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266 results for “experimental models”
Supplementary data frames, AlphaFold models, Normal Mode Analysis (NMA) Data, and NMA of Corresponding NMR Ensembles in the S2RCI, MD, and S2 Datasets for "Gradations in protein dynamics captured by experimental NMR are not well represented by AlphaFold2 models and other computational metrics"
<h1><strong>Changes applied to V2</strong></h1> <p>In addition to the supplementary dataframes and AlphaFold models from each dataset in V1, V2 includes the additional data outlined below.</p> <p>The <strong>S2RCI</strong> and <strong>MD</strong> datasets include comprehensive analyses of AlphaFold2 models (both before and after truncation). These datasets feature: </p> <ul> <li><strong>AlphaFold2 Models</strong>: Both original and truncated structures. </li> <li><strong>WEBnma Modes</strong>: `modes.txt` files generated from WEBnma analysis, available for both non-truncated and truncated AF2 models. </li> <li><strong>Root-Mean-Square-Fluctuations (RMSF)</strong>: Profiles calculated before and after truncation of AF2 models. </li> <li><strong>NMR Data: Normal Mode Analysis (NMA)</strong>: Performed on corresponding NMR ensembles (see below). </li> </ul> <p> </p> <p>The <strong>NMR Data</strong> of NMA in these datasets includes: </p> <ul> <li>NMR ensembles </li> <li>Individual NMR models extracted from each ensemble </li> <li>STRIDE secondary structure calculations per-individual NMR models</li> <li>RMSF profiles per-individual NMR models</li> </ul> <p>For detailed information, please refer to the `Readme.txt` file within each corresponding folder. </p> <p>The <strong>S2 dataset</strong> includes all the features listed above, except for the NMR analysis.</p>
Compositional discovery of architecture-aware and sound process models from event logs of multi-agent systems: experimental data.
<p>This repository contains the experimental data used for the evaluation of the compositional approach to the discovery of process models from event logs of multi-agent systems, where agents interact according to specific patterns of synchronous and asynchronous interactions.</p> <p>According to the experiment plan, there is the folder for each interface pattern containing:</p> <ol> <li>The reference model (Petri net encoded in PNML-file)</li> <li>The event log obtained by simulating the behavior of the reference model (XES-file)</li> <li>The model discovered directly from the generated event log (Petri net encoded in PNML-file)</li> <li>The model discovered by composing the agent model w.r.t. the interface pattern (Petri net encoded in PNML-file)</li> </ol>
Experimental and model data for "Nitrogen oxide production in laser-induced breakdown simulating impacts on the Hadean atmosphere"
<p>This is raw data and supporting figures associated with the publication: Heays, A. N., Kaiserová, T., Rimmer, P. B., Knížek, A., Petera, L., Civiš, S., et al. (2022). Nitrogen oxide production in laser-induced breakdown simulating impacts on the Hadean atmosphere. <em>Journal of Geophysical Research: Planets</em>, 127, e2021JE006842. <a href="https://doi.org/10.1029/2021JE006842">https://doi.org/10.1029/2021JE006842</a></p> <p>Two data files contain model output of the ARGO atmospheric photochemistry code that was used to generate figures for Sec. 3 of the paper:</p> <ul> <li>ARGO_model_data_neutral_case.txt</li> <li>ARGO_model_data_reducing_case.txt</li> </ul> <p>The following data files contain a tabulation of laboratory-measured and modelled photoabsorption spectra as described in Sec. 2 of the paper. The A-G letter-encoding of these files follows Table 1 of the paper, and the spectral ranges correspond to the strongest bands of NO, N2O, and