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6,452 results for “Application”
[dataset] Performance Analysis of Microservice Applications via Automated Load Testing and Bayesian Inference
<p>Anonymized replication package of the experiments presented in the research paper: "Performance Analysis of Microservice Applications via Automated Load Testing and Bayesian Inference".</p> <p>See the README.md file.</p>
Application of JTI to GWAS
<p>Please cite the following: </p> <p>Zhou, D. & Gamazon, E. R. (2020). Application of JTI to GWAS (Version 1). Zenodo. http://doi.org/10.5281/zenodo.3884387 </p> <p>Zhou, D., Jiang, Y., Zhong, X., Cox, N. J., Liu, C., & Gamazon, E. R. (2020). <em>A unified framework for joint-tissue transcriptome-wide association and Mendelian randomization analysis</em>. Nature Genetics. (<a href="https://www.nature.com/articles/s41588-020-0706-2">https://www.nature.com/articles/s41588-020-0706-2</a>)</p> <p>Correspondence should be addressed to: ERG (ericgamazon@gmail.com) and DZ (dan.zhou@vumc.org) </p>
LeafByte: A mobile application that measures leaf area and herbivory quickly and accurately
<ol> <li>In both basic and applied studies, quantification of herbivory on foliage is a key metric in characterizing plant-herbivore interactions, which underpin many ecological, evolutionary, and agricultural processes. Current methods of quantifying herbivory are slow or inaccurate. We present LeafByte, a free iOS application for measuring leaf area and herbivory. LeafByte can save data automatically, read and record barcodes, handle both light and dark colored plant tissue, and be used non-destructively. </li> <li>We evaluate its accuracy and efficiency relative to existing herbivory assessment tools.</li> <li>LeafByte has the same accuracy as ImageJ, the field standard, but is 50% faster. Other tools, such as BioLeaf and grid quantification, are quick and accurate, but limited in the information they can provide. Visual estimation is quickest, but it only provides a coarse measure of leaf damage and tends to overestimate herbivory.</li> <li>LeafByte is a quick and accurate means of measuring leaf area and herbivory, making it a useful tool for research in fields such as ecology, entomology, agronomy, and plant science.</li> </ol> <p> </p>
A Deep Learning Based Cardiac Cine Segmentation Framework for Clinicians - Transfer Learning Application to 7T - Additional Data
<p><strong>Automatically Generated Segmentation Masks for Data Science Bowl Cardiac Challenge Data</strong></p> <p>These segmentation masks have been automatically generated with the <a href="https://github.com/baiwenjia/ukbb_cardiac">ukbb_cardiac</a> network by Bai et al. (2018, <a href="https://doi.org/10.1186/s12968-018-0471-x">doi:10.1186/s12968-018-0471-x</a>). In order to reproduce the data cleaning and conversion: download the data from <a href="https://www.kaggle.com/c/second-annual-data-science-bowl/data">Kaggle</a> and follow the data curation and conversion steps outlined in: <a href="https://github.com/chfc-cmi/cmr-seg-tl">cmr-seg-tl</a> and the associated publication (Link to be added).</p> <p>As this is a derived dataset please abide by the data use rules of the original dataset at kaggle and provide proper citation to the original data:</p> <blockquote> <p>The data for the Data Science Bowl is available for research and academic pursuits. Please cite as ‘Data Science Bowl Cardiac Challenge Data’.</p> </blockquote> <p>Please also cite the Bai et al. article for the algorithm and our publication for the data curation.</p>
Codes and Dataset for "Application of Low-Cost Fine Particulate Mass Monitors to Convert Satellite Aerosol Optical Depth to Surface Concentrations in North America and Africa"
<p>This file contains the codes and dataset pertaining to the manuscript "Application of Low-Cost Fine Particulate Mass Monitors to Convert Satellite Aerosol Optical Depth to Surface Concentrations in North America and Africa"</p>
