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Maps and real-space refined models for 2024 Frontiers in Molecular Biosciences Perspective
<p>Maps and real-space refined models for our 2024 Frontiers in Molecular Biosciences perspective examining the impact of ML-based map modification tools on cryoEM maps.</p>
Data Package for "A Platform-Agnostic Approach for Automatically Identifying Real-Life Performance Issue Reports with Heuristic Linguistic Patterns"
<p>This Zenodo repository contains the data supporting the findings of the journal paper, titled "A Platform-Agnostic Approach for Automatically Identifying Real-Life Performance Issue Reports with Heuristic Linguistic Patterns", published on IEEE Transactions on Software Engineering, including:</p> <ol> <li><strong>Heuristic Linguistic Pattern Set</strong>: <span>we listed the 80 HLP we derived from </span><span>Apache's JIRA issue tracking system</span><span>. Column "</span><span>Category" </span><span>lists the type of each pattern. Namely, LEX represents lexical pattern, STR represents structural pattern, SEM represents semantic pattern, and PRF represents profiling pattern. Column "Name" is a descriptive name we give to each pattern. Column "Definition" defines the detailed content in each pattern.</span></li> <li><strong>Manual Tagging Results</strong>: manual_tagging.xlsx spreadsheet <span>comprises both sentence-level and issue-level manually tagging results for three datasets: 'Dataset-1: Apache Jira's Homologous Evaluation', '</span><span>Dataset-</span><span>2: Apache Jira's Heterologous Evaluation', and '</span><span>Dataset-</span><span>3: Other Platform's Evaluation'. The tagging results are segmented into sentence-level tabs ("Dataset-1 Sen", "Dataset-2 Sen", "Dataset-3 Sen") and issue-level tabs ("Dataset-1 Issue", "Dataset-2 Issue", "Dataset-3 Issue").</span></li> <li><span><strong>RQ Findings</strong>: </span> <p><span>This section contains detailed data findings from six research questions (RQ1 to RQ6).</span></p> <ul> <li> <p><span>The RQ1 tab provides an evaluation of our HLP-based approach, showing the precision, recall, and F1-Score of eight classifiers. These results are juxtaposed with the corresponding values from baseline methods, at both sentence and issue levels for automatic tagging.</span></p> </li> <li> <p><span>The RQ2 tab illustrates the precision, recall, and F1-Score of eight classifiers under two training conditions: a balanced training dataset (BT+HLP) and an imbalanced training dataset (UBT+HLP). These outcomes are contrasted with the equivalent values from baseline methods, also trained under balanced (BT+BLM) and imbalanced (UBT+BLM) conditions. The results are shown at both sentence and issue levels for automatic tagging.</span></p> </li> <li> <p><span>The RQ3 tab evaluates the dataset transferability of our HLP-based approach in comparison to baseline methods. It achieves this by analyzing the precision, recall, and F1-Score metrics for eight classifiers under two different "training/testing" dataset conditions, i.e., 'D1/D1' and 'D1/D3'. These conditions allow for a direct comparison of performance when applied to the same dataset ('D1/D1') versus when transferred to a different dataset ('D1/D3'). Additionally, the tab includes an 'Avg Change' and 'p-value' section, summarizing the statistical change in performance metrics between the two dataset conditions. </span></p> </li> <li> <p><span>The RQ4 tab presents a direct comparison between strict and fuzzy HLP matching approaches, assessed through precision, recall, and F1-Score metrics across eight issue classifiers.</span></p> </li> <li> <p><span>The RQ5 tab examines the influence of sentence order on the accuracy of eight classifiers within our approach. It shows the change in precision, recall, and F1-Score when the sentence order feature is taken into consideration versus when it is not.</span></p> </li> <li> <p><span>The RQ6 tab explores the impact of feature selection algorithms on both issue and sentence-level tagging accuracy. This tab presents the average precision, recall, and F1-Score for three experiments: Boruta, Recursive Feature Elimination (RFE), and the usage of all 80 features. </span></p> </li> </ul> </li> <li><strong>Qualitative Analysis</strong>: <p><span>This spreadsheet offers a comprehensive examination of the data supporting Section 6.1, which focuses on Qualitative Analysis. It is organized into several tabs, each dedicated to specific research questions (RQs) as outlined below:</span></p> <ul> <li> <p><span>Tab "RQ-1" showcases performance issue reports accurately detected by our High-Level Performance (HLP) approach's top model, XGBoost, which were not identified by the benchmark method's leading model, BERT. This highlights the comparative advantage of our approach in identifying nuanced performance issues.