NO2. </p> <ul> <li>laboratory_spectrum_experiment_A_species_N2O.txt</li> <li>laboratory_spectrum_experiment_A_species_NO2.txt</li> <li>laboratory_spectrum_experiment_A_species_NO.txt</li> <li>laboratory_spectrum_experiment_B_species_N2O.txt</li> <li>laboratory_spectrum_experiment_B_species_NO2.txt</li> <li>laboratory_spectrum_experiment_B_species_NO.txt</li> <li>laboratory_spectrum_experiment_C_species_N2O.txt</li> <li>laboratory_spectrum_experiment_C_species_NO2.txt</li> <li>laboratory_spectrum_experiment_C_species_NO.txt</li> <li>laboratory_spectrum_experiment_D_species_N2O.txt</li> <li>laboratory_spectrum_experiment_D_species_NO2.txt</li> <li>laboratory_spectrum_experiment_D_species_NO.txt</li> <li>laboratory_spectrum_experiment_E_species_N2O.txt</li> <li>laboratory_spectrum_experiment_E_species_NO2.txt</li> <li>laboratory_spectrum_experiment_E_species_NO.txt</li> <li>laboratory_spectrum_experiment_F_species_N2O.txt</li> <li>laboratory_spectrum_experiment_F_species_NO2.txt</li> <li>laboratory_spectrum_experiment_F_species_NO.txt</li> <li>laboratory_spectrum_experiment_G_species_N2O.txt</li> <li>laboratory_spectrum_experiment_G_species_NO2.txt</li> <li>laboratory_spectrum_experiment_G_species_NO.txt</li> </ul> <p>The following file contains a tabulation of the full-spectral-range laboratory-measured photoabsorption spectrum of experiment A, along with a modelled spectrum.</p> <ul> <li><a href="https://zenodo.org/api/files/49f05962-9a34-4bbc-855c-1a0976f62531/laboratory_spectrum_experiment_A_full_spectrum.txt?versionId=79a70ade-63d1-4fd7-b423-176e27f8dc37">laboratory_spectrum_experiment_A_full_spectrum.txt </a></li> </ul> <p>The following file contains plots of the experimental spectra for all NxOy species in all measurements as well as the residual error of models fit to these spectra. Additional residual errors of model neglecting NxOy species indicates their contribution to the spectra.</p> <ul> <li>laboratory_spectrum_figures.pdf</li> </ul> <p> </p>
An Experimental Test of Lanchester's Models of Combat in the Neotropical Termite Nasutitermes corniger (Blattodea: Termitidae)
<p><span>Lanchester's models of combat have been invoked to explain the mechanics of group fighting in social animals. Specifically, Lanchester's square law posits that the fighting ability of the group is proportional to the square of the number of combatants. Although used to explain a variety of ecological phenomena, the models have not been thoroughly tested. We tested the Lanchester models using group battles between colonies of the termite <em>Nasutitermes corniger</em>. Our main goals were to determine if mortality rates fit the Lanchester models, and if so, whether the behavioural mechanisms underlying a group's success match those used in deriving the model. We initiated battles between pairs of colonies with different ratios of fighters and recorded deaths over time. We found that the numerically larger army has an advantage, but that the advantage is not as pronounced as predicted by Lanchester's square law. We also video-recorded battles to analyse individual behaviour, which did not support the mechanisms invoked by Lanchester. Instead, the killing power of an individual is increased by the presence of nestmates, giving the larger group a disproportionate advantage. Although the behavioural mechanisms leading to the advantage may differ, our results still support some of the proposed ecological phenomena.</span></p>
Dataset from Experimental and Nonlinear Finite Element Modeling Investigating an Innovative Buckling Restrained Bracing System for Rehabilitation of Seismic Deficient Structures
<p>The data presented in this paper were collected experimentally and modeled using the finite element method. A total of six BRBs (i.e., duplicates of three types of BRB core bars) specimens were tested experimentally and verified numerically using the finite element method employing the commercial Software ABAQUS. Specific labeling was used to designate each BRB type. Three core bars were used in the tested BRBs: fully-threaded, threaded-notched, and smooth-shaved. The specimens are labeled according to their core bar type and diameter. i.e., BRB-12-Th stands for a full threaded core bar diameter of 12 mm, the threaded notched type was labeled BRB-12-Th-Nd, and the smooth shave one was labeled BRB-12-Sh.</p> <p>Further details of the tested BRBs are included in the excel file called dimensions and properties of BRBs. The worksheet provides details of the BRB components (i.e., core bar, restraining unit, and innovative end units). The dimensions and strength of the materials were obtained from coupon tests. The experimental data are presented in the second excel file labeled hysteresis with three embedded worksheets, one for each type of BRB. The excel sheets provide the cyclic loading data and plots showing the hysteresis behavior of tested BRBs. A sample of the loading protocol included in the second excel file is presented in Fig.1. The third excel file presents the analytical data extracted from experimental data that has two sheets: stiffness and energy dissipation. The sheet labeled stiffness has the secant stiffness versus deformation plot for the push-pull cycles (compression-tension). The second sheet labeled energy dissipation shows the cumulative energy dissipated.</p>
