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47,155 results for “evaluations”
Associated dataset for "Evaluation of Sensor Self-Noise in Binaural Rendering of Spherical Microphone Array Signals"
<p>The conducted instrumental and perceptual evaluation utilize the Real-Time Spherical Microphone Renderer (<a href="https://github.com/AppliedAcousticsChalmers/ReTiSAR">ReTiSAR</a>) for binaural reproduction in Python. However, the provided execution configurations (see below) are probably not exactly in accordance with the latest ReTiSAR code base. Hence, the at the time employed code state should be used in order to exactly reproduce the rendering results in this data set. The frozen code state for this data set is available at:<br> <a href="https://github.com/AppliedAcousticsChalmers/ReTiSAR/releases/tag/v2020.ICASSP">https://github.com/AppliedAcousticsChalmers/ReTiSAR/releases/tag/v2020.ICASSP</a></p> <p>Download the rendering pipeline and follow the setup instructions! Use the here included Conda environment file when setting up the Python environment. In this way you should obtain exactly the same Python setup as utilized in the instrumental and perceptual evaluation in the publication:</p> <pre><code>conda env create --file ReTiSAR_environment_freeze.yml</code></pre> <pre><code>source activate ReTiSAR_ICASSP_freeze</code></pre> <p>Directory "SNR":</p> <ul> <li>Tools for instrumental evaluation (Section 4)</li> <li>Shell script to capture input and output signals of rendering pipeline for sound field (target / wanted) and self-noise (unwanted) components for all specified configurations</li> <li>Matlab script to analyse captured signal and generate system transfer plots (Figure 1 to Figure 3 and further configurations)</li> </ul> <p>Directory "Relative Output Levels":</p> <ul> <li>Tools for preparation of perceptual evaluation (Section 5)</li> <li>Shell script to capture rendered uniformly contributing noise signals for all specified configurations</li> <li>Matlab script to analyse and level align captured signals and generate plot result plot (Figure 4)</li> </ul> <p>Directory "Absolute Output Levels":</p> <ul> <li>Tools for specification of perceptual evaluation (Section 5)</li> <li>Shell script to capture reproduced uniformly contributing noise signals for all specified configurations</li> <li>Matlab script to analyse the calibrated captured signals yielding the average level in the ear signals of 58.2 dBSPL (Section 5.1)</li> </ul> <p>Files in base directory and directory "Study Results":</p> <ul> <li>Tools for perceptual evaluation / user study (Section 5)</li> <li>Matlab GUI to conduct perceptual user study (employ by executing "ICASSP_gui.m", respective ReTiSAR instances are started and remote controlled by the GUI, raw study results will be stored in "results" directory)</li> <li>Matlab script to "calculate_conclusion.m" to analyse the raw study results and generate individual and conclusive result plots (Figure 5, Figure 6 and more)</li> </ul>
Data from a Large-Scale Experiment to Evaluate the Effects of Trapping to Control Muskrats (Ondatra zibethicus) in The Netherlands
<p>This data set supports the publication 'A Large-Scale Experiment to Evaluate the Effects of Trapping to Control Muskrats (Ondatra zibethicus) in The Netherlands' by Daan Bos, Emiel van Loon, Erik Klop and Ron Ydenberg. (the paper was accepted for publication in Wildlife Society Bulletin in 2020)</p> <p>The Muskrat is an invasive species in Europe and in the Netherlands muskrat burrowing can compromise the integrity of dykes and hence poses a public safety threat. For that reason a control programme has been in effect since the arrival of the species in 1941. To investigate the relation between catch and effort and enhance prediction models, a large randomized controlled experiment was designed and conducted from 2013 till 2016. The publication by Bos et al. (2020) analyses the experimental results and here we present and document the experimental data. See the readme.md file for further information.</p>
Evaluating the microscopic effect of brushing stone tools as a cleaning procedure [Python analysis]