</span></p> </li> <li> <p><span>Tab "RQ-2" continues the exploration of performance issue reports, presenting cases with specific details (to be added).</span></p> </li> <li> <p><span>Tab "RQ-3" delves into the unique capabilities of XGBoost, the leading model in our HLP approach, showcasing its ability to detect performance issues missed by the baseline's top model, BERT. This comparison is drawn under distinct conditions: with pre-training (Dataset 1) and without pre-training (Dataset 3), illustrating the robustness and adaptability of our model.</span></p> </li> <li> <p><span>Tab "RQ-4" focuses on performance issue reports uniquely identified through the implementation of Fuzzy HLP Matching within our HLP approach. This method underscores the innovative matching techniques that enhance issue detection.</span></p> </li> <li> <p><span>Tab "RQ-5" presents performance issue reports pinpointed exclusively by applying the Issue HLP Matrix within our approach. This tab demonstrates the effectiveness of our matrix-based analysis in isolating and identifying specific performance concerns.</span></p> </li> <li> <p><span>Tab "RQ-6" is dedicated to performance issue reports uniquely detected by incorporating feature selection techniques into our HLP approach. This illustrates the value of advanced feature selection in improving the precision of performance issue identification.</span></p> </li> </ul> </li> <li><strong>LLM Experiment Data</strong>: presents the tagging outcomes of Large Language Models (LLMs), specifically ChatGPT-3.5 and ChatGPT-4, across three distinct datasets: 'Dataset-1: Apache Jira's Homologous Evaluation', 'Dataset-2: Apache Jira's Heterologous Evaluation', and 'Dataset-3: Evaluation on Other Platforms'. The results are organized into three separate tabs: 'Dataset-1 Issue', 'Dataset-2 Issue', and 'Dataset-3 Issue'.</li> <li><strong>ChatGPT Operation Python Script</strong>: crafted for automating the evaluation and tagging of issue reports in Excel using Large Language Models (LLMs) like ChatGPT-3.5 and ChatGPT-4. It underscores the importance of administrative rights for file modifications and outlines procedures for reading from and writing responses to Excel files. Key functions include querying LLMs with issue descriptions, processing their responses, and updating the spreadsheet with 'Yes' or 'No' labels and explanatory reasons, thereby facilitating an organized review of LLM performance across different datasets.</li> </ol>
Real Estate Southern Spain 2024
<p>Dataset with 12,086 real estate properties for sale in southern Spain in April 2024. It includes the following files:<br>- properties.csv - comma separated values for 9 data fields<br>- descriptions.tar.gz - compressed archive with a file for each property including a textual description of it<br>- images.tar.gz - compressed archive including a folder with images for each property</p> <p>The fields in the CSV are ordered as follows:<br>reference, location, price, title, bedrooms, bathrooms, indoor surface area in sqm, outdoor surface area in sqm, pipe-separed list of features of the property</p> <p>The descriptions files are extracted into a "descriptions" folder and inside there is a file with the reference of each property in the CSV as the filename and .txt as extension.</p> <p>The image files are extracted into a "images" folder and inside there is a folder for each property with the folder name being the reference of the property in the CSV file. The images have been resized to 300px as maximum dimension, keeping the aspect ratio.</p>
Dataset real estate
<p>Trabajo realizado con fines didácticos y de aprendizaje en el Máster de Ciencia de Datos de la UOC. </p> <p>Extracción de datos mediannte webscrapping empleando Selenium y BeatifulSoup de la página idealista.com, centrado en la opción venta de 3 ciudades: Almería, Madrid y Teruel. </p>
