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3,690 results for “Computing”
Data from: Energy landscape for the insertion of amphiphilic nanoparticles into lipid membranes: a computational study
Amphiphilic, monolayer-protected gold nanoparticles (NPs) have been shown to enter cells via a non-endocytic, non-disruptive pathway that could be valuable for biomedical applications. The same NPs were also found to insert into a series of model cell membranes as a precursor to cellular uptake, but the insertion mechanism remains unclear. Previous simulations have demonstrated that an amphiphilic NP can insert into a single leaflet of a planar lipid bilayer, but in this configuration all charged end groups are localized to one side of the bilayer and it is unknown if further insertion is thermodynamically favorable. Here, we use atomistic molecular dynamics simulations to show that an amphiphilic NP can reach the bilayer midplane non-disruptively if charged ligands iteratively ``flip'' across the bilayer. Ligand flipping is a favorable process that relaxes bilayer curvature, decreases the nonpolar solvent-accessible surface area of the NP monolayer, and increases attractive ligand-lipid electrostatic interactions. Analysis of end group hydration further indicates that iterative ligand flipping can occur on experimentally relevant timescales. Supported by these results, we present a complete energy landscape for the non-disruptive insertion of amphiphilic NPs into lipid bilayers. These findings will help guide the design of NPs to enhance bilayer insertion and non-endocytic cellular uptake, and also provide physical insight into a possible pathway for the translocation of charged biomacromolecules.
Data from: Demographic inferences using short-read genomic data in an Approximate Bayesian Computation framework: in silico evaluation of power, biases, and proof of concept in Atlantic walrus
Approximate Bayesian Computation (ABC) is a powerful tool for model-based inference of demographic population histories from large genetic data sets. For most organisms its implementation has been hampered by the lack of sufficient genetic data. Genotyping-by-sequencing (GBS) provides cheap genome-scale data to fill this gap, but its potential has not fully been exploited. Here, we explored power, precision and biases of a coalescent-based ABC approach where GBS data were modeled with either a population mutation parameter (θ) or with a fixed sites (FS) approach, allowing single or several segregating sites per locus. With simulated data ranging from 500 to 50,000 loci a variety of demographic models could be reliably inferred across a range of timescales and migration scenarios. Posterior estimates were informative with 1,000 loci for migration and split time in simple population divergence models. In more complex models posterior distributions were wide and almost reverted to the uninformative prior even with 50,000 loci. ABC parameter estimates, however, were generally more accurate than an alternative composite-likelihood method. Bottleneck scenarios proved particularly difficult and only recent bottlenecks without recovery could be reliably detected and dated. Notably, minor allele frequency filters – usual practice for GBS data – negatively affected nearly all estimates. With this in mind, we used a combination of FS and θ approaches on empirical GBS data generated from the Atlantic walrus (Odobenus rosmarus rosmarus), collectively providing support for a population split before the last glacial maximum followed by asymmetrical migration and a range-wide bottleneck. Overall, this study evaluates the potential and limitations of GBS data in an ABC-coalescence framework and proposes a best-practice approach.
