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6,452 results for “Application”
Application demonstrating results of application of show view updates developer option on MainActivity with onBind Recyclerview call
<p>Results demonstrating results of application of show view updates developer option on MainActivity with onBind Recyclerview call</p>
Data from: First application of dental microwear texture analysis to infer theropod feeding ecology
<p>Theropods were the dominating apex predators in most Jurassic and Cretaceous terrestrial ecosystems. Their feeding ecology has always been of great interest, and new computational methods have yielded more detailed reconstructions of differences in theropod feedings behaviour. Many approaches however rely on well-preserved skulls. Dental microwear texture analysis (DMTA) is potentially applicable to isolated teeth, and here employed for the first time to investigate dietary ecology of theropods. In particular, we test whether tyrannosaurids show DMT associated with more hard-object feeding than compared to Allosaurus – which would be a sign for higher levels of osteophagy, as has often been suggested. We find no significant difference in complexity and roughness of enamel surfaces between Herrerasaurus, Allosaurus, and tyrannosaurids, which conflicts with inferences of more frequent osteophagic behaviour in Tyrannosaurus as compared to other theropods. Orientation of wear features reveals a more pronounced bi-directional puncture-and-pull feeding mode in Allosaurus than in tyrannosaurids. Our results further indicate ontogenetic niche shift in theropods and crocodylians, significantly larger height parameters in juvenile theropods might indicate frequent scavenging, resulting in more bone-tooth contact during feeding. Overall, DMTA is found to be very similar between theropods and extant large, broad-snouted crocodylians and shows great similarity in feeding ecology of theropod apex predators throughout the Mesozoic.</p>
Companion data of Exploiting system level heterogeneity to improve the performance of a GeoStatistics multi-phase task-based application
<p>This is the companion data repository for the paper entitled <strong>Exploiting system level heterogeneity to improve the performance of a GeoStatistics multi-phase task-based application</strong> by Lucas Leandro Nesi, Lucas Mello Schnorr, and Arnaud Legrand. The manuscript has been accepted for publication in the <a href="https://oaciss.uoregon.edu/icpp21/">ICPP 2021</a>.</p>
The Community Coevolution Model with application to the study of evolutionary relationships between genes based on phylogenetic profiles
<p>Organismal traits can evolve in a coordinated way, with correlated patterns of gains and losses reflecting important evolutionary associations. Discovering these associations can reveal important information about the functional and ecological linkages among traits. Phylogenetic profiles treat individual genes as traits distributed across sets of genomes and can provide a fine-grained view of the genetic underpinnings of evolutionary processes in a set of genomes. Phylogenetic profiling has been used to identify genes that are functionally linked, and to identify common patterns of lateral gene transfer in microorganisms. However, comparative analysis of phylogenetic profiles and other trait distributions should take into account the phylogenetic relationships among the organisms under consideration.</p> <p>Here we propose the Community Coevolution Model (CCM), a new coevolutionary model to analyze the evolutionary associations among traits, with a focus on phylogenetic profiles. In the CCM, traits are considered to evolve as a community with interactions, and the transition rate for each trait depends on the current states of other traits. Surpassing other comparative methods for pairwise trait analysis, CCM has the additional advantage of being able to examine multiple traits as a community to reveal more dependency relationships. We also develop a simulation procedure to generate phylogenetic profiles with correlated evolutionary patterns that can be used as benchmark data for evaluation purposes.</p> <p>A simulation study demonstrates that CCM is more accurate than other methods including the Jaccard Index and three tree-aware methods. The parameterization of CCM makes the interpretation of the relations between genes more direct, which leads to Darwin's scenario being identified easily based on the estimated parameters. We show that CCM is more efficient and fits real data better than other methods resulting in higher likelihood scores with fewer parameters. An examination of 3786 phylogenetic profiles across a set of 659 bacterial genomes highlights linkages between genes with common functions, including many patterns that would not have been identified under a non-phylogenetic model of common distribution. We also applied the CCM to 44 proteins in the well-studied Mitochondrial Respiratory Complex I and recovered associations that mapped well onto the structural associations that exist in the complex.</p>