Data for Sampling Real‐Time Atomic Dynamics in Metal Nanoparticles by Combining Experiments, Simulations, and Machine Learning
<div> <p>Even at low temperatures, metal nanoparticles (NPs) possess atomic dynamics that are key for their properties but challenging to elucidate. Recent experimental advances allow obtaining atomic‐resolution snapshots of the NPs in realistic regimes, but data acquisition limitations hinder the experimental reconstruction of the atomic dynamics present within them. Molecular simulations have the advantage that these allow directly tracking the motion of atoms over time. However, these typically start from ideal/perfect NP structures and, suffering from sampling limits, provide results that are often dependent on the initial/putative structure and remain purely indicative. Here, by combining state‐of‐the‐art experimental and computational approaches, how it is possible to tackle the limitations of both approaches and resolve the atomistic dynamics present in metal NPs in realistic conditions is demonstrated. Annular dark‐field scanning transmission electron microscopy enables the acquisition of ten high‐resolution images of an Au NP at intervals of 0.6 s. These are used to reconstruct atomistic 3D models of the real NP used to run ten independent molecular dynamics simulations. Machine learning analyses of the simulation trajectories allows resolving the real‐time atomic dynamics present within the NP. This provides a robust combined experimental/computational approach to characterize the structural dynamics of metal NPs in realistic conditions.</p> </div> <div></div>
Real Estate Data for Barcelona - Idealista Listings
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Real-Time Dataset of Metheorological Measurements Collected During the Project
<p>This dataset contains a collection of real-time meteorological data during the Resisto project. This information has been recorded and is structured into different fields, each representing a specific meteorological variable of the deployed sensors in the Doñana National Park. </p>
Real-Time Dataset of Fire Sensor Measurements Collected During the Resisto Project
<p>This dataset contains real-time environmental measurements from fire detection sensors across multiple locations. These sensors has been deployed on diferent locations, principally on the Doñana National Park. </p>
Video Supplement for Himes et al. (2024): "Using neural networks for near-real-time aerosol retrievals from OMPS Limb Profiler measurements"
<p>This archive contains the video supplement for</p> <p>Using neural networks for near-real-time aerosol retrievals from OMPS Limb Profiler measurements</p> <p>by Himes et al. (2024), submitted to Atmospheric Measurement Techniques. The file contains an animation of the V2.1 and NRT average retrieved extinction coefficient between 19.5--21.5 km at 997 nm for the 2024 Ruang eruptions.</p>
Tracking and classifying Amazon fire events in near-real time
<p><strong>Summary</strong></p> <p>Time-series (2018-2024) of the Amazon dashboard, including minor updates to the methods.</p> <p>The Amazon dashboard data product tracks individual fire events across most of South America (10N - 25S, 85W - 30W) in near-real time. The model classifies fires into four key fire types (deforestation, forest, small clearing and agricultural, and savanna and grassland fires) and provides estimates of individual fire carbon emissions. Methods are described in Andela et al. (2022). Near-real time estimates are provided at https://amzfire.servirglobal.net/ and here we archive historic time-series.</p> <p><strong>Methods</strong></p> <p>The data archived here (v1.1) include several small updates.</p> <p>Two updates relate to the use of VIIRS active fire detections. First, VIIRS active fire detections have been updated from collection 1 to collection 2. Second, any full day of missing data from either the VIIRS instrument onboard NOAA-20 or Suomi NPP is now replaced by data of the other instrument. This "gap" filling helps reduce the impact of periods with instrument outage, like those of Suomi NPP VIIRS during the 2024 burning season. </p> <p>The other two updates relate to the emissions calculations. First, to convert dry matter burned to carbon emissions, we have introduced fire type specific emissions factors instead of the earlier assumption of 50% carbon content for all fire types. Second, as part of the Sense4Fire project (https://sense4fire.eu/), we provide daily gridded emissions estimates of Dry Matter (DM), C, CO2, CO, and NOx at 0.1 degree resolution. We used emissions factors provided by Andrea (2019) for savanna and grassland fires as well as small clearing and agricultural fires while for forest and deforestation fires we reviewed the literature to select the most relevant emissions factors (Table 1). </p> <p>Table 1: Emissions factors (gram species per kg dry matter burned) used to calculate C, CO2, CO, and NOx emissions. </p> <table> <tbody> <tr> <td>Fire type / trace gas emissions</td> <td>C</td> <td>CO2</td> <td>CO</td> <td>NOx</td> </tr> <tr> <td>Savanna and grassland</td> <td>480</td> <td>1656</td> <td>69.2</td> <td>2.5</td> </tr> <tr> <td>Small clearing and agricultural</td> <td>430</td> <td>1431</td> <td>76.2</td> <td>2.4</td> </tr> <tr> <td>Forest</td> <td>480</td> <td>1561</td> <td>104.0</td> <td>2.0</td> </tr> <tr> <td>Deforestation</td> <td>490</td> <td>1641</td> <td>95.5</td> <td>1.7</td> </tr> </tbody> </table> <p> </p> <p><strong>Dataset description<br></strong></p> <p>For full detail, please see Andela et al. (2022). The tables below (Tables 2 - 4) describe the content of the fire event (polygon) and active fire detections (point) shapefiles as well as the gridded emissions product. The active fire detections and associated estimates of dry matter burned can be combined with emissions factors (Table 1) to derive daily trace gas emissions time series for species and areas of interest.</p> <p>Table 2: Explanation of fire event shapefile attribute table.</p> <table> <tbody> <tr> <td>Attribute class</td> <td>Attribute</td> <td>Explanation / units</td> </tr> <tr> <td>Fire type classification</td> <td>Fire type</td> <td>(1) savanna and grassland, (2) small clearing and<br>agriculture, (3) forest, and (4) deforestation fires</td> </tr> <tr> <td> </td> <td>Confidence</td> <td>(1) low, (2) moderate, and (3) high</td> </tr> <tr> <td>Fire Atlas</td> <td>Size</td> <td>Fire size in km2</td> </tr> <tr> <td> </td> <td>Start day</td> <td>Day of new fire start as day of year (1-366)</td> </tr> <tr> <td> </td> <td>Duration</td> <td>Fire duration in days</td> </tr> <tr> <td> </td> <td>C Emissions</td> <td>Fire carbon emissions (ton C)</td> </tr> <tr> <td>Fire characterization</td> <td>Tree cover</td> <td>Average tree cover fraction within perimeter (%)</td> </tr> <tr> <td> </td> <td>Biomass</td> <td>Average biomass within fire perimeter (ton ha-1)</td> </tr> <tr> <td> </td> <td>Deforestation </td> <td>Fraction of 550 m grid cells with historic<br>deforestation (five years prior to fire) within fire perimeter (%)</td> </tr> <tr> <td> </td> <td>FRP</td> <td>Average fire radiative power (FRP) for all fire<br>detections within fire perimeter (MW)</td> </tr> <tr> <td> </td> <td>Persistence</td> <td>Average fire persistence across 550 m grid cells<br>within fire perimeter (days)</td> </tr> <tr> <td> </td> <td>Progression</td> <td>Average fire progression fraction across 550 m<br>grid cells within perimeter (%)</td> </tr> <tr> <td> </td> <td>Daytime</td> <td>Fraction of 1:30 pm detections (%) for all fire<br>detections within fire perimeter</td> </tr> <tr> <td> </td> <td>Detections</td> <td>Total active fire detections within fire perimeter</td> </tr> </tbody> </table> <p> </p> <p>Table 3: Explanation of active fire detection shapefile attribute table.</p> <table> <tbody> <tr> <td>Attribute class</td> <td>Attribute</td> <td>Explanation / units</td> </tr> <tr> <td>VIIRS active fire detections</td> <td>FRP</td> <td>Fire radiative power (MW)</td> </tr> <tr> <td> </td> <td>DOY</td> <td>Day of year (1-366)</td> </tr> <tr> <td>Fire type classification</td> <td>Fire type</td> <td>(1) savanna and grassland, (2) small clearing and agriculture, (3) forest, and (4) deforestation fires</td> </tr> <tr> <td> </td> <td>Confidence</td> <td>(1) low, (2) moderate, and (3) high</td> </tr> <tr> <td>Emissions</td> <td>C Emissions</td> <td>Fire carbon emissions (ton C) associated with each active fire detection</td> </tr> <tr> <td> </td> <td>DM Emissions</td> <td>Dry matter burned (ton) associated with each active fire detection</td> </tr> </tbody> </table> <p> </p> <p>Table 4: Content of daily gridded (0.1 degree resolution) emissions netcdf files. The daily emissions product provides emissions estimates of dry matter, C, CO2, CO, and NOx. For DM and CO partitioned emissions are also provided by fire type, for other species these can be derived by multiplying the dry matter burned (DM) estimates with trace gas specific emissions factors (Table 1). Values of each grid cell can be multiplied by the number of seconds per day and grid cell area to calculate total emissions (convert "kg species m-2 s-1" to "kg species day-1 per grid cell").