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47,155 results for “evaluations”
Simulated dataset (Almeida et al., 2018 - GigaScience) treated with various clustering programs to evaluate ReClustOR efficiency and constitency
<p>ReClustOR is a novel clustering method that overcomes some of the problems associated with classical ‘<em>heuristic’</em>clustering methods and consequently increases the stability and quality of the reconstructed OTUs. Moreover, the OTUs database defined with ReClustOR can be used as reference(s) with gradual enrichment of it, with new studies and samples. In this way, huge datasets like<em> </em>the Earth Microbiome Project can be easily used as references for smaller projects, thereby increasing the quality of comparisons between studies and datasets</p> <p>Here, we propose a new approach called ReClustOR (for RE-CLUSTering method using an Open-Reference approach) to improve OTU consistency (see https://doi.org/10.5281/zenodo.2597402). This new strategy combines two of the previously-described clustering methods. Firstly, a classical clustering<em> </em>method (<em>e.g. </em>SWARM, or VSEARCH) is used to define OTU centroids and create a reference database. Secondly, a closed- or open-reference method (depending on the user’s choice) is computed for all reads which are not considered as OTU centroids. Contrary to the classical clustering methods, each read is compared to all centroids using a distance-based greedy clustering technique (Edgar, 2010; He et al., 2015), and then assigned to the nearest one, thereby fixing the erroneous assignments of reads to OTUs.</p> <p>To highlight the improvements provided by ReClustOR in describing microbial diversity in terms of ecological diversity metrics (<em>e.g. </em>richness, OTU composition, Shannon, 1/Simpson) and taxonomic composition, a simulated dataset was subjected to: (i) ESV definition, (ii) multiple conventional <em>de novo</em> methods (<em>i.e.</em> a homemade <em>de novo </em>clustering close to CRUNCHCLUST, VSEARCH and SWARM), and (iii) ReClustOR computation. This dataset is a simulated one (Almeida et al., 2018), containing a diverse set of <em>genera</em> commonly found in three ecosystems different ecosystems: human gut, ocean and soil. The clustering methods were compared for: (i) their ability to describe microbial richness, (ii) the congruence between OTU assignments and sequences taxonomy, (iii) the robustness of each defined OTU, and (iv) their ability to efficiently describe the microbial community based on OTU composition.</p> <p>Here, the simulated dataset (00_Raw_data) and all steps of analysis are available to resue them to test ReClustOR, and also to have a better understanding of files and data produced by this program. More details are available in the Tree_of_data.tree file.</p>
Images associated to the paper "Evaluating the Sensitivity to Virtual Characters Facial Asymmetry in Emotion Synthesis"
<p>We conducted an experiment by presenting 64 pairs of static facial expressions, one symmetric and one asymmetric, illustrating eight emotions (three basic and five complex ones) alternatively for a male and a female character.<br> Each emotion was presented four times by swapping the symmetric and asymmetric positions and by mirroring the asymmetrical expression. Participants were asked to grade, on a continuous scale, the correctness of each facial expression with respect to a short definition</p>
Evaluation Data of the Combined Approach
<p>This dataset contains the programs on which the <a href="http://doi.org/10.1007/978-3-030-02450-5_17">Combined Approach</a> was evaluated.</p> <p>The Java source code of each evaluated program is in the "src" folder.<br> The compiled jar file of each evaluated program is in the "testdata" folder.</p> <p>The .joak file contains the annotated sources and sinks for each evaluated program.<br> Note that you may not be able to load the .joak files directly into the Combined <br> Approach program as the various paths in the .joak files need to be fixed first.<br> The purpose of the .joak files in this repository is to document the sources and sinks.<br> You can also generate new .joak files with the Combined Approach application.</p>
Downscaled 1 km RACMO2 data used in CESM2 Greenland SMB evaluation paper
<p>Post-processed RACMO2.3p2 data used to carry out part of the analysis in the paper titled “Present day Greenland ice sheet climate and surface mass balance in CESM2”, in review with JGR Earth Surface.</p> <p>This data stems from a RACMO2.3p2 regional climate simulation over Greenland at 11 km which was averaged over the period 1961-1990 and statistically downscaled to 1 km. The original resolution of this dataset is 11 km and further described in Noël et al., 2018, <a href="https://doi.org/10.5194/tc-12-811-2018">https://doi.org/10.5194/tc-12-811-2018</a></p> <p>This data is published for archiving purposes only. Data requests for the latest version of RACMO2 output can be made free of charge to Brice Noël (B.P.Y.Noel@uu.nl) and Michiel van den Broeke (M.R.vandenBroeke@uu.nl). In your request, please specify the variables of interest, time period and time frequency, and area of interest.</p> <p> </p>
Data for the publication "Incorporation of inline warm rain diagnostics into the COSP2 satellite simulator for process-oriented model evaluation"