Companion data of Multi-Phase Task-Based HPC Applications: Quickly Learning how to Run Fast
<p>This is the companion data repository for the paper entitled <strong>Multi-Phase Task-Based HPC Applications: Quickly Learning how to Run Fast</strong> by Lucas Leandro Nesi, Lucas Mello Schnorr, and Arnaud Legrand. The manuscript has been accepted for publication in the <a href="https://www.ipdps.org/ipdps2022/2022-organization.html">IPDPS 2022</a>.</p>
A systematic assessment of deep learning methods for drug response prediction: from in-vitro to clinical application
<p>https://github.com/LihongLab/Suppl-data-Benchmark</p> <p>## GDSC dataset</p> <p>**Table S3.** GDSC gene expression profiles for 966 cancer cell lines, where each column represents a cell line in the form of its name and tissue collection site, and each row represents a gene in the form of the HGNC symbol.</p> <p> </p> <p>**Table S4.** GDSC gene mutation profiles for 966 cancer cell lines, where each column represents a cell line in the form of its name and tissue collection site, and each row represents a gene in the form of the HGNC symbol. The wild type is coded as 1 and the wild type as 0.</p> <p> </p> <p>**Table S5.** GDSC copy number variation profiles for 966 cancer cell lines, where each column represents a cell line in the form of its name and tissue collection site, and each row represents a gene in the form of the HGNC symbol. The copy-neutral is coded as 0 and the deletion or amplification as 1.</p> <p> </p> <p>**Table S6.** GDSC drug response data for 966 cancer cell lines and 282 drugs in the form of the natural logarithm of the IC50 readout. The first column shows the cell line name and tissue collection site, the second column shows the drug name, and the third column shows the drug response readout.</p> <p> </p> <p>**Table S7.** GDSC annotations for 282 drugs include drug name, PubChem CID, PubChem canonical SMILES, Rdkit canonical SMILES, Target Pathway, standard deviation, bimodality coefficient and density coverage.</p> <p>## TCGA dataset</p> <p>**Table S8.** TCGA gene expression profiles, where each column represents a patient in the form of TCGA patient ID, and each row represents a gene in the form of the HGNC symbol.</p> <p> </p> <p>**Table S9.** TCGA gene mutation profiles, where each column represents a patient in the form of TCGA patient ID, and each row represents a gene in the form of the HGNC symbol. The wild type is coded as 1 and the wild type as 0.</p> <p> </p> <p>**Table S10.** TCGA copy number variation profiles, where each column represents a patient in the form of TCGA patient ID, and each row represents a gene in the form of the HGNC symbol. The copy-neutral is coded as 0 and the deletion or amplification as 1.</p> <p> </p> <p>**Table S11.** TCGA clinical response data. The first column shows the TCGA patient ID, the second column shows the drug name, the third column shows the clinical response category, the fourth column shows the cancer type, and the last column shows the clinical label as responder or non-responder.</p>
Dataset for: Guidelines for standardising the application of discriminant analysis of principal components to genotype data
<p><span>Data and scripts required to replicate the analyses in Thia (2022) "<span class="fontstyle0">Guidelines for standardising the application of discriminant analysis of principal components to genotype data" in <em>Molecular Ecology</em>.</span></span></p> <p><span>This study aimed to address methodological misunderstandings and misuse of the DAPC method in population genetics. The analyses are used to illustrate that for genotype data comprising <em>k</em> effective populations, there are only <em>k</em><span>−</span>1 PC axes that describe populations structure, and that are biologically informative. These PC axes are the only suitable axes for modelling the among-population differences with a DA. Use of many more than <em>k</em><span>−1 PC axes leads to decreasing biological relevancy of the final DA solution, with implications for misinterpretations of population structure.</span></span></p>
Model for Smart-Agri app for farmers to enable optimum fertilizer application
<p>For the safe management of these fertilizers (i.e., safe application rates to land), a tool was needed to guide growers and processing plants. A parsimonious program was developed in MS Excel<sup>TM</sup> to determine the maximum legal application rate of the different types of DPS and DPS-derived STRUBIAS products based on the soil test P content, the legal limits for N, P and metal application, the dry solid content, and nutrient (N and P) and metal concentration of the DPS and DPS-derived STRUBIAS products. </p>
Dataset for Sound-based Anomalies Detection in Agricultural Robotics Application