Data from: Computed tomography shows high fracture prevalence among physically active forager-horticulturalists with high fertility
<p>Modern humans have more fragile skeletons than other hominins, which may result from physical inactivity. Here we test whether reproductive effort also compromises bone strength, by measuring using computed tomography thoracic vertebral bone mineral density (BMD) and fracture prevalence among physically active Tsimane forager-horticulturalists. Earlier onset of reproduction and shorter interbirth intervals are associated with reduced BMD for women. Tsimane BMD is lower versus Americans, but only for women, contrary to simple predictions relying on inactivity to explain skeletal fragility. Minimal BMD differences exist between Tsimane and American men, suggesting that systemic factors other than fertility (e.g. diet) do not easily explain Tsimane women's lower BMD. Tsimane fracture prevalence is also higher versus Americans. Lower BMD increases Tsimane fracture risk, but only for women, suggesting a role of weak bone in women's fracture etiology. Our results highlight the role of sex-specific mechanisms underlying skeletal fragility that operate long before menopause.</p>
PISA 2012: How do results for the paper and computer tests compare (do-files)
<p>These do-files run the analysis on the PISA 2012 dataset.</p>
Investigating the Competencies and Skills of Computer Professionals
<p>We investigated a set of competencies and skills required of computing professionals for education/training purposes. IS theory: The work was developed based on the Social Learning Theory perspective. This theory explains how people think and what factors determine their behavior. Method: We conducted a Multivocal literature review and an opinion poll with 53 participants (students) for Bachelor's degrees in Computer Science, Computer Engineering, Information Systems, and Software Engineering, as well as a Degree in Computer Science. Results: The nature of the competencies and skills of computing professionals are hard skills and soft skills, which include building hardware, language skills, programming/software development, complex problem-solving, and working in a team. Contributions and Impact in the IS area: The article's main contribution is to make a product possible for any organization/university or individual to develop the competencies and skills of computing professionals. This study also contributes to the Grand Research Challenge "Strengthening the Sociotechnical Approach in Information Systems Research".</p>
Computational data on "Proton Affinity and Conformational Integrity in a 24-atom Triazine Macrocycle Across Physiologically-relevant pH"
<p>The archive contains 5 different folders:<br><br>1. mdp_files, that contains all the input files for the minimization, equilibration and molecular dynamics run (in gromacs format);<br>2. topologies, that contains the equilibrated configurations and topology of the 2 systems studied -protonated and deprotonated macrocycles- (in gromacs format);<br>3. trajectories, that contains the coordinates of the macrocycles during the metadynamics calculations and the relevant metadynamics output files (hills file and energy file);<br>4. plumed_input, that contains the input file for the metadynamics calculations.<br>5. gaussian, that contains input and output for the single-point charge calculations.</p>
Computational insights into the Conformational Dynamics of HIV-1 Vpr in lipid bilayer for ion channel modeling
<p>This is the dataset of input files, parameter files and run files for the various protein conformations generated in the study "Computational insights into the Conformational Dynamics of HIV-1 Vpr in lipid bilayer for ion channel modeling"</p>
Multimodal 2D and 3D microscopic mapping of growth cartilage by computational imaging techniques – a short review including new research
<p>This dataset contains the phase and amplitude maps obtained with Fourier ptychographic microscopy and the X-ray diffraction tensor tomography dataset described in the journal article "Multimodal 2D and 3D microscopic mapping of growth cartilage by computational imaging techniques".</p>
Structural basis of Omicron immune evasion: A comparative computational study of Spike protein-Antibody interaction