<p>Michibata et al. (2019), currently under peer-review for publication in <em>Geoscientific Model Development</em>, incorporated a diagnostic tool for warm rain microphysics into the CFMIP Observation Simulator Package (COSP; Bodas-Salcedo et al. 2011; Swales et al., 2018), designed to evaluate model representations of aerosol–cloud–precipitation interactions at a fundamental process-level. The tool automatically generates two diagnostics related to warm rain microphysics during COSP execution in a host model. One is the contoured frequency by optical depth diagram (CFODD), which visualizes a cloud-to-rain microphysical vertical structure (Suzuki et al., 2015). The other diagnostic is a global map of warm rain fraction classified as non-precipitating clouds (< –15 dBZ<sub>e</sub>), drizzling clouds (–15 < dBZ<sub>e</sub>< 0), and precipitating clouds (0 < dBZ<sub>e</sub>).</p> <p>This repository contains the MIROC6/COSP2 input data and A-Train satellite statistics used in Michibata et al. (2019). A sample of the post-processing scripts for visualization using the GrADS software is also included in this repository.</p>
King Louie: DBMS Availability Evaluation Data Sets
<p>These data sets provide all availability measurements as accompanying material for the research paper <strong><em>King</em> </strong><em><strong>Louie: Reproducible Availability Benchmarking of Cloud-hosted DBMS</strong> </em>that is presented in the 35th ACM/SIGAPP Symposium on Applied Computing (SAC ’20), March 30-April 3, 2020, Brno, Czech Republic.</p> <p> </p> <p> </p>
Mowgli: DBMS Performance & Scalability Evaluation Data Sets
<p>These data sets contain the performance and scalability evaluation data created by the <a href="https://omi-gitlab.e-technik.uni-ulm.de/mowgli/getting-started">Mowgli</a> framework for Apache Cassandra and Couchbase, operated on a private Openstack and the Amazon EC2 cloud.</p>
DATASET Clinical and Radiographic Evaluation Data of Autotransplantation using 3D Replicas
<p>This dataset repository contains detailed data and analysis scripts related to a research study on autotransplantation using 3D replicas. The study aims to evaluate clinical outcomes and radiographic changes over time in dental autotransplantation cases. The dataset includes CSV files containing clinical data, detailed radiographic evaluation results, and HTML files documenting analysis procedures and findings.</p>
Dataset for the evaluation of Supercritical Fluid Chromatography Polar Stationary Phases with OH moieties
<p>Raw data used for the evaluation of supercritical fluid chromatography stationary phases with OH moieties published in article "Advancing Fundamental Understanding of Retention Interactions in Supercritical Fluid Chromatography Using Artificial Neural Networks: Polar Stationary Phases with OH moieties" in Analytical Chemistry, 2024. Data set contains: (i) chromatograms of 107 analytes measured on silica, hybrid silica, and diol column using methanol, 10 mmol/L ammonium in methanol, and 2% water in methanol as organic modifiers in 8 points during 1 year (Empower project, Excel sheets of retention times and measured mixtures), (ii) 226 molecular descriptors calculated by CDK Descriptor Calculator (v.1.4.8) from 3D structures of the 107 analytes optimized by semi-empirical AM1 quantum mechanical calculations using the MOPAC application of Chem 3D Pro version 14.0 software (CambridgeSoft) (Excel sheet), (iii) weights assigned to each molecular descriptor at each chromatographic conditions by artificial neural network created using the neural network simulator in Matlab R2023a with the deep learning toolbox V.23.2 (The MathWorks, Inc., Massachusetts, USA) and a sigmoid activation function, a backpropagation learning algorithm with 500 learning cycles (Excel sheet). </p>
Templates for BWS IPA and NPS project evaluations
<p>Templates with example data to facilitate the completion of project evaluations using Excel to undertake three analyses:</p> <p>1. Importance-Performance Analysis (IPA) with Gap Analysis</p> <p>2. Net Promoter Score</p> <p>3. Best-Worst-Scaling template in seperate file in version 1</p>
Evaluating the impact of shade on Nitrogen fixation in sulla (Hedysarum coronarium L.): a 15N natural abundance study
<p>This dataset refers to the experimental raw data (csv version) collected within the trial reported in the concerned article on the following parameters:</p> <p>1. total nitrogen, delta N15, nitrogen derived from atmosphere, root biomass, nitrogen yield, nitrogen fixed, splitted per experiment, mowing, crop, treatment and replicate (15N_root.csv).</p> <p>2. total nitrogen, delta N15, nitrogen derived from atmosphere, shoot biomass, nitrogen yield, nitrogen fixed, splitted per experiment, mowing, crop, treatment and replicate (15N_shoot.csv).</p> <p>3. shoot cumulative nitrogen yield, root cumulative nitrogen yield, shoot cumulative nitrogen fixed, root cumulative nitrogen fixed, shoot:root ratio of nitrogen yield, shoot:root ratio of nitrogen fixed, splitted per experiment, treatment and replicate (shoot root ratio and N cumulative value.csv).</p>
A new in vitro blood flow model for the realistic evaluation of antimicrobial surfaces
<p>Dataset to the publication</p> <p>A new <em>in vitro</em> blood flow model for the realistic evaluation of antimicrobial surfaces</p> <p>Juliane Valtin, Stephan Behrens, André Ruland, Florian Schmieder, Frank Sonntag, Lars D. Renner, Manfred F. Maitz, Carsten Werner</p> <p><em>Adv. Healthcare Mater.</em> 2023, 2301300. <a href="https://doi.org/10.1002/adhm.202301300">https://doi.org/10.1002/adhm.202301300</a></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>
