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506 results for “assessment model”
Data for The importance of cloud phase when assessing surface melting in an offline coupled firn model over Ross Ice shelf, West Antarctica
<p>This is the data used in the paper "The importance of cloud phase when assessing surface melting in an offline coupled firn model over Ross Ice shelf, West Antarctica"</p>
Population models used in: Method to assess potential magnitude of terrestrial European avian population reductions from ingestion of lead ammunition
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Assessing patterns and risk to Chilean freshwater fish distributions using multi-species occupancy models
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Data from: A hierarchical model for jointly assessing ecological and anthropogenic impacts on animal demography
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Data from: In vitro to in vivo extrapolation from three-dimensional hiPSC-derived cardiac microtissues and physiologically based pharmacokinetic modeling to inform next-generation arrythmia risk assessment
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Assessing predictive performance of supervised machine learning algorithms for a diamond pricing model
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Data for: An integrated population model and population viability assessment for the southern population of a data-poor species
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Model output dataset used in "Assessment of Ch in the Noah-MP LSM over China"
<p>1. The Noah-MP LSM v3.6 was used in an offline standalone mode to execute single-site and regional-scale land surface experiments. Single-point experiments were executed at nine flux tower sites, while the simulated regional domain covered all of China.</p> <p>2. Three cases were designed: (1) the original M-O option with identical <em>Z<sub>om</sub></em> and <em>Z<sub>ot</sub></em> (Default), (2) a constant <em>C<sub>zil</sub></em> specified as 0.1 (Czil), and (3) a dynamic canopy-height-dependent <em>C<sub>zil</sub> </em>( Newczil).</p> <p>3. The model output data files for single-site land surface experiements are named in accordance with the following convention:</p> <p>SiteName_SchemeName_start{year/month/day/hour/minute}_end{year/month/day/hour/minute}UTC_noahmp.nc</p> <p>For regional-scale land surface experiments (UTC):</p> <p>NoahMP.{year/month/day}T{hour}0000.nc</p> <p>The file "Domain_regional-scale.nc" contains the static geographic information, such as land cover.</p>
Model outputs: Vegetation biomass change in China in the 20th century: An assessment based on a combination of multi-model simulations and field observations
<p>This dataset contains six model outputs of vegetation biomass on plant functional type level and total vegetation biomass on grid cell with and without bias-correction in different sensitivity experiments, as described in Readme.txt.</p>
Ultimate strength assessment of stiffened panel using non-linear mechanical behavior of an equivalent single layer: grillage FE model used for analysis
<p>This example shows how the ESL can be applied in the ultimate strength structural analysis in Abaqus finite element software. In other words, ESL methodology is applied only in some parts of the structure while larger structural supporting components like girders and webframes are still modeled explicitly. FIles include also the Full_3D_FEM model used for validating the ESL model.</p> <p>Dataset includes following files:</p> <p>1. ESL_nonlinear_grillage.inp - this is Abaqus input file for running the ESL nonlinear grillage model.</p> <p>2. ugensFINALv_master.for - this defines the nonlinear stiffness or ABD matrix. This is called by input file (ESL_nonlinear_grillage.inp ).</p> <p>3. Full_3D_FEM.inp - Full_3D_FEM model used for validating the ESL model.</p> <p> </p>
Supporting data for "A convolution method to assess subgrid-scale interactions between flow and patchy vegetation in biogeomorphic models"
<p>Dataset necessary to reproduce the results and analyses presented in the paper:</p> <p>Gourgue, O., van Belzen, J., Schwarz, C., Bouma, T.J., van de Koppel, J. & Temmerman, S. (2020) A convolution method to assess subgrid-scale interactions between flow and patchy vegetation in biogeomorphic models, Journal of Advances in Modeling Earth Systems, submitted.</p> <p>The dataset contains:</p> <ul> <li>Process-based model simulations, including their input files and the Python scripts to generate them (pre-processing), as well as the output files and Python scripts to post-process them.</li> <li>Flume experiment data processed for the model calibration.</li> <li>Python scripts to generate the figures and tables of the manuscript.</li> </ul>
Assessing confidence in root placement on phylogenies: an empirical study using non-reversible models for Mammals
