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3,673 results for “practices”
Digital Twins - from industrial management to healthcare practice
<p>A guest seminar offered by SCImPULSE Foundation CTO Taghi Aliyev for the University of Parma (IT) master "ARTE" https://www.masterarte-unipr.it/</p>
Digging deeper into colonial palaeontological practices in modern day Mexico and Brazil
<p>Scientific practices stemming from colonialism, whereby middle- and low-income countries supply data for high-income countries and the contributions of local expertise are devalued, are still prevalent today in the field of palaeontology. In response to these unjust practices, countries such as Mexico and Brazil adopted protective laws and regulations during the twentieth century to preserve their palaeontological heritage. However, scientific colonialism is still reflected in many publications describing fossil specimens recovered from these countries. Here, we present examples of ‘palaeontological colonialism’ from publications on Jurassic–Cretaceous fossils from NE Mexico and NE Brazil spanning the last three decades. Common issues that we identified in these publications are the absence of both fieldwork and export permit declarations and the lack of local experts among authorships. In Mexico, access to many fossil specimens is restricted on account of these specimens being housed in private collections, whereas a high number of studies on Brazilian fossils are based on specimens illegally reposited in foreign collections, particularly in Germany and Japan. Finally, we outline and discuss the wider academic and social impacts of these research practices, and propose exhaustive recommendations to scientists, journals, museums, research institutions and government and funding agencies in order to overcome these practices.</p> <p> </p> <p><strong>Files included:</strong></p> <p><strong>Table S1.</strong> Sabinas, La Popa and Parras basins fossil publications by foreign authors</p> <p><strong>Table S2.</strong> Araripe fossil publications by foreign authors (vertebrates and plants)</p> <p><strong>Table S3.</strong> Preliminary list of Araripe fossil arthropod publications</p> <p><strong>Table S4.</strong> List of palaeontology museums and postgraduate courses in Brazil with palaeontology advisors</p> <p><strong>Table S5.</strong> List of palaeontology museums and postgraduate courses in Mexico with palaeontology advisors</p> <p><strong>Translation S1.</strong> Complete article in Portuguese</p> <p><strong>Translation S2.</strong> Complete article in Spanish</p> <p><strong>Appendix A.</strong> Laws in Brazil (includes English translations)</p> <p><strong>Appendix B.</strong> Laws in Mexico (includes English translations)</p>
Artifact: "If security is required": Engineering and Security Practices for Machine Learning-based IoT Devices
<p>Artifact for "If security is required": Engineering and Security Practices for Machine Learning-based IoT Devices</p>
Studying the Practices of Deploying Machine Learning Projects on Docker
<p>This repository contains the dataset for our study titled above:</p> <p>Below is the abstract:</p> <p>Docker is a containerization service that allows for convenient deployment of websites, databases, applications' APIs, and machine learning (ML) models with a few lines of code. Studies have recently explored the use of Docker for deploying general software projects with no specific focus on how Docker is being used to deploy ML-based projects. In this study, we conducted an exploratory study to understand how Docker is being used to deploy ML-based projects. As the initial step, we examined the categories of ML-based project that use Docker. We then examined why and how these projects use Docker, and the characteristics of the resulting Docker images. Our results indicate that six categories of ML-based projects use Docker for deployment, including ML Applications, MLOps/ AIOps, Tookits, DL Frameworks, Models, and Documentation. We derived the taxonomy of 21 major categories representing the purposes of using Docker, including those specific to models such as model management tasks (e.g., testing, training), data management (e.g., migration, persistent storage, sharing), software testing, interactive development. We then showed that ML engineers use Docker images mostly to help with the platform portability, such as transferring the software across the operating systems, runtimes such as GPU-accelerated, and language constraints. However, we also found that more resources may be required to run the Docker images for building ML-based software projects due to the large number of files contained in the image layers with deeply nested directories. Through this study we hope to shed light on the emerging practices of deploying ML software projects using containers and highlight aspects that should be improved.</p>
Phylogenomics and biogeography of Torreya (Taxaceae) – Integrating data from three organelle genomes, morphology, and fossils and a practical method for reducing missing data from RAD-seq