<p>The COVID-19 pandemic has caused more than 424 million infections and 5.9 million deaths so far. The vaccines used against SARS-COV-2 by now have been able to develop some neutralising antibodies in the vaccinated human population and slow down the infection rate. The effectiveness of the vaccines has been challenged by the emergence of the new strains with numerous mutations in the spike (S) protein of SARS-CoV-2. Since S protein is the major immunogenic protein of the virus and also contains Receptor Binding Domain (RBD) that interacts with the human Angiotensin-Converting Enzyme 2 (ACE2) receptors, any mutations in this region should affect the neutralisation potential of the antibodies leading to the immune evasion. Several variants of concern (VOC) of the virus have emerged so far. Among them, the most critical are Delta (B.1.617.2), and recently reported Omicron (B. 1.1.529) which have acquired a lot of mutations in the spike protein. We have mapped those mutations on the modelled RBD and evaluated the binding affinities of various human antibodies with it. Docking and molecular dynamics simulation studies have been used to explore the effect of the mutations on the structure of the RBD and the RBD-antibody interaction. The analysis shows that the mutations mostly at the interface of a nearby region lower the binding affinity of the antibody by ten to forty per cent, with a downfall in the number of interactions formed as a whole and therefore, it implies the generation of immune escape variants. Notable mutations and their effect was characterised by performing various analyses that explain the structural basis of antibody efficacy in Delta and a compromised neutralisation effect for the Omicron variant. Our results pave the way for robust vaccine design that can be effective for many variants.</p>
Datasets used in: Modelling eye-level visibility of urban green space: Optimising city-wide point-based viewshed computations through prototyping
<p>Research data supporting our publication. Full workflows using the R programming language have been provided on <a href="https://github.com/STBrinkmann/protoVS">GitHub</a>. Here we provide external data that has been used for our research, as well as the resulting Viewshed Greenness Visibility Index (VGVI) raster.</p> <p><strong>Datasets</strong></p> <p>Digital Terrain Model (DTM):</p> <ul> <li>Spatial Resolution: 1 m</li> <li>Source: Canada’s Open Government Portal</li> <li>Licence: <a href="https://open.canada.ca/en/open-government-licence-canada">Open Government Licence - Canada</a></li> <li>File name: Vancouver_DTM_1m.tif<br> </li> </ul> <p>Digital Surface Model (DSM):</p> <ul> <li>Spatial Resolution: 1 m</li> <li>Source: Canada’s Open Government Portal</li> <li>Licence: <a href="https://open.canada.ca/en/open-government-licence-canada">Open Government Licence - Canada</a></li> <li>File name: Vancouver_DSM_1m.tif<br> </li> </ul> <p>Landuse</p> <ul> <li>Spatial Resolution: 2 m</li> <li>Source: Land Cover Classification 2014 - 2m LiDAR</li> <li>Licence: <a href="http://www.metrovancouver.org/data">Metro Vancouver</a></li> <li>File name: Vancouver_LULC_2m.tif<br> </li> </ul> <p>VGVI map</p> <ul> <li>Spatial Resolution: 5 m</li> <li>Source: Resulting dataset from our analysis</li> <li>Licence: MIT License</li> <li>File name: vgvi_van.tif</li> </ul>
Establishing trust in quantum computations
<p>This is supplemental data and code for: T. Proctor et al., <em><a href="https://arxiv.org/abs/2204.07568">Establishing trust in quantum computations</a></em><em>, </em>arXiv 2204.07568 (2022).</p> <p>This folder contains all the data and the analysis code to generate the results presented in that paper. The simulation code uses PyGSTi, which can be found at <a href="https://github.com/pyGSTio/pyGSTi">https://github.com/pyGSTio/pyGSTi</a>.</p> <p>The `code_for_release` folder contains all code, and processed data required for reproducing the results presented in the paper. The `data_for_release` folder contains all raw data (this folder is ~70 Gb when uncompressed), which was generated using the code in `code_for_release`.</p> <p>Please direct any questions to Timothy Proctor (tjproct@sandia.gov).</p>
Exploiting Strict Constraints in the Computation of Cylindrical Algebraic Coverings - Illustration
<p>Graphical illustration of the running example in the bachelor thesis "Exploiting Strict Constraints in the Computation of Cylindrical Algebraic Coverings".</p>
Raw data for Reservoir computing on silicon platform with a ferroelectric field-effect transistor
<p>Raw data of publication "Reservoir computing on silicon platform with a ferroelectric field-effect transistor"</p>
Figure 6 from: Faulwetter S, Vasileiadou A, Kouratoras M, Dailianis T, Arvanitidis C (2013) Micro-computed tomography: Introducing new dimensions to taxonomy. ZooKeys 263: 1-45. https://doi.org/10.3897/zookeys.263.4261
Figure 6 - Eunice sp., transaxial cross section at mid-body (iodine-stained individual).
Figure 14 from: Faulwetter S, Vasileiadou A, Kouratoras M, Dailianis T, Arvanitidis C (2013) Micro-computed tomography: Introducing new dimensions to taxonomy. ZooKeys 263: 1-45. https://doi.org/10.3897/zookeys.263.4261
Figure 14 - Syllis gracilis, false-colour volume rendering of virtually dissected proventricle.
LAMMPS input files and analysis for estimating the glass transition temperature using ensemble molecular dynamcs of a selection of epoxy resins using different protocols for computing the density-temperature behaviour.