Dataset: A methodological framework to analyse determinants of host-microbiota networks, with an application to the relationships between Daphnia magna's gut microbiota and bacterioplankton
<p>Dataset and R codes for the publication "A methodological framework to analyse determinants of host-microbiota networks, with an application to the relationships between <em>Daphnia magna</em>’s gut microbiota and bacterioplankton"</p>
Music and Medicine: applications in Neurology, Neuropsychiatry and Speech Therapy
<p>Scientists are showing growing interest on Music Therapy. However, there is still a need to raise awareness among the public on the potential clinical applications of the use of Music. </p> <p>This popularised video is part of a series included in the Certificate in the Fundamentals of Music Therapy CPD activity held at Weill Cornell Medicine Qatar.</p>
Cluster analysis and its application in geochemistry
<p>This is the fourth session video recording of the Goldschmidt 2020 Virtual Workshop: Earth Science meets Data Science - Services & Systems, Policies & Procedures, Tools & Techniques for Geochemistry. Moderated by Shaunna Morrison (Carnegie Earth and Planets Laboratory)</p> <p>Github repository: <a href="https://github.com/wadesnoopy/Goldschmidt-2020-cluster">https://github.com/wadesnoopy/Goldschmidt-2020-cluster</a></p>
CO2 sequestration by olivine for three different applications in Knowledge Mile Park, Amsterdam
<p>The concentration of atmospheric CO<sub>2</sub> is still increasing according to numerous projections of future greenhouse gas emissions. Nations must make every effort to achieve the target of keeping the global average temperature to below 2 ̊C above pre-industrial levels, agreed on in the Paris Agreement. A relatively new and promising geo-engineering approach to possibly combat this worldwide problem is the use of olivine ((Mg,Fe)<sub>2</sub>SiO<sub>4</sub>). During the weathering process of olivine, carbon dioxide (CO<sub>2</sub>) is extracted from the atmosphere and converted to insoluble carbonate minerals, consequently reducing the atmospheric CO<sub>2</sub> concentration. This research aim is to investigate whether olivine can be effectively implemented and within environmental safety boundaries in the Knowledge Mile Park, a project in commission of the Municipality of Amsterdam, to sequester atmospheric CO<sub>2</sub> in three scenarios i.e. tree sand, green rooftop substrate and footpath substrate. With the Olivine Weathering and CO<sub>2</sub> Sequestration model and PNEC-pro V6, the dissolution and CO<sub>2</sub> sequestration rate of olivine were examined and the released nickel concentration with the effects on various plant and aquatic species was analysed. Green rooftop substrate was identified as the most effective possible scenario in terms of the magnitude of CO<sub>2</sub> binding in 40 years that can be implemented in the Knowledge Mile Park remaining within the safety boundaries of environmental and ecotoxicological effects. To deepen the knowledge on olivine applications, further research should incorporate practical experimental work based on the modelled input of this report.</p>
Figure 2 from: Chen H-Y, Olmi M, Pang H, Liu J-X (2020) Application of DNA barcoding confirms the host of Gonatopus viet Olmi, 1986 (Hymenoptera, Dryinidae). ZooKeys 944: 115-120. https://doi.org/10.3897/zookeys.944.53054
Figure 2 Gonatopus viet Olmi, female (SCAU 3040953) A habitus, lateral view B habitus, dorsal view C head and mesosoma, lateral view D head and mesosoma, dorsal view E head, anterior view F chela.
Figure 1 from: Chen H-Y, Olmi M, Pang H, Liu J-X (2020) Application of DNA barcoding confirms the host of Gonatopus viet Olmi, 1986 (Hymenoptera, Dryinidae). ZooKeys 944: 115-120. https://doi.org/10.3897/zookeys.944.53054
Figure 1 A, BStirellus capitatus (Distant, 1918) nymph parasitized by Gonatopus viet Olmi, 1986 (SCAU 3040955) A habitus, dorsal view B habitus, ventral view C, DStirellus capitatus (Distant, 1918) C habitus, female (SCAU 3040956), dorsal view D habitus, male (SCAU 3049598), dorsal view.