<p>This data set contains data related to a Mowing Intelligent Tool (MowIT).</p> <p>Two different microphones were used to collect the sound samples, recording the audio with just one single channel, with a sampling rate of 44100 Hz and 16 bits resolution.</p> <p>The data provided by an inertial measurement unit (IMU) was also recorded since that was already integrated into the MowIT.</p> <p>Two different data collections were performed in different open-air environments with grass to cut.</p> <p>In each collection, eight different sample sets were made, five with the machine cutting using a trimmer line and the other three using the blades. Various combinations were used in each set, and tools were or were not placed on each of the three cutting axes of the MowIT. For each group, the acquisitions were designated from 0 to 7.</p> <p>Each folder of the first collection is a combination containing two audio files, one for each microphone used, the IMU data and a photograph of the lower part of the MowIT to understand the configuration used.</p> <p>In the second collection, to improve the variety of data, three distinct sub-sets were performed for combination: the first with the MowIT turned on but not cutting grass and the next two cutting grass. </p> <p>In samples 4 and 7, there is one audio where the MowIT cuts but stops due to motor stress. In sample 6, the initial recording was not made without cutting grass, and only the two recordings were made cutting grass.</p> <p> </p> <p> </p> <p> </p>
First steps in the development of a support application for Easy-to-Read adaptation: Questionnaire Responses
<p>This csv document contains the responses obtained in our user study performed in the context of the paper entitled "First steps in the development of a support application for Easy-to-Read adaptation".</p>
Shadow Spaces for Water Stress Adaptation: Supplemental Irrigation Application in Rainfed Fig Production
<p>Data Sources is a SPSS file. Common descriptive statistics and inferential statistics are used.</p>
Data from: Improving performance of hurdle models using rare-event weighted logistic regression: An application to maternal mortality data
<p>In this paper, the performance of hurdle models in rare events data is improved by modifying their binary component. The rare-event weighted logistic regression model is adopted in place of logistic regression to deal with class imbalance due to rare events. Poisson Hurdle Rare Event Weighted Logistic Regression (REWLR) and Negative Binomial Hurdle (NBH) REWLR are developed as two-part models which use the REWLR model to estimate the probability of a positive count and a Poisson or NB zero-truncated count model to estimate non-zero counts. The obtained results are numerically validated and then discussed from both the mathematical and the maternal mortality perspective. Numerical simulations are also presented to give a more complete representation of the model dynamics. Results obtained suggest that NB Hurdle REWLR is the best-performing model for zero-inflated count data due to rare events.</p>
Seismic analysis of the detachment and impact phases of a rockfall and application for estimating rockfall volume and free-fall height
<p>Digital Elevation models of the Mount Granier and Mount Saint-Eynard.</p> <p>Mount Saint-Eynard DEMs were carried out using an Optech Ilris-LR laser scanner.</p> <p>Mount Granier DEMs were carried out by photogrammetry.</p> <p> </p>
EEG Data for: "Composing only by thought: novel application of the P300 brain-computer interface"
<p>EEG Data for: "Composing only by thought: novel application of the P300 brain-computer interface". See the file "Information about the Dataset.pdf" for further information.</p>
myVCF: a desktop application for high-throughput mutations data management
<p>Next-generation sequencing technologies have become the most powerful tool to discover genetic variants associated with human diseases. Although the dramatic reductions in the costs facilitate the use in the wet-lab and clinics, the huge amount of data generated renders their management by non-expert researchers and physicians extremely difficult. Therefore, there is an urgent need of novel approaches and tools aimed at getting the ‘end-users’ closer to the sequencing data, facilitating the access by non-bioinformaticians, and to speed-up the functional interpretation of genetic variants. We developed myVCF, a standalone, easy-to-use desktop application, which is based on a browser interface and is suitable for Windows, Mac and UNIX systems. myVCF is an efficient platform that is able to manage multiple sequencing projects created from VCF files within the system; stores genetic variants and samples genotypes from an annotated VCF files into a SQLite database; implements a flexible search engine for data exploration, allowing to query for chromosomal region, gene, single variant or dbSNP ID. Besides, myVCF generates a summary statistics report about mutations distribution across samples and across the genome/exome by aggregating the information within the VCF file. In summary, the myVCF platform allows end-users without strong programming and bioinformatics skills to explore, query, visualize and export mutations data in a simple and straightforward way.</p>