<p>This upload includes the following files related to the Python analysis:</p> <ol> <li>Raw data as a XLSX table (brushing_v2.xlsx), i.e. results from R Script #1 (see <a href="https://doi.org/10.5281/zenodo.3632517">https://doi.org/10.5281/zenodo.3632517</a>)</li> <li>Python script of the whole analysis (RunEveryParameter.py)</li> <li>Convenience script for running RunEveryParameter.py in background and logging all output (RunSingleParametesBash.sh)</li> <li>Log file for output of sampling from the model for each parameter in a loop (logAll.txt)</li> <li>Jupyter notebooks of the analysis run on <em>epLsar</em> as an example (Notebook_SingleParameter.inpyb) and of a summary of the whole analysis (Notebook_Overview.ipynb), plus associated HTML output files (*.html)</li> <li>For each parameter:</li> </ol> <ul> <li>Full samples of parameter values (*.pkl)</li> <li>Energy plots of Hamiltonian Monte Carlo (*_Energy.pdf)</li> <li>Contrast plots between each treatment (BrushDirt = Is_Is, BrushNoDirt = Is_No, RubDirt = No_Is) and the control (No_No) (*_Contrasts.pdf)</li> <li>Trace plots for each parameter (*_Trace.pdf)</li> <li>Distribution of posteriors for each parameter (*_Posterior.pdf)</li> <li>Prior and posterior predictive distributions for each parameter (*_PriorPosterior.pdf)</li> </ul> <p>Instructions to download all files at once are given here: <a href="https://doi.org/10.5281/zenodo.4011952">https://doi.org/10.5281/zenodo.4011952</a></p>
Elevation Models for Reproducible Evaluation of Terrain Representation - Inventory of Renderings
<p>This is an inventory of 155 renderings from 78 publications on terrain visualization techniques. The renderings guided the selection of landform types in the elevation models that are proposed in the following article:</p> <p><em>Kennelly, P. J., Patterson, T., Jenny, B., Huffman, D. P., Marston, B. E., Bell, S. and Tait, A. M. (2021). Elevation models for reproducible evaluation of terrain representation. Cartography and Geographic Information Science, 48:1, 63–77. DOI: <a href="http://doi.org/10.1080/15230406.2020.1830856">10.1080/15230406.2020.1830856</a></em></p> <p>Visualization techniques include colored aspect, contour lines, hypsometric tints, plan oblique relief, relief shading, rock and scree representation, and spot heights. The inventory contains information about display scale of the sample renderings, landform types, cell size, and geographic location of the digital elevation models. Also inventoried are how authors evaluated their renderings, how scale was indicated on the renderings, and whether the cell size and source of elevation data was included.</p> <p>The inventory is formatted as a single table in CSV UTF-8 and MS Excel .xlsx formats. Papers are grouped by visualization type; attributes of each rendering are stored on a single row.</p>
Ground Truth for DCASE 2020 Challenge Task 2 Evaluation Dataset
<p><strong>Description</strong></p> <p>This data is the ground truth for the "<a href="https://zenodo.org/record/3841772">evaluation dataset</a>" for the <strong>DCASE 2020 Challenge Task 2 "Unsupervised Detection of Anomalous Sounds for Machine Condition Monitoring" </strong><a href="http://dcase.community/challenge2020/task-unsupervised-detection-of-anomalous-sounds">[task description]</a>. </p> <p>In the task, three datasets have been released: "<a href="http://zenodo.org/record/3678171">development dataset</a>", "<a href="https://zenodo.org/record/3727685">additional training dataset</a>", and "<a href="https://zenodo.org/record/3841772">evaluation dataset</a>". The evaluation dataset was the last of the three released and includes around 400 samples for each Machine Type and Machine ID used in the evaluation dataset, none of which have any condition label (i.e., normal or anomaly). This ground truth data contains the condition labels.</p> <p> </p> <p><strong>Data format</strong></p> <p>The ground truth data is a CSV file like the following:</p> <p>---------------------------------</p> <p>fan<br> id_01_00000000.wav,normal_id_01_00000098.wav,0<br> id_01_00000001.wav,anomaly_id_01_00000064.wav,1<br> ...