Artifacts: An Efficient Approach for Reviewing Security-Related Aspects in Agile Requirements Specifications of Web Applications
<p><strong>Abstract:</strong> Defects in requirements specifications can have severe consequences during the software development lifecycle. Some of them result in time and cost overruns due to incorrect or missing quality characteristics, such as security. This characteristic requires special attention in web applications because they have become a target for manipulating sensible data. Several concerns make security difficult to deal with. For instance, (1) when stakeholders discuss general requirements they are often unaware that they should also discuss security-related aspects, because (2) they typically do not have enough expertise in security. This often leads to unspecified or ill-defined security requirements. These concerns become even more challenging in agile contexts, where lightweight documentation is typically produced. To tackle this problem, we designed an approach for reviewing security-related aspects in agile requirements specifications of web applications. Our proposal considers user stories and security specifications as inputs and relates those user stories to security properties via Natural Language Processing. Based on the related security properties, our approach identifies high-level security requirements from the Open Web Application Security Project (OWASP) to be verified, and generates a reading technique to support reviewers in detecting defects. We evaluate our approach via three experiment trials conducted with 56 novice software engineers, measuring effectiveness, efficiency, usefulness, and ease of use. We compare our approach against using: (1) the OWASP high-level security requirements, and (2) a perspective-based approach as proposed in contemporary state of the art. The results strengthen our confidence that using our approach has a positive impact (with large effect size) on the performance of inspectors in terms of effectiveness and efficiency.</p> <p>The files below contains the following data:</p> <p><strong>1) Consent form.docx</strong>: This document provides to the research subjects information to decide whether to participate in a research study or not based on an explanation of the proposed research and the nature of the participation that is requested of them.</p> <p><strong>2) Characterization_Questionnaire.docx:</strong> This document shows the questions used to characterize the working experience and knowledge of the participants of the controlled experiment. The answers obtained through this questionnaire allowed us to identify some key characteristics about three knowledge areas: Agile Software Development, Software Security and Software Inspection.</p> <p><strong>3) Experiment_Results.xlsx: </strong>This Excel document shows a summary of the results of the experiments by participant ID, trial and technique. It also synthesizes the defects found by the reviewers and the characterization, follow up and TAM questionnaire. </p> <p><strong>4) FollowUp_Questionnaire_AdHoc_Technique.docx: </strong>This document shows the questions used to acquire information about the review conducted by inspectors who used the ad hoc technique.</p> <p><strong>5) FollowUp_Questionnaire_Reading_Technique.docx: </strong>This document shows the questions used to acquire information about the review conducted by inspectors who used the proposed reading technique. </p> <p><strong>6) Repository of Keywords.docx: </strong>This document shows the keywords used by our proposed approach and that indicate some security concern. </p> <p><strong>7) Task_description_AdHoc_A.docx: </strong>This document shows textual instructions on how to follow the ad hoc review for a set of user stories. </p> <p><strong>8) Task_description_AdHoc_B.docx: </strong>This document shows textual instructions on how to follow the ad hoc review for another set of user stories.</p> <p><strong>9) Task_description_RT_A.docx: </strong>This document shows textual instructions on how to follow the proposed reading technique for a set of user stories.</p> <p><strong>10) Task_description_RT_B.docx: </strong>This document shows textual instructions on how to follow the proposed reading technique for another set of user stories.<strong> </strong></p> <p><strong>11) Training_Experiment.pptx: </strong>This document contains the material used to explain the topics involved in the experiment. It was used to train the subjects. </p>
Homogenization of heterogeneous materials for aerospace applications