<p>Using time-reversible Markov models is a very common practice in phylogenetic analysis, because although we expect many of their assumptions to be violated by empirical data, they provide high computational efficiency. However, these models lack the ability to infer the root placement of the estimated phylogeny. In order to compensate for the inability of these models to root the tree, many researchers use external information such as using outgroup taxa or additional assumptions such as molecular-clocks. In this study, we investigate the utility of non-reversible models to root empirical phylogenies and introduce a new bootstrap measure, the <i>rootstrap</i>, which provides information on the statistical support for any given root position.</p> <p>Availability and implementation: rootstrap support is implemented in IQ-TREE 2 and a tutorial is available at the iqtree webpage <a href="http://www.iqtree.org/doc/Rootstrap">http://www.iqtree.org/doc/Rootstrap</a>. In addition, a python script is available at <a href="https://github.com/suhanaser/Rootstrap">https://github.com/suhanaser/Rootstrap</a></p>
Data from: Assessing cetacean populations using integrated population models: an example with Cook Inlet beluga whales
<p>Effective conservation and management of animal populations requires knowledge of abundance and trends. For many species, these quantities are estimated using systematic visual surveys. Additional individual-level data are available for some species. Integrated population modelling (IPM) offers a mechanism for leveraging these datasets into a single estimation framework. IPMs that incorporate both population- and individual-level data have previously been developed for birds, but have rarely been applied to cetaceans. Here, we explore how IPMs can be used to improve the assessment of cetacean populations. We combined three types of data that are typically available for cetaceans of conservation concern: population-level visual survey data, individual-level capture-recapture data, and data on anthropogenic mortality. We used this IPM to estimate the population dynamics of the Cook Inlet population of beluga whales (CIBW; <i>Delphinapterus leucas</i>) as a case study. Our state-space IPM included a population process model and three observational submodels: 1) a group detection model to describe group size estimates from aerial survey data; 2) a capture-recapture model to describe individual photographic capture-recapture data; and 3) a Poisson regression model to describe historical hunting data. The IPM produces biologically plausible estimates of population trajectories consistent with all three datasets. The estimated population growth rate since 2000 is less than expected for a recovering population. The estimated juvenile/adult survival rate is also low compared to other cetacean populations, indicating that low survival may be impeding recovery. This work demonstrates the value of integrating various data sources to assess cetacean populations and serves as an example of how multiple, imperfect datasets can be combined to improve our understanding of a population of interest. The model framework is applicable to other cetacean populations and to other taxa for which similar data types are available.</p>
Questionnaires and Raw Data for the Paper "Operationalised Product Quality Models and Assessment: The Quamoco Approach"
<p>This paper contains the quantitative data from several interviews along with a used questionnaire for empirically investigating the software quality models created in the project Quamoco.</p>
Data for "Assessment of using field-aligned currents to drive the Global Ionosphere Thermosphere Model: A case study for the 2013 St Patrick's Day geomagnetic storm"
GITM Simulation results for the paper "Assessment of using field-aligned currents to drive the Global Ionosphere Thermosphere Model: A case study for the 2013 St Patrick's Day geomagnetic storm"
Application of flow cytometry using advanced chromatin analyses for assessing changes in the sperm structure and DNA integrity in a porcine model
<p><span>Chromatin status is critical for sperm fertility. We tested a multivariate approach for studying pig sperm chromatin, aiming to capture the chromatin structure's complexity with a set of quick and simple techniques, not only DNA damage. Sperm doses from 36 boars (3 ejaculates/boar) were analyzed at days 0 and 11 (cooled storage). Analyses were: CASA (motility) and flow cytometry to assess sperm functionality and chromatin structure by SCSA (DNA fragmentation %DFI and chromatin maturity %HDS), monobromobimane (mBBr, tiol status/disulfide bridges between protamines), chromomycin A3 (CMA3, protamination) and 8-hydroxy-2'-deoxyguanosine (8-oxo-dG, DNA oxidative damage). Data were analyzed by linear models for effects of boar and storage, correlations, and multivariate analysis as hierarchical clustering and principal component analysis (PCA). Storage reduced sperm quality parameters, mainly motility, with no critical oxidative stress increases, while chromatin status worsened slightly (%DFI and 8-oxo-dG increased while mBBr MFI and disulfide bridges decreased). Boar