<p><span>Restriction site-associated DNA sequencing (RAD-seq) enables obtaining thousands of genetic markers for phylogenomic studies. However, RAD-seq data are subject to allele dropout (ADO) due to polymorphisms at enzyme cutting sites. We developed a new pipeline, RADADOR, to mitigate the ADO in outgroups by recovering missing loci from previously published transcriptomes in our study of a gymnosperm genus </span><em>Torreya</em><span>. Using the supplemented RAD-seq data in combination with plastome and mitochondrial gene sequences, morphology, and fossil records, we reconstructed the phylogenetic and biogeographic histories of the genus and test hypotheses on diversity anomaly in eastern Asian-North American floristic disjunction. Our results showed that our pipeline recovered many loci missing from the outgroup, and the improved data yielded a more robust phylogeny for </span><em>Torreya</em><span>. Using the fossilized-birth-death model and divergence-extinction-cladogenesis method we resolved detailed biogeographic history of </span><em>Torreya</em><span> that suggested a Jurassic origin in the Laurasia and differential speciation and extinction among continents accounting for the modern diversity anomaly biased toward Eastern Asia (EA). The history also supported a vicariance origin of the modern </span><em>Torreya</em><span> from a widespread ancestor in EA and NA in the mid-Eocene, cross-Beringia exchange in the early Paleogene before the vicariant isolation, in contrast to the "Out of NA" pattern common to gymnosperms and in contrast to the "Out of EA" hypothesis previously proposed for the genus. Furthermore, we observed phylogenetic discordance between the nuclear and plastid phylogenies on </span><em>T. jackii</em><span>, suggesting differential lineage sorting of plastid genomes among </span><em>Torreya</em><span> species or plastid genome capture in </span><em>T. jackii</em><span>.</span></p>
DASP: A Framework for Driving the Adoption of Software Security Practices
<p>Online appendix for the publication:</p> <p>DASP: A Framework for Driving the Adoption of Software Security Practices.</p>
i-SoMPE Inventory A: List and description of 58 innovative soil management practices
<p>List and description of 58 innovative soil management practices (inventory A)</p>
i-SoMPE Inventory A: Adoption rate of 58 innovative soil management practices
<p>Adoption rate of 58 innovative soil management practices (maps of inventory A)</p>
Karuk ecological fire management practices promote elk habitat in Northern California
<p>After a century of fire suppression and accumulating fuel loads in North American forests, prescribed burns are increasingly used to prevent conditions leading to catastrophic megafire. There is widespread evidence that prescribed fire was used by Indigenous communities to manage natural and cultural resources tribes for thousands of years. Wildlife habitat is an example of an ecological response that was actively managed with prescribed burns by Indigenous American peoples and is an important factor in western U.S. forest management planning, restoration and climate resilience efforts. We analyzed the effects of modern prescribed burns informed by traditional ecological knowledge (TEK) on the predicted change in elk winter habitat in Karuk aboriginal territory in Northern California between 2013 and 2018 using species distribution and simultaneous autoregressive modeling techniques. Burn types most closely resembling Karuk traditional practices, specifically those incorporating multiple-year broadcast burns, had significant positive effects on elk winter habitat suitability. Conversely, concentrated burns focused solely on reducing fuel loads had significant negative effects on elk winter habitat suitability. However, areas where these fuel-reduction burns were combined with multiple years of broadcast burns featured the highest increases in habitat. Our results suggest that transitioning to prescribed burns that more closely follow Karuk TEK will promote elk habitat in the region. This would be best achieved through continuing to work closely with Indigenous representatives to plan and implement cultural fire prescriptions on a landscape-scale, a trend we posit would benefit environmental management efforts across the globe.</p>
command line interface practical - 2022 bioinformatics summer school
<p>Files and folders for the comman line interface practical of the 2022 bioinformatics summer school. Second release</p>
VINDICTA project, Practice 3, egg masses photo survey, code ENGA22060401
<p>ENGA22060401</p>
Dataset Practical Performance and User Experience of Novel DUAL-Flush Vacuum Toilets
<p>Dataset for paper "Practical Performance and User Experience of Novel DUAL-Flush Vacuum Toilets" <a href="https://doi.org/10.3390/w13162228">https://doi.org/10.3390/w13162228</a> <em>Water</em> <strong>2021</strong>, <em>13</em>(16), 2228</p> <p> </p>
Code and Additional Files for the Manuscript "The Impact of Farming Practices on Resistance to Critically Important Antimicrobials in ESBL or AmpC-producing Escherichia coli in Thailand"
<p>These scripts were used in the"The Impact of Farming Practices on Resistance to Critically Important Antimicrobials in ESBL or AmpC-producing Escherichia coli in Thailand" manuscript. The scripts are ordered for ease of use. It also contains intermediate files and files necessary for the mapping. Table S1 containing the metadata is available in the supplementary information of the manuscript.</p>