Segmentation models and experimental results on segmenting slide scans of diatom preparations from river Menne
<p>This archive contains the models and the results of the deep learning experiments published in Kloster et al. 2022: Improving deep learning-based segmentation of diatoms in gigapixel-sized virtual slides by object-based tile positioning and object integrity constraint.</p> <p>The folders contain models and results of each of the 24 training runs, the files “metrics.experiments.pt[prediction score threshold].csv contain segmentation score thresholds the models obtained on unknown evaluation data.</p> <p>The data pertaining to each model is stored in a separate folder. Its name follows the convention “experiment.[model architecture].[tiling method].[dataset size].[timestamp]”. Please note that the naming of the tiling method differs from the manuscript; “fixed” refers to fixed-stride tiling, “objectcentred” object-based positioning, and “objectcentred_with_cropped” to object-based positioning + object integrity constraint. Dataset size “10p” refers to a 10% subsample of the complete training data set, “25p” to a 25% subsample and so on.</p> <p>Each folder contains the best performing model of the corresponding training run as pth (Mask R-CNN, PyTorch) or h5 (U-Net, Tensorflow/Keras) file, along with a files describing setup and conduction of the training. Subfolders “test_images_segmented*” contain the segmentation predicted by the models on the evaluation data. These are supplied as 1.) mask image either with the intensity value representing the prediction score (score 0.0 – 1.0 = intensities 0 – 255) or thresholded by the prediction score threshold given in the folder name; 2.) input image overlayed with ground truth (red) and segmentation mask (green), resulting in TP marked in yellow; 3.) a CSV file giving info on the filenames and the segmentation performance metrics.</p> <p>Please refer to the manuscript for further details.</p>
Experimental data for Distributed parametric model checking timed automata under non-Zenoness assumption
<p>This is the experimental data mentioned in the paper "Distributed parametric model checking timed automata under non-Zenoness assumption", published in FMSD (Formal Methods in System Design), 2022.</p> <p>Experiments were conducted using the distributed version of IMITATOR 2.9.2 (Butter Incaberry) on two Intel Xeon Silver 4114 at 2.2GHz (20 cores in total), and 96GiB of memory, running under Ubuntu 16.04 LTS 64-bit.</p>
3D models and raw data for the "Photogrammetric 3D modelling and experimental archaeology reveals new technological insights into engraved soapstone sinker production in Western Norway (6400-3300 cal. BC)" paper, Radchenko et al. in prep.
<p>3D models and raw data for the "Photogrammetric 3D modelling and experimental archaeology reveals new technological insights into engraved soapstone sinker production in Western Norway (6400-3300 cal. BC)" paper, Radchenko et al. in prep.</p> <p>5 models of soapstone sinkers and 5 models of experimentally produced objects.</p>
The state-of-the-art machine learning model for Plasma Protein Binding Prediction: computational modeling with OCHEM and experimental validation
<p><span>Institute of Materia Medica, Chinese Academy of Medical Sciences purchased 10,000 ChemDiv databases.</span></p>
Figure 1. Experimental unit model built with a 150 in Design and optimization of an experimental maintenance system for yellow clam broodstock Amarilladesma mactroides (Reeve, 1854)
Figure 1. Experimental unit model built with a 150 mm PVC pipe and coupling, used in the maintenance of yellow clam (Amarilladesma mactroides) broodstock in the laboratory.