<p>The lecture discusses the micromechanical analysis of heterogeneous can be effectively carried out using the variational asymptotic method (VAM) unit cell homogenization technique. The governing equations obtained by adopting this technique can be solved using numerical methods by conformal discretization of the domain. In the case of heterogeneous materials, conformal discretization of the domain becomes difficult and time-consuming. It is preferable to have a non-conformal discretization procedure for problems involving complex geometries, for example, woven composites. A novel numerical framework for the micromechanical analysis of heterogeneous materials based on VAM is proposed, where the level-set method is used to define the interface as well as to decompose the domain into voxel regions of inclusions and matrix. The point interpolation method (PIM) is used to connect these voxel regions. The PIM-VOXEL framework thus developed is validated using examples having complex geometries taken from open literature for predicting elastic, thermal, thermo-elastic, and visco-elastic properties. The proposed methodology alleviates the requirement for conformal meshing without compromising the accuracy and is capable of automation for homogenization and localization applications. Finally, the application of the numerical framework to capture damage initiation and progression in woven composites is demonstrated.</p>
Application of spectral library prediction for parallel reaction monitoring of viral peptides_PRM_data
<p><strong>Project description: </strong></p> <p>A major part of the analysis of parallel reaction monitoring (PRM) data is the comparison of observed fragment ion intensities to a library spectrum. Classically, these libraries are generated by data-dependent acquisition (DDA). Here we test Prosit, a published deep neural network algorithm, for its applicability in predicting spectral libraries for PRM. For this purpose, we targeted 1,529 precursors derived from synthetic viral peptides and analyzed the data with Prosit and DDA-derived libraries. Additionally, we used a spectral library predicted by Prosit and a DDA library to identify SARS-CoV-2 peptides from a simulated oropharyngeal swab.</p> <p> </p> <p><strong>Sample processing protocol:</strong></p> <p>A total of 1,569 crude synthetic viral peptides were ordered in six pools from JPT (Berlin, Germany). Synthetic peptides were separated on a 200 cm μPAC™ column (PharmaFluidics) by using an EASY-nLC1200 system (Thermo Fisher Scientific) equipped with a μPAC™ trapping column (PharmaFluidics). The flow rate was set to 300 nL/min and a stepped linear 160 min gradient was applied: 3-10% B in 22 min, 10-33%B in 95 min, 33-49% B in 23 min, 49-80% B in 10 min and 80% B for 10 min. Solvent A was 0.1% (v/v) formic acid (FA) in water, solvent B consisted of 80% (v/v) acetonitrile in 0.1% (v/v) FA. The column temperature was set to 50 °C. The Q Exactive Plus (Thermo Fisher Scientific) operated in Full MS/dd-MS2 or unscheduled PRM mode. For MS/dd-MS2 the following parameters were used. MS1 resolution was 70.000 with an AGC target of 3x10<sup>6</sup>, max. injection time of 20 ms and a scan range of 300-1650 m/z. MS2 resolution was 17.500 with an AGC target of 10<sup>5</sup>, max. injection time of 50 ms and an isolation window of 2 m/z. The analysis parameters in PRM mode were set as follows. MS1 parameters were identical to DDA. MS2 resolution was 17.500 with an AGC target of 10<sup>6</sup>, max. injection time of 55 ms and an isolation window of 1.4 m/z.</p> <p>Potential SARS-CoV-2 target peptides belonging to the N protein were identified by DDA of SARS-CoV-2 infected Calu-3 cells. Peptides were diluted in 0.1% TFA (0.2 µg/µL) and 5 µL were separated on a 50 cm μPAC™ column (PharmaFluidics) using an EASY-nLC1200 system (Thermo Fisher Scientific). The flow rate was set to 800 nL/min and a stepped 30 min gradient was applied: 6-11% B in 2:58 min, 11-30% B in 17:10 min, 30-35% B in 2:41 min, 35-47% B in 3:11 min, 47-80% B for 0:10 min, 80% B for 1:50 min, 80-0% B in 0:10 min and 100% A for 1:50 min. Solvent A was 0.1% (v/v) formic acid (FA) in water, solvent B consisted of 80% (v/v) acetonitrile in 0.1% (v/v) FA. The column temperature was set to 50 °C. The Q Exactive HF (Thermo Fisher Scientific) operated in Full MS/dd-MS2 (Top20) using the following parameters. MS1 resolution was 60.000 with an AGC target of 3x10<sup>6</sup>, max. injection time of 20 ms and a scan range of 300-1650 m/z. MS2 resolution was 17.500 with an AGC target of 10<sup>5</sup>, max. injection time of 50 ms and an isolation window of 2 m/z.</p> <p> </p> <p>To simulate a SARS-CoV-2 positive patient sample, we spiked cell-culture derived virus in a negative oropharyngeal swab and targeted the N protein by PRM. LC parameters were identical to DDA analysis of SARS-CoV-2 infected Calu-3 cells. The PRM parameters of the The Q Exactive HF (Thermo Fisher Scientific) were set as follows. MS1 parameters were identical to DDA. MS2 resolution was 45.000 with an AGC target of 10<sup>6</sup>, max. injection time of 100 ms and an isolation window of 1.4 m/z.</p> <p> </p> <p> </p> <p><strong>Data processing protocol:</strong></p> <p>DDA Raw files were searched with MaxQuant against the respective virus database (UniProt) with a peptide FDR of 1%. Detailed MaxQuant parameters can be found in the parameters.txt files of the according results. MaxQuant .msms output files were used to generate spectral libraries with BiblioSpec implemented in the Skyline environment using a cut-off score of 0.95. Peptide identification of PRM runs was done in Skyline using the top 6 fragment ions of the DDA spectral library or according Prosit derived library (Prosit_2020_intensity_model).</p>