Application Of Substantial And Sustained Force To Vertical Surfaces Using A Quadrotor
<p><strong>One of the challenges in the interaction between aerial manipulators (drones with manipulator arms) and the environment is to maintain stability under high interaction forces. The dynamics of the system change, and due to limitations to the drone-platform-- the drone not being to apply sideways forces and having limited yaw-torque-- stability is not naturally guaranteed. </strong></p> <p> </p> <p><strong>In this video we demonstrate a new control approach to overcome these limitations. The video shows a quadrotor drone with manipulator pushing on the environment. More precisely, the stability is achieved using a state-feedback approach to compensate for the roll and yaw errors. This approach uses the linearized contact dynamics under pseudo-static conditions. The key element is that non-zero roll-states are used to compensate for errors in the yaw-state. At a certain point the drone reaches pitch angles of over 45º. Given that the drone has a mass of 1.5 kg, this means that the drone is pushing with 15N(!) of force on the environment. The video demonstrates that the drone is easily able to maintain stability over a longer time period.</strong></p> <p> </p> <p><strong>These high interaction forces can be extremely useful when operating tools on the environment, as tasks such as grinding and brushing require sufficient contact pressure to function.</strong></p>
Data supplementing the article "Avoiding quantification bias in metabarcoding: application of a cell biovolume correction factor in diatom molecular biomonitoring" V. Vasselon, A. Bouchez, F. Rimet, S. Jacquet, R. Trobajo, M. Corniquel, K. Tapolczai, I. Domaizon submitted to Methods in Ecology and Evolution journal
<p>These data supplement the article "Avoiding quantification bias in metabarcoding: application of a cell biovolume correction factor in diatom molecular biomonitoring" V. Vasselon, A. Bouchez, F. Rimet, S. Jacquet, R. Trobajo, M. Corniquel, K. Tapolczai, I. Domaizon submitted to Methods in Ecology and Evolution journal</p> <p>The directory contains the following files:</p> <p>1<strong>5 fastq files raw reads (5 mock communities, 3 replicates)</strong><strong>.rar </strong>- contains the 15 fastq files provided by the sequencing platform with demultiplexed DNA reads (raw data prior any bioinformatics treatments).</p> <p><strong>15 fastq files information.xlsx</strong> :</p> <p>- contains the information relative to the 15 fastq files corresponding to the PGM raw data of the 5 mock communities (sequenced with 3 replicates), including: the ID of the fastq files, the mock community name, the replicate number, the final sample Id and the number of raw reads per fastq file.</p> <p>- contains the information of the proportion of the 8 diatoms species (%) used to create the 5 mock communities (estimated from microscopy).</p>
Data for "Depressed-cladding thulium-doped fiber for applications below 1800 nm"
<p>Dataset includes simulation results as well as confirming experimental data for depressed-cladding thulium-doped fiber presented in the graphs.</p>
MD3F Simulation and Application Code
<p>MD3F is a method developed to model longitudinal, multivariate trajectories for high-dimensional data. Herein we include reference code for the simulation, bias, and application analyses reported in our manuscript, “MD3F: Multivariate Distance Drift Diffusion Framework for High-Dimensional Datasets.” Data is made available to supplement the code where needed (see folder contents below).</p> <p> </p> <p><strong>Folder Contents: </strong></p> <p>1. MD3F_Simulation_Code.Rmd – Simulation R markdown file. Simulation results with 10k replicates included in MD3F_Simulation_Data.RData file.</p> <p>2. MD3F_Kostic_DataCode.Rmd – MD3F Application to Kostic data (available below).</p> <p>3. MD3F_BiasEstimation_Code.Rmd – Bias estimation and plotting examples.</p> <p>4. KosticData_withSampleData.Rdata (see above)</p> <p>5. MD3F_Simulation_Data.RData (see above)</p>
The workload of manual data entry for integration between mobile health applications and eHealth infrastructure
<div> <p>In this study, we conducted a time-motion study observing healthcare workers (HCWs) completing data management activities including monitoring and evaluation (M&E) and manual data linkage of individual-level app data to electronic medical records (EMRS). This study served as a baseline study for an open-source app to mirror EMRS and reduce HCW workload while improving care in the Nurse-led Community-based Antiretroviral therapy Program (NCAP) in Lilongwe, Malawi.</p> </div>
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.