</p> <table> <tbody> <tr> <td>/ancill</td> <td>grid_cell_area</td> </tr> <tr> <td>/partitioned_DM_emissions</td> <td>Deforestation emissions</td> </tr> <tr> <td> </td> <td>Forest emissions</td> </tr> <tr> <td> </td> <td>Savanna and grassland emissions</td> </tr> <tr> <td> </td> <td>Small clearing and agricultural emissions</td> </tr> <tr> <td>/partitioned_CO_emissions</td> <td>Deforestation emissions</td> </tr> <tr> <td> </td> <td>Forest emissions</td> </tr> <tr> <td> </td> <td>Savanna and grassland emissions</td> </tr> <tr> <td> </td> <td>Small clearing and agricultural emissions</td> </tr> <tr> <td>/total_emissions</td> <td>DM emissions</td> </tr> <tr> <td> </td> <td>C emissions</td> </tr> <tr> <td> </td> <td>CO2 emissions</td> </tr> <tr> <td> </td> <td>CO emissions</td> </tr> <tr> <td> </td> <td>NOx emissions</td> </tr> </tbody> </table> <p> </p> <p><strong>Results</strong></p> <p>Despite the various small improvements to the dataset, the data are largely consistent with the original dataset published for 2019-2020 (Table 5). </p> <p>Table 5: Comparison of model versions (original from Andela et al., 2022 and v1.1 published here) for April-December 2019 (equator-25S, 85W - 30W). Note that the current version (v1.1) is complete for 2019, but the original dataset had missing data due to incomplete active fire detections from NOAA-20 VIIRS at that time.</p> <table> <tbody> <tr> <td>Dataset</td> <td>Fire type</td> <td>Fire detections (x1,000)</td> <td>Mean fire radiative power (MW)</td> <td>Number of events (x1,000)</td> <td>Emissions (Tg C)</td> </tr> <tr> <td>Original</td> <td>Deforestation</td> <td>756.65</td> <td>15.15</td> <td>24.24</td> <td>99.18</td> </tr> <tr> <td>Original</td> <td>Forest</td> <td>637.58</td> <td>12.73</td> <td>5.28</td> <td>85.46</td> </tr> <tr> <td>Original</td> <td>Small clearing and agricultural</td> <td>348.49</td> <td>10.91</td> <td>154.68</td> <td>10.55</td> </tr> <tr> <td>Original</td> <td>Savanna and grassland</td> <td>1935.06</td> <td>12.11</td> <td>296.42</td> <td>71.75</td> </tr> <tr> <td>v1.1</td> <td>Deforestation</td> <td>742.64</td> <td>14.81</td> <td>24.02</td> <td>97.18</td> </tr> <tr> <td>v1.1</td> <td>Forest</td> <td>626.92</td> <td>12.06</td> <td>5.16</td> <td>77.84</td> </tr> <tr> <td>v1.1</td> <td>Small clearing and agricultural</td> <td>350.7</td> <td>10.89</td> <td>155.56</td> <td>9.27</td> </tr> <tr> <td>v1.1</td> <td>Savanna and grassland</td> <td>1877.16</td> <td>11.89</td> <td>299.17</td> <td>70.55</td> </tr> </tbody> </table> <p> </p> <p><strong>Acknowledgements</strong></p> <p>The Sense4Fire project is funded by ESA under ESA Contract Number: 4000134840/21/I-NB. </p> <p><strong>References</strong></p> <p>Andela, N., Morton, D.C., Schroeder, W., Chen, Y., Brando, P.M. and Randerson, J.T., 2022. Tracking and classifying Amazon fire events in near real time. Science advances, 8, eabd2713. https://doi.org/10.1126/sciadv.abd2713.</p> <p>Andreae, M.O., 2019. Emission of trace gases and aerosols from biomass burning–an updated assessment. Atmospheric Chemistry and Physics, 19, 8523-8546. https://doi.org/10.5194/acp-19-8523-2019.</p>
CARA: Benchmarking Compound Activity Prediction for Real-World Drug Discovery Applications
<p>Identifying active compounds for target proteins is fundamental in early drug discovery. Recently, data-driven computational methods have demonstrated promising potential in predicting compound activities. However, there lacks a well-designed benchmark to comprehensively evaluate these methods from a practical perspective. To fill this gap, we propose a benchmark, named CARA.Through carefully distinguishing assay types, designing train-test splitting schemes and selecting evaluation metrics, CARA can consider the biased distribution of current real-world compound activity data and avoid overestimation of model performances. We observed that current models can make successful predictions for certain proportions of assays, while the performances varied across different assays. In addition, evaluation of several few-shot training strategies demonstrated different performances related to task types. Overall, we provide a high-quality dataset for developing and evaluating compound activity prediction models, and the analyses in this work may inspire better applications of data-driven models in drug discovery.</p>