</p> <p>id_05_00000456.wav,anomaly_id_05_00000033.wav,1<br> id_05_00000457.wav,normal_id_05_00000049.wav,0<br> pump<br> id_01_00000000.wav,anomaly_id_01_00000049.wav,1<br> id_01_00000001.wav,anomaly_id_01_00000039.wav,1<br> ...</p> <p>id_05_00000346.wav,anomaly_id_05_00000052.wav,1<br> id_05_00000347.wav,anomaly_id_05_00000080.wav,1<br> slider<br> id_01_00000000.wav,anomaly_id_01_00000035.wav,1<br> id_01_00000001.wav,anomaly_id_01_00000176.wav,1<br> ...</p> <p>---------------------------------</p> <p>"Fan", "pump", "slider", etc mean "Machine Type" names. The lines following a Machine Type correspond to pairs of a wave file in the Machine Type and a condition label. The first column shows the name of a wave file. The second column shows the original name of the wave file, but this can be ignored by users. The third column shows the condition label (i.e., 0: normal or 1: anomaly).</p> <p> </p> <p><strong>How to use</strong></p> <p>A system for calculating AUC and pAUC scores for the "evaluation dataset" is available on the Github repository <a href="https://github.com/y-kawagu/dcase2020_task2_evaluator">[URL]</a>. The ground truth data is used by this system. For more information, please see the Github repository.</p> <p> </p> <p><strong>Conditions of use</strong></p> <p>This dataset was created jointly by <strong>NTT Corporation</strong> and <strong>Hitachi, Ltd.</strong> and is available under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) license.</p> <p> </p> <p><strong>Publication</strong></p> <p>If you use this dataset, please cite <strong>all the following three papers</strong>:</p> <p>Yuma Koizumi, Shoichiro Saito, Noboru Harada, Hisashi Uematsu, and Keisuke Imoto, "ToyADMOS: A Dataset of Miniature-Machine Operating Sounds for Anomalous Sound Detection," in Proc. of IEEE Workshop on Applications of Signal Processing to Audio and Acoustics (WASPAA), 2019. <a href="https://ieeexplore.ieee.org/document/8937164">[pdf]</a></p> <p>Harsh Purohit, Ryo Tanabe, Kenji Ichige, Takashi Endo, Yuki Nikaido, Kaori Suefusa, and Yohei Kawaguchi, “MIMII Dataset: Sound Dataset for Malfunctioning Industrial Machine Investigation and Inspection,” in Proc. 4th Workshop on Detection and Classification of Acoustic Scenes and Events (DCASE), 2019. <a href="http://dcase.community/documents/workshop2019/proceedings/DCASE2019Workshop_Purohit_21.pdf">[pdf]</a></p> <p>Yuma Koizumi, Yohei Kawaguchi, Keisuke Imoto, Toshiki Nakamura, Yuki Nikaido, Ryo Tanabe, Harsh Purohit, Kaori Suefusa, Takashi Endo, Masahiro Yasuda, and Noboru Harada, "Description and Discussion on DCASE2020 Challenge Task2: Unsupervised Anomalous Sound Detection for Machine Condition Monitoring<em>,"</em> in Proc. 5th Workshop on Detection and Classification of Acoustic Scenes and Events (DCASE), 2020. <a href="https://dcase.community/documents/workshop2020/proceedings/DCASE2020Workshop_Koizumi_3.pdf">[pdf]</a></p> <p><br> <strong>Feedback</strong></p> <p>If there is any problem, please contact us:</p> <ul> <li>Yuma Koizumi, <a href="mailto:koizumi.yuma@ieee.org">koizumi.yuma@ieee.org</a></li> <li>Yohei Kawaguchi, <a href="mailto:yohei.kawaguchi.xk@hitachi.com">yohei.kawaguchi.xk@hitachi.com</a></li> <li>Keisuke Imoto, <a href="mailto:keisuke.imoto@ieee.org">keisuke.imoto@ieee.org</a></li> </ul>
Occurrence data used to create species distribution models and apply an evaluation method
<p>These two files containing a table with three columns: species names, longitude, latitude. Each row of the tables represents a georeferenced presence record for the corresponding species. The original presence data were downloaded from the GBIF database and after going through a cleaning process, we ended with these records that passed all the tests.</p> <p>These datasets were used to create species distribution models (SDMs) that were then used to apply a new method to evaluate the performance of different SDMs. Jiménez & Soberón (2020)</p>
CEPHIA Evaluation Panel data for Maxim and Sedia Limiting Antigen Avidity assays