UnientrezDB: Large-scale Gene Ontology Annotation Dataset and Evaluation Benchmarks with Unified Entrez Gene Identifiers
<p>Our work focuses on providing a comprehensive dataset and benchmarks for evaluating gene ontology annotations using a unified system of Entrez Gene Identifiers.</p>
Supporting information of a study for the definition and evaluation of a graphical user interface for housing co-design
<p>This dataset is from a study that intends to define, prototype and test a graphical user interface for a housing co-design system. To define the requirements of the interface, we conducted interviews with professionals of architecture, urbanism and social sciences areas, as well as with housing cooperatives and inhabitants of these institutions. An interface solution was prototyped, tested and refined. Then we conducted a heuristic evaluation and a summative evaluation. Such evaluations involved the testing of a high-fidelity prototype, to receive feedback from UX/UI experts, potential users (inhabitants) and architects.</p> <p>S1_File refers to the interview protocol used with the three groups of interviewees. We share the English and Portuguese versions of the interviews with professionals and the original (Portuguese) and translated versions of the remaining ones since these were conducted in Portuguese.</p> <p>S2_File is a dataset reporting the results of the interviews. Each question includes the answers given and the identification (anonymized) of the interviewees who responded to that question.</p> <p>S3_File describes the usability issues identified by the experts during the heuristic evaluation of the high-fidelity prototype. The first page organizes the issues by severity (left) and priority (right). The remaining pages have a table for each issue, including rows for problem designation, heuristic violated, problem description, solution proposal, severity degree, and an image of the interface pointing to the referred issue.</p> <p>S4_File refers to the results of the heuristic evaluation. It includes the identification of each issue, which expert (anonymized) identified such issue, and the heuristic it violates, with the sum of the times each heuristic was violated at the end of each column. At the right, a table presents the consolidation of issues, organized by priority, with columns identifying the issue, severity level, frequency, and priority.</p> <p>S5_File is the script given to potential users to experiment with the interface during the summative evaluation. This script guides the user through the tasks to perform since the prototype does not have all the features functioning.</p> <p>S6_File refers to the questionnaires applied during the summative evaluation with inhabitants. It includes a preliminary questionnaire, a Single Ease Question (SEQ) questionnaire, a System Usability Scale (SUS) questionnaire, and a Graphical User Interface (GUI) questionnaire.</p> <p>S7_File refers to the results of the summative evaluation with inhabitants (potential users).</p> <ul> <li>Page A refers to the preliminary questionnaire with demographic information such as age, gender, education, relationship with digital technologies, etc. Each field corresponds with each inhabitant (anonymised) and the sum and percentage. In the middle, a table presents a summary of the consolidation. In the right possible relations are presented. </li> <li>Page B presents the results of the SEQ questionnaire, identifying the ratings each inhabitant (anonymized) gave each task. A summary of such values is at the right. </li> <li>On page C, the result of each rating for the SUS questionnaire given by each inhabitant (anonymized) is shown. At the bottom is the calculation of the SUS score.</li> <li>Page D presents the GUI questionnaire results for each inhabitant (anonymized), with the average and SD identified for each question. A summary of such results is on the right.</li> <li>Page E holds the notes taken by the researchers based on their observations regarding task performance. The information is organized in tables for each step of each task and includes the completeness, attempts, and time taken for each inhabitant (anonymized) to complete such task. Also, the sum, percentage, average, and SD are registered. Next to each task is a table identifying how many participants accomplished the task at the first attempt.</li> <li>Page F refers to the strong and weak aspects identified by the inhabitants. Strong and weak aspects are identified, as well as which inhabitant (anonymized) has identified them. The sum and percentage are also given. At the right, there is a table with the consolidation of results by combining similar answers. </li> </ul> <p>S8_File refers to the results of the discussion with architects after experiencing the interface. Such results relate to the positive and negative aspects that the architects identified in the interface and its usefulness for architecture. The left table identifies the strong and weak aspects that architects (anonymized) identified and the sum and percentage associated with them. The table on the right consolidates such results, with similar responses combined.</p>
Evaluating Changes in the Local Protein Physicochemical En-vironment induced by Molecular Dynamics Simulation