Data related to publication "Coherent phase transfer for real-world twin-field quantum key distribution"
<p>These datasets have been used to produce Figure 3, 4 and 5 of manuscript: "Coherent phase transfer for real-world twin-field quantum key distribution". The files contain two arrays: time in seconds and normalised intensity.</p> <p>Explanation for "Data_fig3_XXX.txt": the files contains the raw data used to produce Fig. 3. The following timespans have been used:</p> <p>Data_fig3_stabilised.txt: t_start= 0.29 s, t_stop=0.292 s</p> <p>Data_fig3_unstabilised.txt: t_start=0.00225 s, t_stop=0.00424 s</p> <p>Explanation for "Data_fig4_XXX.txt" files: the procedure to obtain the phase deviation from the normalised interference is detailed in the text (Methods section). Datasets with different sampling rate have been combined to obtain the phase deviation on the long and short term.</p> <p>Explanation for "Data_fig5.txt": the files contains the raw data used to produce Fig. 5.</p>
Datasets corresponding to publication: Machine learning assisted Real-time deformability cytometry of CD34+ cells allows to identify patients with Myelodysplastic Syndromes
<p>This repository contains all dataset that correspond to the publication "Machine learning assisted Real-time deformability cytometry of CD34+ cells allows to identify patients with Myelodysplastic Syndromes". Furthermore, Python scripts are provided which allow to reproduce all analyses shown in the manuscript. Execution of the scripts requires a Python environment with packages as stated in the Methods section of the manuscript, or by using PyBox 0.1.0. PyBox is a readily installed Python environment containing all packages at the required version. PyBox is publicly available on GitHub: <a href="https://github.com/maikherbig/PyBox">https://github.com/maikherbig/PyBox</a>.</p>
Testing hormonal responses to real and simulated social challenges in a competitive female bird
<p>Competitive interactions often occur in series; therefore animals may respond to social challenges in ways that prepare them for success in future conflict. Changes in the production of the steroid hormone testosterone (T) are thought to mediate phenotypic responses to competition, but research over the past few decades has yielded mixed results, leading to several potential explanations as to why T does not always elevate following a social challenge. Here, we measured T levels in tree swallows (<i>Tachycineta bicolor</i>), a system in which females compete for limited nesting cavities and female aggression is at least partially mediated by T. We experimentally induced social challenges in two ways: (1) using decoys to simulate territorial intrusions and (2) removing subsets of nesting cavities to increase competition among displaced and territory-holding females. Critically, these experiments occurred pre-laying, when females are physiologically capable of rapidly increasing circulating T levels. However, despite marked aggression in both experiments, T did <i>not</i> elevate following real or simulated social challenges, and in some cases, socially-challenged females had lower T levels than controls. Likewise, the degree of aggression was negatively correlated with T levels following a simulated territorial intrusion. Though not in line with the idea that social challenges prompt T elevation in preparation for future challenges, these patterns nevertheless connect T to territorial aggression in females. Coupled with past work showing that T promotes aggression, these results suggest that T may act rapidly to allow animals to adaptively respond to the urgent demands of a competitive event.</p>
Real time CO2 emissions 2012-2021 at 3 minutes interval
<p>This dataset includes the power generated split by fuel and related CO2 emissions based on production and consumption. </p> <p>Geographical: Finland, Sweden, Norway, Russia, Estonia</p> <p>Time: 01-01-2013 - 01-10-2021</p> <p>time resolution: 3 minutes</p> <p>This repository is only keeping track of historical data and was used in an analysis. Real-time data can be accessed through the API of a the project. </p> <p><a href="https://app.swaggerhub.com/apis-docs/jean-nicolas.louis/emission-and_power_grid_status/1.1.0">API documentation</a></p>