<p>CEPHIA Evaluation Panel dataset containing final ODn values for each assay. The first file contains results on all standard panel samples, and the second contains results on blinded control samples tested in replicate.</p>
Comparing Perturbation Modes for Evaluating Instabilities in Neuroimaging: Processed NKI-RS Subset (08/2019)
<p>The processed subset of the NKI-RS dataset for evaluation of various perturbation modes when studying instabilities. Linked to the <a href="https://arxiv.org/abs/1908.10922">pre-print found here</a>, can be visualized using the <a href="https://github.com/gkiar/stability-mca/blob/master/code/dipy_exploratory/mca_dipy_exploratory_analysis.ipynb">plotting code here</a>, and generated with various <a href="https://github.com/gkiar/stability/tree/master/code/experiments/paper0_comparing_perturbation_modes">scripts and launch configurations found here</a>.</p>
Land cover, landscape metrics and typology of European cities for Urban Forest Ecosystem Services (UFES) evaluation
<p>The data refers to the paper "<em>Urban Forests as Regulating Ecosystems: Types and Ranking of European Cities</em>"</p> <p>The datasets provide a typology for 689 European urban areas, the land cover metrics and landscape metrics used to create the typology and the Urban Forest Ecosystem Services (UFES) indexes created from them.</p> <p>The typology of Urban Forest Ecosystem Services (UFES) presents 10 clusters of cities aggregated into 4 groups: Forest cities, Anthropogenic cities, Herbaceous cities and Standard European cities. The data can be used to support urban planning policies at local and regional scales; in urban forestry, urban form and ecosystem services work related at different spatial scales. The metrics used capture the spatial integration of different layers of natural, semi-natural and artificial land within functional urban areas.</p> <p> </p> <p>The datasets are a csv file (<code>Metrics.csv</code>) and a shapefile (<code>UFES.shp</code>) of polygons with attributes.</p> <ul> <li> <p><code>UFES.shp</code> attributes' are the following: FUA codes, country name, main city name, clusters and groups of FUAs resulting from the hierarchical cluster analysis (HCA), the R color codes used in the article, the five UFES budget indexes as well as an aggregated global UFES index for each FUA.</p> </li> <li> <p><code>Metrics.csv</code> contains the FUA codes, the land cover and landscape metrics used in the HCA.</p> </li> </ul> <p> </p>
A comprehensive evaluation of binning methods to recover human gut microbial species from a non-redundant reference gene catalog - Supporting Data
<p><strong>Description </strong></p> <p>The following files are available : </p> <ul> <li>Simulated non-redundant Gene Catalog (SGC) composed of 128267 genes;</li> <li>Gene abundance profiles across 40 samples: raw read counts, gene length normalized base counts, depth file computed by the jgi_summarize_bam_contig_depth script provided by MetaBAT;</li> <li>Gold Standard (GS) and Gold Standard Single Assignment (GS_SA) binning results;</li> <li>Binning results obtained on the SGC with nine binning methods: MSPminer, MGS-canopy, DAS Tool, MaxBin2, MetaBAT2, SolidBin, CONCOCT, COCACOLA and MyCC.</li> </ul> <p><strong>License</strong></p> <p>These files are licensed under a <a href="http://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution 4.0 International License</a>.</p>
Human assemblies evaluated in the hifiasm paper
<p>Human assemblies evaluated in the <a href="https://www.nature.com/articles/s41592-020-01056-5">Cheng et al (2021)</a>. Non-human assemblies are available at <a href="https://zenodo.org/record/4393750">doi:10.5281/zenodo.4393750</a>. File "*.ONT.*" were generated by <a href="https://www.nature.com/articles/s41587-020-0503-6">Shafin et al (2020)</a>, "*.DipAsm*" by <a href="https://www.nature.com/articles/s41587-020-0711-0">Garg et al (2020)</a> and "*.PAGS*" by <a href="https://www.nature.com/articles/s41587-020-0719-5">Porubsky et al (2020)</a>. The rest of the assemblies were generated by Cheng et al.</p>
Data and materials from: "Towards Auditory Profile-based Hearing-aid Fitting: Fitting Rationale and Pilot Evaluation"