<p><span>Mutation of a single amino acid residue may significantly affect the structure and function of an entire protein. The effect of single amino acid substitutions can be assessed by examining the physicochemical environment surrounding the amino acid of interest, an emerging form of quantification of which is multidimensional tensors. However, the effect with respect to a protein variant’s inherent dynamics in tensor space is rarely assessed despite the potential importance of this form of analysis in revealing local physicochemical properties of the protein and response to mutation. Using the wild-type and 936 mutant structures of the protein domain 1pga, the present research evaluated the effects of local protein context and single amino acid substitutions on molecular dynamics simulation-derived structural distributions via the use of tensors capturing a range of biochemical properties. It was observed that the extent of simulated </span><span>physicochemical</span><span> variation local to a substituted amino acid is positively associated with local mechanical stiffness, loss of protein thermostability and decreased local hydrophobicity. In addition, it was observed that the largest tensor variation occurs in densely-packed, hydrophobic core-associated regions of protein structures. In summary, the pattern of tensor change aligns with prior knowledge about protein stability and physicochemical properties.</span></p>
Comprehensive Evaluation of Alternative API, Excipient, and Packaging Material Sources: A Regulatory Perspective
<p>Incorporating alternative sources for Active Pharmaceutical Ingredients (API), excipients, and primary packaging materials in approved pharmaceutical products necessitates rigorous evaluation to ensure product quality, safety, and efficacy are maintained. Regulatory agencies, including the World Health Organization (WHO), the United States Food and Drug Administration (US FDA), the European Medicines Agency (EMA), and the UK Medicines and Healthcare products Regulatory Agency (UK MHRA), require comprehensive data to assess such changes. This abstract summarizes the key data requirements across these agencies, focusing on API, excipients, and primary packaging materials.</p> <p>For APIs, critical data include comparative analytical testing, impurity profiling, stability studies under ICH conditions, and bioequivalence studies when applicable. Agencies mandate risk assessments and process validation to ensure the new API source does not compromise the product's critical quality attributes (CQAs) or therapeutic performance.</p> <p>For excipients, regulatory bodies require detailed information on the new supplier’s compliance with Good Manufacturing Practices (GMP), certificate of analysis (CoA), and comparative studies to demonstrate equivalence in performance, stability, and compatibility with the drug product. Stability testing, extractables and leachables analysis, and risk assessment play crucial roles in ensuring the excipient change does not negatively impact product quality or patient safety.</p> <p>Primary packaging material changes require a thorough evaluation of mechanical and barrier properties, container-closure integrity (CCI), and extractables and leachables studies. Stability testing with the new packaging material under ICH conditions, risk assessments, and functional equivalence testing are essential to confirm the packaging material’s suitability in protecting the drug product throughout its shelf life.</p> <p>In conclusion, stringent regulatory expectations underscore the importance of comprehensive data generation and risk mitigation strategies when incorporating alternative sources for APIs, excipients, and packaging materials in pharmaceutical products. Adherence to these guidelines ensures product safety, efficacy, and compliance with global regulatory standards.</p>
A Bioconductor workflow for processing, evaluating and interpreting expression proteomics data
<p>Files for users of the workflow "A Bioconductor workflow for processing, evaluating and interpreting expression proteomics data". Files include Proteome Discoverer (v2.5) processing and consensus workflows for both TMT and LFQ expression proteomics data. Also provided are the output .txt files of a corresponding Proteome Discoverer identification search, as required for users to follow the workflow themselves. For raw data please refer to PRIDE. Appendix is provided as a PDF.</p>
Regional scale shear wave velocity profiles for ground response analyses and uncertainties evaluations – the Piedmont Region (NW Italy) Database
<p>The databases provide detailed information for the Piedmont region in Northwest Italy, offering a view of its geological and geophysical characteristics:</p> <ul> <li><strong>Geological-Geomorphological Database</strong>: Includes 13 distinct Geological-Geomorphological Domains (GGD) in shapefile format. It supports spatial analysis and visualization, based on data from the Geological Map of the Piedmont Region at a 1:250,000 scale.</li> <li><strong>Geotechnical Database</strong>: Contains geotechnical data on bedrock depth and texture attributes derived from available logs in CSV format. Georeferenced using UTM coordinates (WGS84 UTM32N), it includes depth values and texture codes (C for clay, G for gravel, S for sand, R for rock, X for not available).</li> <li><strong>Geophysical Database</strong>: Provides data on shear wave velocity (Vs) profiles in CSV format. Georeferenced with UTM coordinates (WGS84 UTM32N), it includes layer interface depth and shear wave velocity above each layer.</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>
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.