A comparative study of the effectivity of MSC-based, NP-based and combined therapies in an experimental model of NaIO3-induced retinal degeneration
<div><strong>Background</strong></div> <div>Mesenchymal stem cells (MSCs) are currently tested as one of the promising options for the therapy of retinal diseases, due to their immunomodulatory and neuroprotective abilities. However, there are several limitations associated with this type of treatment. Therefore, combinations of MSCs with other therapeutic agents are being considered. One of such approaches is represented by the application of MSCs with nanoparticles (NPs), which are widely used in medicine for their antimicrobial and immunomodulatory properties. Nevertheless, there is a possibility of negative effects of NPs on MSCs.</div> <div><strong>Methods</strong></div> <div>In this study, we tested the <em>in vitro</em> and <em>in vivo</em> effect of silver (Ag) NPs on the properties of MSCs in an experimental mouse model of chronic retinal degeneration induced by sodium iodate.</div> <div><strong>Results</strong></div> <div>The results showed that simultaneous intravitreal administration of MSCs with AgNPs had no effect on the survival of MSCs in the eye, but a less effective regulation of Iba-1 (activated microglia/macrophages) and interleukin-1β expression in the retinal tissue compared to MSCs or AgNP only treated groups was observed. However, all treated groups had decreased expression of the gene for galectin-3 compared to the untreated control. In addition, MSCs applied alone or in combination with AgNPs and sorted from the degenerated retina on day 7 after application had increased expression of genes for specific retinal markers, and for transforming growth factor-β and insulin-like growth factor-1 compared to untreated naïve MSCs. On the contrary, the increased expression of the gene for glial cell-derived growth factor was observed only in the MSCs combined with AgNPs. However, the application of MSCs with AgNPs triggered increased expression for the IL-6 gene in the CD45 cells separated from the retina.</div> <div><strong>Conclusion</strong></div> <div>Overall, the results show that the application of MSCs or AgNPs has an immunomodulatory effect in chronic retinal degeneration, but the combined application of MSCs and AgNPs could decrease the effects of a single therapy.</div>
Code and data associated with Christiansen et al. 2021 "Facilitating population genomics of non-model organisms through optimized experimental design for reduced representation sequencing"
<p>All code and data input and output files (except reference genome and raw sequencing data) needed to reproduce the results of Christiansen et al. 2021 as released on <a href="https://github.com/notothen/radpilot">https://github.com/notothen/radpilot</a> alongside journal publication. See published paper:</p> <p>Christiansen, H., Heindler, F.M., Hellemans, B. <em>et al.</em> Facilitating population genomics of non-model organisms through optimized experimental design for reduced representation sequencing. <em>BMC Genomics</em> <strong>22, </strong>625 (2021). <a href="https://doi.org/10.1186/s12864-021-07917-3">https://doi.org/10.1186/s12864-021-07917-3</a></p>
Experimental and numerical study of the effect of model geometric distortion on laboratory modelling of urban flooding
<p>The supporting datasets includes: </p> <p>(1) All the figures in the manuscript in .fig format (in case possible)</p> <p>- Figures in main text</p> <p>- Figure in Support Information</p> <p>(2) Datasets for generating the main outcomes of the manuscript</p> <p>- two files that explain detailed data content in three structure</p> <p>- 3 sub-repositories which contains the results for the three models</p> <p>- one repository contains the data for Figure 8</p> <p> </p>
Describing ion transport and water splitting in an electrodialysis stack with bipolar membranes by a 2-D model: Experimental validation
<p>Electrodialysis with bipolar membranes (EDBM) has drawn attention motivated by their application in gener- ating reagents from salts. Due to the water splitting (WS) occurring at the junction of the bipolar membranes (BPMs), where the anion and cation layers are in strict contact, H+ and OH- are released from the BPM producing acid and alkali on the respective compartment. Considering this application, the interest of this work is to provide further understanding of the mechanisms of WS and transport of species in EDBM. This work develops and utilizes, for the first time, an experimentally validated two-dimensional (2-D) computational model, in which the Navier-Stokes and Nernst-Planck equations are coupled with the description of WS given by the Second Wien effect. In addition, a 1-D geometry is also proposed to perform a comparison between electroneutrality and Poisson charge conservation. The model is computationally solved using COMSOL Multiphysics. According to simulations, electroneutrality is valid for 2-D geometries. Moreover, the semipermeable characteristics of the membranes are assessed by means of evidencing a polarization effect resulting in a double-electric layer. The model proposed predicts a significant proton leakage, and facilitates the study of WS within the BPMs.</p>
