of phylogenomics and coalescent species delimitation. To address this issue, we generated RADseq assemblies of representatives of the amphibian genera <em>Discoglossus</em>, <em>Rana</em>, <em>Lissotriton</em> and <em>Triturus</em> using a wide range of clustering thresholds. Particularly, we studied the effects of the intra-sample Clustering Threshold (iCT) and between-sample Clustering Threshold (bCT) separately, as both are expected to differ in multi-species data sets. The obtained assemblies were used for downstream inference of concatenation-based phylogenies, and multi-species coalescent species trees and species delimitation. The results were evaluated in the light of a reference genome-wide phylogeny calculated from newly generated Hybrid-Enrichment markers, as well as extensive background knowledge on the species' systematics. Overall, our analyses show that the inferred topologies and their resolution are resilient to changes of the iCT and bCT, regardless of the analytical method employed. Except for some extreme clustering thresholds, all assemblies yielded identical, well-supported inter-species relationships that were mostly congruent with those inferred from the reference Hybrid-Enrichment data set. Similarly, coalescent species delimitation was consistent among similarity threshold values. However, we identified a strong effect of the bCT on the branch lengths of concatenation and species trees, with higher bCTs yielding trees with shorter branches, which might be a pitfall for downstream inferences of evolutionary rates. Our results suggest that the choice of assembly parameters for RADseq data in the context of shallow phylogenomics might be less challenging than previously thought. Finally, we propose a pipeline for empirical optimization of the iCT and bCT, implemented in optiRADCT, a series of scripts readily usable for future RADseq studies.</span></p>
Co-manipulation of soft-materials estimating deformation from depth images [Dataset]
<p>The dataset and training results used in the paper "Co-manipulation of soft-materials estimating deformation from depth images" G. Nicola, E. Villagrossi, N.Pedrocchi submitted at Robotics and Computer Integrated Manufacturing.</p>
Figure S51 in Supplementary Materials for Precipitation is the main axis of tropical plant phylogenetic turnover across space and time
Figure S51. Higher resolution version of Figure 1. See Figure 1 for caption.
Supporting data for: Optical properties of electrochemically gated La1-xSrxCoO3-δ as a topotactic phase-change material
<p>The data included here contain the information necessary to recreate the figures in a manuscript titled "<em>Optical Properties of Electrochemically Gated La<sub>1-x</sub>Sr<sub>x</sub>CoO<sub>3-δ</sub> as a Topotactic Phase-Change Material</em>". The data files include scanning transmission electron microscopy (STEM) images of electrochemically gated La<sub>1-x</sub>Sr<sub>x</sub>CoO<sub>3-δ</sub> (LSCO) films, finite-difference time-domain (FDTD)-simulated electric field and reflectance data for LSCO-based metasurfaces, transfer-matrix model reflectance data for LSCO films on gold substrates, complex refractive index data for LSCO films before and after electrochemical gating, electronic resistivity data for LSCO films before and after electrochemical gating, source-drain current measurements of LSCO films during electrochemical gating, and X-ray diffraction data for LSCO films before and after electrochemical gating.</p>
Figure S12 in Supplementary Materials for Precipitation is the main axis of tropical plant phylogenetic turnover across space and time
Figure S12 (lef). Numbers of taxa per alignment.
Figure S8 in Supplementary Materials for Precipitation is the main axis of tropical plant phylogenetic turnover across space and time
Figure S8 (lef). Percentages of reads on target per sample.
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.