significantly affected most chromatin variables except for CMA3, with storage affecting most except %HDS. At day 0, sperm chromatin variables clustered closely, except for CMA3, and %HDS and 8-oxo-dG correlated with many variables (notably, mBBr). After storage, the relation between %HDS and 8-oxo-dG remained, but correlations among other techniques disappeared, and mBBr variables clustered separately. The PCA suggested a considerable influence of mBBr on sample variance, especially regarding storage, with SCSA and 8-oxo-dG affecting between-sample variability. Overall, CMA3 was the least informative, in contrast with results in other species. The combination of DNA fragmentation, DNA oxidation, chromatin compaction, and tiol status seems a good candidate for obtaining a complete picture of the pig sperm nucleus status, raising many questions for future molecular studies and deserving further research to establish its usefulness as fertility predictors in multivariate models. The meaning of CMA3 should be clarified.</span></p>
Induced pluripotent stem cell-derived cardiomyocyte in vitro models: tissue fabrication protocols, assessment methods, and quantitative maturation metrics for benchmarking progress
<p>The advent of human induced pluripotent stem cells (hiPSCs) and techniques to differentiate cardiomyocytes from them has opened a viable path to creating <em>in vitro</em> models of normal and diseased hearts, accelerating more predictive drug screening and therapeutic strategies for cardiac pathologies. Currently, hiPSC-derived cardiomyocytes (hiPSC-CMs) are more similar to fetal than adult cardiomyocytes, leading many in the field to explore approaches to enhance cell and tissue maturation. There are over 2,000 studies utilizing hiPSC-CMs in models composed of various combinations of cell and extracellular matrix components, using a plethora of differentiation protocols, culture formats, and methods for quantifying cardiomyocyte function. To assess the current state of this rapidly growing area, we systematically analyzed 300 studies using hiPSC-CM models for their selection of hiPSC lines, hiPSC-CM differentiation protocols, types of <em>in vitro </em>models, maturation techniques, and metrics used to assess cardiomyocyte functionality and maturity. Here, we provide the data compiled from our analysis of these papers so others in the field can utilize it to inform their research.</p> <p>Based on this analysis, we highlight the diversity of, and current trends in, <em>in vitro</em> model designs and highlight the most common and promising practices for functional assessments. We further analyzed outputs spanning structural maturity, contractile function, electrophysiology, and gene expression and note field-wide improvements over time. Finally, we observe that a persistent lack of coordination amongst investigators is limiting the field's ability to benchmark and advance hiPSC-CM function against previous studies. We discuss opportunities to collectively pursue the common goal of hiPSC-CM model development, maturation, and assessment that we believe are critical to drive the entire community forward in engineering mature cardiac tissue.</p>
EyeCatchingMaps, a Dataset to Assess Saliency Models on Maps
<div>EyeCatchingMaps, a Dataset to Assess Saliency Models on Maps</div> <div> </div> <div> <p>This dataset is made up of a total of 322 maps. It is made up of maps from google maps, ign and osm.</p> <p>It also includes maps from school textbooks.</p> </div> <div> </div> <div>In the folder map we have all the map of the datatset</div> <div> </div> <div>in the folder coord_on_map, for each map, a file containing all the fixation points of each participant, named ’coord_fixation_name_map.png.csv’ in CSV format with the following elements and during a fixation, a person looks at an area and can move slightly. The fixation will then be represented by a few points:</div> <div>- worl_index : the id of fixation</div> <div>- id_fixation : the id of fixation point</div> <div>- time : the time of the fixation point in relation to the time of the survey</div> <div>- x : x coordinate of the point of fixation on the image</div> <div>- y : y coordinate of the point of fixation on the image</div> <div>- dispersion : distance between all gaze locations during a fixation, in degree</div> <div>- accuracy : in degree</div> <div>- precision :in degree</div> <div>- participant : Participant ID</div> <div>- distance : distance between eye-tracker and screen incm</div> <div>- time_to_map : the time of the fixation point in relation to the map display</div> <div>- height : height of the map</div> <div>- width : width of the map</div> <div> </div> <div>In the folder heatmap we have heatmaps for each map named ’heatmap_name_map.png’.</div> <div> </div> <div> </div> <div> <div> <div>in the folder 'script' there are the different scripts used to produce the data</div> </div> </div>
Audio recordings and soundscape assessments from the study: "Indoor soundscape assessment: A principal components model of acoustic perception in residential buildings"