Experimental measurements and uncertainty analysis for validation of the Building Electrical Efficiency Analysis Model (BEEAM)
<div> <div> <div> <div> <div>This dataset includes experimental measurements taken on a laboratory testbed at Colorado State University that was used for model validation of a software toolkit, the Building Electrical Efficiency Analysis Model (BEEAM). This toolkit was developed for comparing electrical efficiency of AC versus DC distribution systems in buildings. The testbed emulated loads found in a small office building and included laptop computer chargers, LED lighting systems, and miscellaneous DC and AC loads. Measurements were taken under AC and DC configurations in electrically balanced and unbalanced loading conditions. Also included in the dataset is an uncertainty analysis. A complete description of the testbed, hardware, measurements and uncertainty analysis is contained in the paper cited below.</div> </div> </div> </div> </div> <div> </div> <div>Avpreet Othee, James Cale, Arthur Santos, Stephen Frank, Daniel Zimmerle, Omkar Ghatpande, Gerald Duggan and Daniel Gerber, <em>"A Modeling Toolkit for Comparing AC and DC Electrical Distribution Efficiency in Buildings," Energies, 2023 (accepted, publication in progress).</em> </div>
Experimental data analyzed in: Signal detection models as contextual bandits
<p>Signal detection theory (SDT) has been widely applied to identify the optimal discriminative decisions of receivers under uncertainty. However, the approach assumes that decision-makers immediately adopt the appropriate acceptance threshold, even though the optimal response must often be learned. Here we recast the classical normal-normal (and power-law) signal detection model as a contextual multi-armed bandit (CMAB). Thus, rather than starting with complete information, decision-makers must infer how the magnitude of a continuous cue is related to the probability that a signaller is desirable, while simultaneously seeking to exploit the information they acquire. We explain how various CMAB heuristics resolve the trade-off between better estimating the underlying relationship and exploiting it. Next, we determined how naïve human volunteers resolve signal detection problems with a continuous cue. As anticipated, a model of choice (accept/reject) that assumed volunteers immediately adopted the SDT-predicted acceptance threshold did not predict volunteer behaviour well. The Softmax rule for solving CMABs, with choices based on a logistic function of the expected payoffs, best explained the decisions of our volunteers but a simple midpoint algorithm also predicted decisions well under some conditions. CMABs offer principled parametric solutions to solving many classical SDT problems when decision-makers start with incomplete information.</p>
Experimental Results for "A Unified Perspective on Natural Gradient Variational Inference with Gaussian Mixture Models"
<p>This package contains the raw data / logs (fetched from WandB) for the experiments of the following publication:</p> <p>O. Arenz, P. Dahlinger, Z. Ye, M. Volpp, and G. Neumann. A unified perspective on natural gradient variational inference with gaussian mixture models. Transactions on Machine Learning Research, 2023. URL: <a href="https://openreview.net/forum?id=tLBjsX4tjs">https://openreview.net/forum?id=tLBjsX4tjs</a>.</p> <p> </p>
Practical Cell Design for PTMA-Based Organic Batteries: an Experimental and Modeling Study - Supporting Dataset
<p>The cycling and impedance data used in the work "Practical Cell Design for PTMA-Based Organic Batteries: an Experimental and Modeling Study" are provided in this repository.<br> The data are reported both as original .txt files with the raw data from the instruments and as processed Matlab files, where the data are structured in cycles.<br> The Excel sheet "Metadata" explains the type of battery associated to each code and file(s).</p> <p><br> </p>
Characterizing the Neural Substrates of Irritability in Women: an Experimental Neuroendocrine Model
ClinicalTrials.gov study NCT04051320. IPD Sharing: YES. Countries: 1. Publications: 98.
Data from: Experimental validation of a linear momentum and bluff-body model for high-blockage cross-flow turbine arrays
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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.