Continuous Integration and Delivery Practices for Cyber-Physical Systems: An Interview-Based Study - Online Dataset
<p>This package contains the online dataset of the manuscript:</p> <p>Continuous Integration and Delivery Practices for Cyber-Physical Systems: An Interview-Based Study</p>
Video Examples from: Establishment and Implementation of Guidelines for Narrative Audio-based Room-scale Virtual Reality using Practice-based Methods
<p>This video accompanies our paper: Popp, C. and Murphy, D.T., "Establishment and Implementation of Guidelines for Narrative Audio-based Room-scale Virtual Reality using Practice-based Methods", held at the 2022 AES International Conference on Audio for Virtual and Augmented Reality.</p> <p>Room-scale Virtual Reality (VR) presents sound designers with new challenges to tell stories with audio in games with player-driven narratives. These challenges arise from the player moving in and interacting with the virtual environment. The paper performs a small scoping review of VR/non-VR games and associated literature to identify issues and solutions to the placement of speech-based audio using practice-based research methods. The review leads to the proposition of design guidelines and strategies for their implementation. The paper advocates that each instance of speech-based audio should be short, interactive, and complemented by non-speech audio. Furthermore, each instance’s spatial, interactive, visual, aural, and narrative representation should be considered in combination. The paper also suggests that 3D-binaural audio informed by physics can aid storytelling and make virtual environments player-responsive.</p> <p>The paper is part of the research project SuperCharging Audio Storytelling: 3D Audio in Virtual Reality, funded by UK Arts and Humanities Research Council (AHRC) XR Stories Creative Industries Cluster project, grant no. AH/S002839/1. More information about the project can be found at <a href="https://xrstories.co.uk/project/supercharging-audio-storytelling-3d-audio-in-virtual-reality/">XR Stories</a>. Firelight Technologies Pty Ltd and Unity Technologies kindly provided non-commercial licenses for research purposes as part of this research project.</p>
Landsat-based maps of cropping practices in the irrigated drylands of the Aral Sea Basin (1987-2019)
<p><strong>Overview</strong></p> <p>A set of maps revealing agricultural land use patterns in the irrigated drylands of the Amu Darya and Syr Darya basin between 1987 and 2019. The maps were produced using time series of 30m Landsat TM, ETM+ and OLI Collection 1 surface reflectance products and a Random Forest classification model trained with ~30,000 samples from the years 1987, 1998, 2008, and 2018. All processing steps were conducted in Google Earth Engine. The target classes of this product are "wet season cropping", "dry season cropping", "double cropping including fodder crops", and "non-cropland". Mapping was conducted across nine provinces in Uzbekistan, two in Turkmenistan, and three in Tajikistan, and post-processing was used to constrain the study area to regions which were irrigated in at least two years in the study period, areas below 2,000 m above sea level, and regions/years with a sufficient number of cloud-free Landsat images (n>6). Annual maps were aggregated temporally and spatially, resulting in different datasets described below.</p> <p>We advise map users to read the <a href="https://doi.org/10.1088/1748-9326/ac8daa">open access paper</a> and the associated supplementary materials for detailed insights. In case of further questions please contact the lead author of the work.</p> <p><strong>Data</strong></p> <p>This download contains three folders:</p> <ul> <li><em>landuse_30m</em>: Land use layers with 30m spatial resolution, representing the percentage (0-100%) of the three key land use types ("wet season cropping", "dry season cropping", "double cropping including fodder crops") within two time frames (1987-2000 and 2001-2019). Years with insufficient cloud-free Landsat observations were excluded from the calculation of percentages.</li> <li><em>landuse_3km</em>: Land use metrics with 3km spatial resolution, representing - for each grid cell and year - the "percentage of cropland", "percentage of dry-season cultivation", and "cropping frequency". The layers in these datasets are ordered chronologically, with the layer 1 representing the year 1987, and layer 33 the year 2019. Gaps in the time series were filled using linear interpolation for subsequent trend calculation using <a href="https://github.com/morrowcj/remotePARTS/">remotePARTS</a>.</li> <li><em>mask</em>: A mask with 30m spatial resolution constraining the study area to regions below 2,000 m above sea level and regions which were irrigated at least twice in the study period.