ReCANVo: A Dataset of Real-World Communicative and Affective Nonverbal Vocalizations
<p>A dataset of 7077 labeled vocalizations made by non-speaking individuals. Each vocalization lasts approximately 0.5-4 seconds and is labeled with its affective or communicative meaning. Data were acquired in real-world settings (homes, schools, etc.) and were labeled in real-time by parents or caregivers who knew the non-speaking communicator well. </p> <p>dataset_file_directory.csv provides the name of each vocalization file, the corresponding participant ID, and the vocalization meaning or label (delighted, frustrated, request, etc.).</p> <p>If you use this dataset, please <strong>cite Johnson & Narain et al., "ReCANVo: A Database of Real-World Communicative and Affective Nonverbal Vocalizations"</strong>. The authors are Jaya Narain, Kristina T. Johnson, Thomas Quatieri, Pattie Maes, and Rosalind Picard. This paper provides more information about the dataset, including data acquisition methodology, pre-processing procedures, and participant demographics. </p> <p>**J.N. and K.T.J. are joint first authors on this project. Please include both names in attribution when possible (e.g., Johnson & Narain et al.).</p>
Spectral imaging enables contrast agent-free real-time ischemia monitoring in laparoscopic surgery
<p>Sample video showing the 'ischemia index' computed with a deep-learning model trained on multispectral images recorded during partial nephrectomy before a clamp is applied to the renal artery (perfused) and after clamping the artery (ischemic).</p>
Simulated and Real datasets used for benchmarking MARGARET
<p>A collection of real and simulated datasets used for benchmarking MARGARET against other state-of-the-art TI methods</p>
Data from: Predicting habitat suitability and connectivity for management and conservation of urban wildlife: A real-time web application for grassland water voles
<ol> <li>Natural habitats in urban areas provide benefits for both humans and biodiversity. However, to achieve biodiversity gains we require new techniques to determine habitat suitability and ecological connectivity that will inform urban planning and development.</li> <li>Using an example of an urban population of water voles (<i>Arvicola amphibius</i>) we developed a habitat suitability model and a resistance-surface-based model of landscape connectivity to identify potential connectivity between areas of suitable habitat. We then updated the environmental variables according to new urban development plans and used our models to generate spatially explicit predictions of both habitat suitability and connectivity.</li> <li>To make models accessible to urban and conservation planners we developed an interactive mapping tool that provided users with a graphical user interface (GUI) to inform conservation planning for this species.</li> <li>The model found that habitat suitability for water voles was related to distance from key environmental variables, such as built-up areas and urban green spaces, while the connectivity model identified important corridors connecting areas of potential distribution for this species.</li> <li>Future development plans altered the potential spatial distribution of the water vole population, reducing the extent of suitable habitat in some core areas. The interactive mapping tool made available suitable habitat and connectivity maps for conservation managers to assess new planning applications and for the development of a conservation action plan for water voles.</li> <li>Synthesis and applications: We believe this approach provides a framework for future development of nature conservation tools that can be used by planners to inform ecological decision making, increase biodiversity and reduce human-wildlife conflict in urban environments.</li> </ol>
Data and Source codes for: Real-time Radial Tagging for Quantification of Left Ventricular Torsion
<p> </p> <p>Magnetic Resonance Imaging measurement raw data, simulation, and reconstruction codes used in our paper about ‘Real-time Radial Tagging for Quantification of Left Ventricular Torsion' (DOI:10.1002/mrm.29169).</p> <p> </p> <p> </p> <p> </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.