<p>This repository contains materials and data used and described in:</p> <p><strong>Sanchez-Lopez, R., Fereczkowski, M., Santurette, S., Dau, T., Neher, T. (2021). Towards Auditory Profile-based Hearing-aid Fitting: Fitting Rationale and Pilot Evaluation. <em>Audiol. Res.</em> 11, no. 1: 10-21. <a href="https://doi.org/10.3390/audiolres11010002 ">https://doi.org/10.3390/audiolres11010002 </a></strong></p> <p> </p> <p><strong>Abstract</strong></p> <p><strong>Background</strong> - The clinical characterization of hearing deficits for hearing-aid fitting purposes is typically based on the pure-tone audiogram only. In a previous study, a group of hearing-impaired listeners completed a comprehensive test battery designed to tap into different dimensions of hearing abilities. A data-driven analysis of the data yielded four clinically relevant patient subpopulations or “auditory profiles”. The purpose of the current study was to propose and pilot-test profile-based hearing-aid settings to explore their potential for providing more targeted hearing-aid treatment.<br> <strong>Methods </strong>- Four candidate hearing-aid settings were developed and evaluated by a subset of the participants tested previously. The evaluation consisted of multi-comparison preference ratings carried out in realistic sound scenarios.<br> <strong>Results </strong>- Listeners belonging to the different auditory profiles showed different patterns of preference for the tested hearing-aid settings that were largely consistent with the expectations.<br> <strong>Conclusion</strong> - The results of this pilot evaluation support further investigations into stratified, profile-based hearing-aid fitting with wearable hearing aids.</p> <p>Please cite this article when using the data</p> <p> </p> <p><strong>Description of the files:</strong></p> <ul> <li><strong>APBHAF_Audiofiles.zip: </strong>Audio files used in the SenseLabOnline environment. Each folder corresponds to one participant.</li> <li><strong>APBHAF_MUSHA.xlsx: </strong>Raw Data of the MUSHA experiment.</li> <li><strong>APBHAF_MUSHA_Analysis.R: </strong>R code for the data analysis.</li> <li><strong>MUS_SoundScenes.mat</strong>: Mat file with a structure 1x9 MUS with the raw acoustic signals before processing with the hearing-aid simulator. <ul> <li>CurrentMixture: matrix consisting of the simulated acoustic signal recorded by the 4 microphones of the hearing-aid satellites: 1) front-left, 2) back-left, 3) front-right, 4) back-right.</li> <li>CurrentAnchor: matrix consisting of the simulated acoustic signal recorded by the 4 microphones of the hearing-aid satellites: 1) front-left, 2) back-left, 3) front-right, 4) back-right. The Anchor is -6 dB SNR.</li> <li>SampleLabel: Either "Kantine", "Traffic" or "Quiet"</li> <li>ConditionLabel: Either "Cond1", "Cond2" or "Cond3"</li> <li>fsmix: sampling frequency. For all signals must be 32000Hz</li> </ul> </li> <li><strong>MUSHA_Instruction: </strong>Instructions used for explaining the task and the environment.</li> </ul> <p>* The participant IDs in each of the files has been assigned randomly to ensure the anonymization of the data. The pseudo-anonymized data might be shared under request by direct correspondence with the authors.</p>
Evaluating demand forecasting models using multi-criteria decision-making approach
<p>The datasets added include the raw data, ANP weights calculations and TOPSIS ranking calculations for the demonstration case in the article titled: Evaluating demand forecasting models using multi-criteria decision-making approach.</p> <p>The files include a data explanation text file.</p>
Supplementary material for "Decomposing fecundity and evaluating demographic influence of multiple broods in a migratory bird"
<p>Data and code files used in the paper. The four data files are provided in ASCII format (marr_S.TXT, broods_S.TXT, marr_G.TXT, broods_G.TXT). The code file (script_IPM_wryneck_Tenan_etal.txt) is a space delineated text file. The code file is written for R, but models are run in NIMBLE from R. The code file also contains the description of the data files and code for data management.</p>