</li> </ul> <p><strong>Map accuracy</strong></p> <p>We conducted an area-adjusted accuracy assessment based on a stratified random sample (n = 2,784 per year), which yielded important insights regarding accuracies and error types. The median area-adjusted overall accuracy of the maps across the study period is 91.4%, but class-specific user´s and producer´s accuracies vary substantially. Users should consult the supplementary materials of the article for details on accuracies, confusion matrices, and the most important error types.</p> <p><strong>Further resources</strong><br> The production of this map was made possible through the Landsat Program of the United States Geological Survey (USGS) and the Google Earth Engine cloud computing platform for preprocessing of the satellite data and classification. The code for preprocessing the Landsat time series is based on the Google Earth Engine Python API and made available at <a href="https://github.com/philipperufin/eepypr/">https://github.com/philipperufin/eepypr/</a>.</p>
Pre- and post-intervention responses to a knowledge, attitudes, and practices survey for the study, "Disseminating vaccination information in baby soap products increases knowledge and vaccine uptake in central Uganda: A non-randomized controlled trial"
<p>This dataset contains responses to the pre- and post-intervention knowledge, attitudes, and practices surveys utilized for the study, "Disseminating vaccination information in baby soap products increases knowledge and vaccine uptake in central Uganda: A non-randomized controlled trial."</p>
Fast kinetics data of binding of azide to myoglobin, training data -- MetBio practicals
<p>These data files were acquired during the course of the 3rd <a href="http://frenchbic.cnrs.fr/">FrenchBIC</a> <a href="http://frenchbic.cnrs.fr/2021/01/25/3rd-frenchbic-summer-school-on-methods-for-studying-metals-in-biology/">MetBio summer school</a> taking place in and around Marseille. The data were acquired during the “stopped flow” practicals.</p> <p>The data correspond to the reaction of Myoglobin with various concentrations of azide, triggered using a stopped-flow apparatus and followed by UV/Visible spectroscopy.</p> <p>The concentrations of azide can be deduced from the names of the files and are expressed in millimolar. The concentrations of myoglobin are variable but always much lower than that of azide.</p> <p>The purpose of this dataset is to be used as training data for analysing multiwavelength kinetic data. It will be the subject of a data analysis tutorial using the free software <a href="https://bip.cnrs.fr/groups/bip06/software/">QSoas</a>, to be published <a href="https://vince-debian.blogspot.com/">there</a>.</p> <p>With the exception of the <code>WTV-Azide-0.5mm_3.txt</code>, all the files are in a “matrix” format, in which the first column gives the time and each column after the first corresponds to the absorbances over time of a single wavelength.</p> <p>The <code>WTV-Azide-0.5mm_3.txt</code> uses a different format, in which each line corresponds to a <em>wavelength</em> <em>time</em> <em>absorbance</em> triplet.</p> <p>Useful background reading:</p> <ul> <li> <p>Coletta <em>et al</em>, <strong>1996</strong>, DOI: 10.1111/j.1432-1033.1996.00049.x</p> </li> <li> <p>De Sanctis <em>et al</em>, <strong>2007</strong>, DOI: 10.1529/biophysj.106.098764</p> </li> </ul>
A practice-led assessment of landscape restoration potential in a biodiversity hotspot
<p>Effective restoration planning tools are needed to mitigate global carbon and biodiversity crises. Published spatial assessments of restoration potential are often at large scales or coarse resolutions inappropriate for local action. Using a Tanzanian case study, we introduce a systematic approach to inform landscape restoration planning, estimating spatial variation in cost-effectiveness, based on restoration method, logistics, biomass modelling and uncertainty mapping. We found potential for biomass recovery across 77.7% of a 53,000 km<sup>2</sup> region, but with some natural spatial discontinuity in moist forest biomass, that was previously assigned to human causes. Most areas with biomass deficit (80.5%) were restorable through passive or assisted natural regeneration. However, cumulative biomass gains from planting outweighed initially high implementation costs meaning that, where applicable, this method yielded greater long-term returns on investment. Accounting for ecological, funding and other uncertainty, the top 25% consistently cost-effective sites were within protected areas and/or moderately degraded moist forest and savanna. Agro-ecological mosaics had high biomass deficit but little cost-effective restoration potential. Socio-economic research will be needed to inform action towards environmental and human development goals in these areas. Our results highlight value in long-term landscape restoration investments and separate treatment of savannas and forests. Furthermore, they contradict previously asserted low restoration potential in East Africa, emphasising the importance of our regional approach for identifying restoration opportunities across the tropics.</p>
Making Data Work: A Systematic Mapping of Collaborative Data Curation Practices
<p>This file contains dataset associated with the paper Making Data Work: A Systematic Mapping of Collaborative Data Curation Practices</p>
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.