Systematic evaluation of ReaxFF reactive force fields for biochemical applications
<p>The tar archive contains supporting information to accompany the publication. The data includes the ReaxFF force field files, XYZ and BGF geometry files for amino acid conformers and dipeptides, pathways of initial DNEB interpolations and full connected pathways of condensation reactions.</p>
Using a custom mobile application for change management in an electronic health record implementation
<p><b><i>Objectives </i></b></p> <p>Institutions cite managing the modification in infrastructure, technical support, and process change as substantial barriers to a successful electronic health record (EHR) implementation. In an effort to organize and centralize the complex scheduling, task completion and communication needs of a "big-bang" EHR go-live, we developed a unified communication system with the goal of improving implementation process efficiency. Our goal was to create a platform that would work across the medical enterprise.</p> <p><b><i>Materials and Methods</i></b></p> <p>We employed an agile process to design the application, called Hubbl, based on initial requirements and iteratively obtained stakeholder user. The final feature set included role specific organization, integrated communication, task and content management tooling, and embedded project information retrieval, all embedded into the end user's day to day activities.</p> <p><b><i>Results </i></b></p> <p>User enrollment continually increased from launch in February of 2017 through go-live day. During the pre-go-live period, usage increased from an average of 7.37 events/user/day to 18.65 events/user/day with over 97 communications sent across all periods. 5,400 unique users accessed tip sheets and information retrieval tools averaged 28.84 searches/user/day during the go-live period with an average high of 46.33 searches/user/day five days post go-live. User access during go-live and post-go-live averaged 12.82 accesses/user/day and decreased from 20.42 average accesses on day one of go live to 14.07 averaged accesses on day 60 of post go live with over 727 tasks monitored to completion during all periods.</p> <p><b><i>Conclusion</i></b></p> <p>Hubbl was an essential component of our communication, task coordination, and change management strategy, for our EHR go live. Institutions that choose a unified mobile and web based platform during a substantial IT (information technology) implementation can feasibly ensure task completion, project coordination, and timely information dissemination.</p>
Application of Different Building Representation Techniques in HEC-RAS 2-D for Urban Flood Modeling Using the Toce River Experimental Case
<p>The output of numerical simulation in HEC-RAS 2-D</p>
Performance Curves for better Performance Predictions of Parallel Applications in Multicore Environments
<p><br> Model-based performance prediction for parallel applications on architectural models suffers from significant inaccuracies. <br> A major reason is that current model-based performance prediction approaches consider CPU speed as a single metric for multicore performance. </p> <p>Thus, in this paper, we investigate performance-influencing factors for multicore environments, execute extensive experiments to determine their impact on the performance, and extract performance curves for characteristic behaviours.</p> <p>As a result, we present a set of performance curves to software engineers which enables them to increase the performance prediction power in an easy to use manner. <br> Further, we evaluate the approach using 13 SPEC Benchmarks and could show that our approach reduces the prediction error by up to 60% and increases the accuracy by up to 98% for certain scenarios. </p>
Hierarchical Inference With Bayesian Neural Networks: An Application to Strong Gravitational Lensing - Model Weights, Chains, BNN Samples, and Simulated Datasets
<p>The model weights, chains, simulated datasets, and BNN samples used to produce the results shown in LSST DESC Collaboration paper "Hierarchical Inference With Bayesian Neural Networks: An Application to Strong Gravitational Lensing." All files presented here are meant for use in tandem with the python package "ovejero" (<a href="https://github.com/swagnercarena/ovejero">https://github.com/swagnercarena/ovejero</a>).</p>
Supplementary material 3 from: Evans T, Blackburn TM, Jeschke JM, Probert AF, Bacher S (2020) Application of the Socio-Economic Impact Classification for Alien Taxa (SEICAT) to a global assessment of alien bird impacts. In: Wilson JR, Bacher S, Daehler CC, Groom QJ, Kumschick S, Lockwood JL, Robinson TB, Zengeya TA, Richardson DM. NeoBiota 62: 123-142. https://doi.org/10.3897/neobiota.62.51150
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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.