An Empirical Evaluation of Video Conferencing Systems Used in Industry, Academia, and Entertainment
<p>Video Conferencing Systems~(VCS) are used daily--at work, in online education, and for get-togethers with friends and family. Many new VCSs have emerged in the past decade and a new market-leader has risen during the coronavirus period of 2020. Understanding how these systems work could help us improve them rapidly. However, no experimental comparison of such systems currently exists. </p> <p>We propose a method to compare VCSs in real-world operation and implement it as a tool. Our method considers 4 main real-world experiments. Each captures different aspects, such as communication channels~(audio, video, audio-video), types of network environments~(e.g., Ethernet, WiFi, 4G), and reports system and network utilization. We conduct real-world experiments with 3 VCSs, Zoom, Microsoft Team, and Discord.</p> <p>This dataset is the result of our experiments conducted with the Online Video Conference Benchmarking tool.</p>
Interlaboratory study for the evaluation of three microtiter plate-based biofilm quantification methods
<p>Data collected in the Print-aid interlaboratory study (ring trial) to evaluate the repeatability and reproducibility of three microtiter plate based methods: crystal violet, resazurin and plate counts. The files contain all the raw data collected for each laboratory as well as the tranformed data. Analysis and protocol details can be found in the following publication https://www.nature.com/articles/s41598-021-93115-w </p>
Global dataset for evaluating impact of topographic factors on hydrologic response to climate variability
<p>The dataset contained here was used to document the biomes in the world that show high sensitivity in their hydrologic response to interannual changes in climatic forcing during the 2001-2016 period, while evaluating the role of major topoclimatic factors in modulating these responses. To do this we generated a hydrologic sensitivity index (HSi). HSi evaluates the absolute ratio between the changes of the climatic conditions (dryness index, DI) and hydrologic response (evaporative index, EI<sub>R</sub>) between consecutive years (e.g. HSi= |∆ EI<sub>R</sub> /∆ DI|). HSi was computed for every successive pair of years from 2001 to 2016. A total of 15 HSi maps were obtained representing the HSi for each consecutive pair of years. For each map, where HSi >1, regions are classified as <strong><em>Sensitive</em></strong> and for HSi ≤1, <strong><em>Resilient</em></strong>. To provide a synthesis of the general trend of global hydrologic sensitivity, we display the frequency of HSi, showing the recurrence of HSi >1 for every non-ocean location with a range of 0 (low frequency) to 15 (high frequency). Regions where frequency HSi≥7 are considered highly recurring and as such are deemed as the most hydrologically sensitive. </p> <p><strong>This dataset includes the code and raster data to evaluate the effect of the topography on HSi to plot the average frequency HSi for all elevations, aspects, and slope steepness against latitudinal change.</strong> We used global digital elevation models (DEMS) from the Shuttle Radar Topography Mission (SRTM) data (90 m resolution; version 4, for latitudes < 60◦ N and GTOPO30 (1◦ resolution; http://lta.cr.usgs.gov/GTOPO30) for latitudes > 60◦ N. Slope and aspect maps were derived from the DEMs using standard GIS-based methods in ArcMap 10.7.Elevation range used is [0,7000] meters above sea level (m.a.s.l), aspect (N, NE, E, SE, S, SW, W, NW) specifically above slope values greater than 10-degrees (no flat areas used), and slope [0,90] degrees.</p> <p><strong>Contents:</strong></p> <ul> <li>1 MATLAB with the code ready to use</li> <li>1 PDF file with the same code</li> <li>27 geotiff files for elevation (dem#1-27.tif)</li> <li>27 geotiff files for frequency HSi (freq#1-27.tif) </li> </ul> <p>Note: the following files of slope and aspect could not upload in repository due to exceedance in storage limit: 50MG. The DEM files must be run in ArcMap using slope and aspect tool to produce the following files with the following names.</p> <ul> <li>27 geotiff files for slope (slope#1-27.tif)</li> <li>27 geotiff files for aspect (aspect#1-27.tif)</li> </ul>