<p>LAMMPS input files and analysis for estimating the glass transition temperature using ensemble molecular dynamcs of a selection of epoxy resins using different protocols for computing the density-temperature behaviour. </p>
Computational Data - Role of Molecular Orientation: Comparison of Nitrogenous Aromatic Small Molecule Inhibitors for Area-Selective Atomic Layer Deposition
<p><span><span>Area-selective atomic layer deposition (AS-ALD) shows great potential for meeting the stringent demands of the semiconductor industry for precision nanopatterning. Small molecule inhibitors (SMIs) have recently proven to be a promising, industry-compatible means of achieving AS-ALD. In this work, we compare three nitrogenous aromatic SMIs – aniline, pyrrole, and pyridine – for their ability to block Al</span></span><sub><span><span>2</span></span></sub><span><span>O</span></span><sub><span><span>3</span></span></sub><span><span> ALD on copper with (CuO</span></span><sub><span><span>x</span></span></sub><span><span>) and without (Cu) a native oxide. We find that pyrrole and aniline perform much better as inhibitors than does pyridine. Furthermore, when redosed on copper before every ALD cycle in an ABC scheme, pyrrole and aniline provide outstanding inhibition, facilitating the selective deposition of over 11 nm of Al</span></span><sub><span><span>2</span></span></sub><span><span>O</span></span><sub><span><span>3</span></span></sub><span><span> on an SiO</span></span><sub><span><span>2</span></span></sub><span><span> growth surface in the presence of Cu with 99.9% selectivity. By combining both theory and experiment, we provide new understanding of the mechanisms by which selectivity is prolonged and lost. First, we show that the CuO</span></span><sub><span><span>x</span></span></sub><span><span> surface is inherently more reactive than the Cu surface, leading to an eventual loss of selectivity, even when the inhibitor is redosed. Second, we find that whereas pyrrole and aniline adsorb in a planar bonding orientation, pyridine binds upright at the copper surface and we propose that the upright orientation is the origin of the ineffective inhibition of pyridine. Finally, we observe that redosing of aniline protects the copper surface from undesired oxidation, whereas the redosing of pyridine does not. As such, we posit that a likely benefit of redosing is preventing oxidation and thus reducing reactive site formation during ALD. Through this work, we demonstrate the capability of nitrogenous aromatics to serve as SMIs for AS-ALD, and we contribute valuable insights regarding the impact of ALD process parameters on selectivity. </span></span></p>
Supplemental Material: Computational experiments in Computer Science: A bibliometric study
<p>This laboratory package contains supplemental material from the study: "Supplemental Material: Computational experiments in Computer Science: A bibliometric study". The supplementary material contains:</p> <p>1. The .xlsx files of the dataset used to analyze the RQs.</p> <p>2. The .pdf files of the figures published in the paper.</p> <p>3. The .xlsx files of the tables published in the paper.</p>
Benchmarking Recent Computational Tools Available for DNA Binding Protein Identification
<p><strong>Train_Test_PSSM.pickle:</strong></p> <p>We have provided a train and a test fasta file containing DNA binding and non-binding protein sequences. The PSSM matrices for these sequences are available inside this .pickle file. You will need to provide the path of this .pickle file when running predictions on the provided train or test fasta file sequences using the two provided tools (LocalDPP and LSTM-CNN_Fusion)</p> <p><strong>db.zip:</strong></p> <p>You will need to unzip this database file and provide the unzipped folder as path to the PSSM generation method. The PSSM creation method provided in github uses this database to generate the .pickle file (full of PSSM matrices) from user provided fasta file sequences.</p>
Data from "Cross-Domain Foundation Model Adaptation: Pioneering Computer Vision Models for Geophysical Data Analysis"
<p>This dataset includes the collected geoscientific data of<strong> lunar images, seismic data, and DAS arrays</strong>.</p> <p>It can be used to test the foundation model adaptation in the geophysical domain.</p> <p>Below are some brief desription of the datasets:</p> <p>1) Lunar images for<strong> crater detection<a href="https://moon.bao.ac.cn/">[CAS]</a></strong> : 1000 are used for training and 199 for testing, each with a size of 1022x1022.</p> <p>2) Seismic data for <strong>geobody identification<a href="https://kaggle.com/competitions/tgs-salt-identification-challenge">[TGS]</a></strong> : 3000 are used for training and 1000 for testing, each with a size of 224x224.</p> <p>3) Seismic data for <strong>facies classification<a href="https://www.aicrowd.com/challenges/seismic-facies-identification-challenge">[SEAM]</a></strong> : 250 are used for training and 45 for testing, each with a size of 1006x782.</p> <p>4) Seismic data for <strong>deep fault detection </strong>: 1081 are used for training and 269 for testing, each with a size of 896x896.</p> <p>5) DAS arrays for <strong>seismic event detection<a href="../records/8270895">[Biondi]</a></strong> : 115 are used for training and 28 for testing, each with a size of 512x512.</p> <p><strong>Tips: All the images are “float32” and the labels are "int8".</strong></p> <p>The test code has been published on GitHub: <strong><a href="https://github.com/ProgrammerZXG/Cross-Domain-Foundation-Model-Adaptation/">Cross-Domain-Foundation-Model-Adaptation</a></strong>.</p>
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.