<h1><strong><span>Content</span></strong></h1> <p><span>The dataset contains processed audio files employed in a listening test performed at the Here East Audio Lab of the University College London to derive a model of acoustic perception in residential buildings [1]. The study followed a full factorial design by combining five urban environments (Factor A) and four indoor sound scenarios (Factor B). The audio files are available in both B-format (Ambix) and A-format. Furthermore, the component scores of each participant in the three derived perceptual dimensions (i.e., comfort, content, familiarity) are made available, along with the psychoacoustic analysis of 20 binaural recordings, each lasting 1 minute, corresponding to the 20 acoustic scenarios to which the 32 participants were exposed.</span></p> <h1><strong><u><span>Audio files</span></u></strong></h1> <p><strong><span>Factor A (Outdoor sounds)</span></strong></p> <p><span>Factor A audio recordings were performed in indoor spaces without audible indoor sound sources and with windows partially opened to different urban contexts in the city of London. Sound material was recorded @24bit/48kHz using a First Order Ambisonics (FOA) microphone (Sennheiser AMBEO VR Mic) positioned at the average listener’s ear height in endfire position, with accompanying portable multi-channel audio recorder (Sound Devices MixPre-10T) with channels 1-4 linked for the FOA setting, together with a sound level meter (NTi Audio XL2), both microphones oriented towards the window openings. By recording outdoor acoustic environments in indoor spaces, the effects of reverberation and window filtering were intrinsically embedded in the collected recordings.</span></p> <p><strong><span>Factor B (Indoor sounds)</span></strong></p> <p><span>Factor B audio recordings were made in low-noise indoor environments using the equipment described above with both microphones oriented roughly towards the sound source of interest.</span></p> <p><strong><span>Combinations of Factors A & B</span></strong></p> <p><span>Excluding the two “no added sounds” scenarios, a total of seven audio stimuli were played and combined during the listening tests, as described in [1], resulting in total 20 scenarios where no more than 2 sounds were overlapped. </span></p> <p><strong><span>Audio Editing and Processing</span></strong></p> <p><span>Audio samples were edited and processed in A format in the Digital Audio Workstation Reaper (Cockos) @24bit/48kHz. The edits were performed in terms of removing extraneous sound events by trimming the audio track and creating the necessary crossfades, in order to bring the audio material as close as possible to the scenario it represented. Audio processing was conducted using the Sennheiser Ambeo plugin to generate the B-format audio files, to be correctly spatialized using a playback system of choice. In the process of conversion to B format, the default Ambisonics Correction Filter was engaged and the Low Cut Filter was switched off, while the Microphone Rotation was set to correct for the endfire position used during the recordings. One-minute excerpts were finally extracted. No further audio editing, nor processing was done. Full details about sound recordings and playback levels used in the experiment are available in [1] and in the supplementary materials.</span></p> <p><span>The audio files are intended to be employed in future listening tests.</span></p> <h1><strong><u><span>Psychoacoustic Analysis and Soundscape scores (.xlsx file)</span></u></strong></h1> <p><span>The xlsx file is formatted with a row for each individual participant's component scores per each of the 20 experimental conditions, then includes the psychoacoustic analysis of the 60s binaural recording corresponding to each acoustic condition. Details about the psychoacoustic analyses and component scores derivation are provided in [1] and in the related supplementary material. In the sheet "Legend_Exposure_Conditions", the coding of the 20 conditions is provided. The numbers of the levels for factors A and B refer to Table 1 in [1].</span></p> <p><span> </span></p> <p><span>[1] Torresin, S., Albatici, R., Aletta, F., Babich, F., Oberman, T., Siboni, S., & Kang, J. (2020). </span><span>Indoor soundscape assessment: A principal components model of acoustic perception in residential buildings. Building and Environment, 182, 107152.</span></p>
The Awareness Assessment Model repository
<p>Dataset of the paper "The Awareness Assessment Model: Measuring Awareness and Collaboration Support Over Participant's Perspective". This dataset contains the supplementary materials about:</p> <p>+ the systematic mapping study;</p> <p>+ the taxonomy elaboration;</p> <p>+ the awareness assessment process;</p> <p>+expert panel validation;</p> <p>+ the case study validation;</p> <p>+ R scripts and observations.csv</p> <p>For more information, please get in touch with us (marcio.mantau@gmail.com).</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.