Fluorescent Confocal Laser Scanning Microscopy of White Blood Cells, Cancer Cell Line MCF7, and Mixtures of these Cells: A Model System for Circulating Tumor Cell Biomarker Evaluation V.1
<p>This is a confocal laser scanning microscopy data set of white blood cells (leukocytes), the cancer cell line MCF7, and mixtures of these cells acquired on a Zeiss LSM 780 microscope in the University of Colorado Anschutz Medical Campus Advanced Light Microscopy Core. Cells are fluorescently labeled for DNA with DAPI (Sigma D9542), lipids with Bodipy 495/503 (Thermo Fisher D3922), the filament protein cytokeratin (CK) with pan-cytokertain-alexa555 antibodies (Cell Signaling Technologies 3478S) and the surface membrane antigen CD45 with CD45-alexa647 antibodies (Biolegend 304020). Bodipy was excited with a continuous wave (CW) 488 nm laser, alexa555 was excited with CW 561 nm laser, and alexa647 was excited with a CW 633 nm laser. The acquiring instrument does not have a CW 405 nm source so DAPI was excited by two photon process using a Coherent Cameleon ultrafast pulsed laser tuned to 765 nm. The objective used was a Zeiss Plan-Apochromat 20x, 0.8 NA, air.</p> <p>The data consists of 4 channel 8x8 mosaic z-stacks. The Zeiss software performed stitching of the mosaics. These stitched data images are included and marked with _Stitched at the end. Those interested in performing the stitching themselves can do this with the raw data files (without the _Stitched). The jpeg images are processed from the stitched LSM images. The LSM files contain additional meta data on the experiment including power levels and acquisition settings.</p> <p>The _Stiched .lsm files will load in ImageJ (tested with V.1.49) as 4 channel 3 stack images.</p> <p>This data is a model system for evaluating the DNA/Lipids/CK/CD45 biomarker panel to identify circulating tumor cells (CTCs). The D- population of the model is the WBCs and the D+ population is the MCF7 cancer cell line. The amount of separation the biomarker panel plus analysis algorithm can produce between these populations (D+/D-) is an estimate the sensitivity and specificity of the biomarker panel plus algorithm to CTCs.</p> <p>Experiments generating the data were performed over the course of 15 days. Peripheral blood samples were collected from the Gynecological Tissue and Fluid Bank (COMIRB 07-0935 / COMIRB 05-1081) from consenting patients undergoing surgery at the University of Colorado Hospital. Blood samples were used the same day they were collected. Blood samples were collected from 3 patients with benign conditions, labeled WBBN#, and 3 patients with ovarian cancer, labeled WBCA#. We do not expect there to be any difference in the isolated white blood cells samples prepared from the cancer and benign patients. Samples were stored at room temperature until white blood cells were isolated. Mixed samples were prepared by passaging a MCF7 flask and mixing it with isolated white blood cells before fixation. A schedule showing the time duration between collection, processing and imaging is included as “experimental schedule.gif”.</p> <p>The MCF7 cancer cell line was a kind gift from Dr. Heide Ford. Genomic DNA was isolated from the MCF7 cell line after the experiment and sent for cell line authentication. The gDNA was a match to MCF7. The authentication report and data are included in this submission.</p> <p>CD45 antibodies were exhausted on day 7. New antibody was purchased and received on day 8. The day 7 images only has labels for DAPI and Bodipy. The samples prepared with the old antibodies on days 4 and 7 were relabeled and imaged with the new antibodies on days 14 and 15. This labeling was also done to confirm the pan-CK antibodies remained good since they are dim in the MCF7 cells imaged on days 12 and 13. The pan-CK on days 14 and 15 looks the same as it did on days 5 and 7 confirming the antibodies are good.</p> <p>Four of the filters containing cells were not sufficiently flat to be acquired with a 3 slice z-stack so a 5 slice z-stack was used. These files have been zipped to compress them under the 2 GB limit permitted by zenodo.org</p> <p>Further information on how these samples were prepared, processed, and analyzed can be found in our associated 2016 SPIE Photonics West BIOS conference proceeding titled, “Quantitative image cytometry measurements of lipids, DNA, CD45 and cytokeratin for circulating tumor cell identification in a model system”, http://dx.doi.org/10.1117/12.2222317.</p> <p>This work was supported by funding provided to the University of Colorado Cancer Center by the American Cancer Society and awarded as Institutional Research Grant Number 57-001-53, by funding provided by the Defense Advanced Research Projects Agency under grant number N66001-10-4035, and by funding provided by NIH/NCATS Colorado CTSI Grant Number TL1 TR001081. The University of Colorado Anschutz Medical Campus Advanced Light Microscopy Core is also supported in part by NIH/NCATS Colorado CTSI Grant Number UL1 TR001082. The funders had no role in the study design, data collection, analysis, or decision to publish.</p>
Evaluation of dynamically downscaled CMIP6-CCAM models over Australia
<p>Downscaled CCAM-CMIP6 model data used in the evaluation of CCAM-CMIP6 models against AGCD observations:</p><ol><li>Data required for daily evaluation of precipitation and temperature variables, and calculation of Perkins skill score</li><li>Data required for evaluation of bias for precipitation and temperature variables</li><li>Data required for KGE skill score</li></ol>
Dataset for the project "Evaluation of the effects of trace elements from street dust under urban – industrial conditions on the ecophysiology of Acer platanoides L. and Tilia cordata Mill.
<p>Description of the project: The rapid growth of cities, industry and transport has significantly deteriorated environmental quality, especially in areas with the highest population densities. It applies to water, soil, and air, especially in urban areas. Air pollutants include particulate matter (PM), which harms human health. According to WHO reports (2021), PM pollution is the cause of cardiovascular and respiratory diseases, leading to 4.2 million premature deaths worldwide in 2016. Although improving every year, the situation in Poland is still worse than in many European countries. The particulate matter also includes heavy metals, which have a toxic effect on plants. Plants in urban areas are particularly vulnerable, especially trees, which perform several vital functions, including mitigating climate change, filtering pollutants, and improving air quality. The aim of the project was to determine and compare the morphological and physiological responses of selected tree species to particulate pollution stress under urban conditions. Tree leaves are an essential barrier to atmospheric dust by trapping it on their surface. However, this may come at the cost of reduced light absorption, increased leaf temperature, damage to leaf blades and consequently impaired photosynthesis and plant productivity. However, the ability to absorb dust varies between tree species. It depends on the leaf surface structure, and the response may be due to the species' sensitivity to pollutants. Investigations were conducted in the Upper Silesian Industrial Area around various emission sources, such as heavy metal smelters, combined heat and power plants, and busy streets. The research focused on two tree species common in urban areas, the Norway maple (<i>Acer platanoides</i>) and the small-leaved lime (<i>Tilia cordata</i>). It included measurement of heavy metal concentrations in leaf blades and dust collected on their surface, analysis of concentrations of selected pigments and ascorbic acid as markers of environmental stress. The study provided a preliminary assessment of the impact of particulate pollution on tree function under harsh urban conditions and determined the potential of the studied species to reduce atmospheric dust.</p>
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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.