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982 results for “interface”
Data associated to the manuscript "Size-dependence of hydrophobic hydration at electrified gold/water interfaces"
<p>Contains input files and data used to generate the figures of the article: </p> <p>Size-dependence of hydrophobic hydration at electrified gold/water interfaces </p> <p>Alessandra Serva, Mathieu Salanne, Martina Havenith and Simone Pezzotti, <em>arXiv</em>, 2011.08825, 2020</p> <p><a href="https://arxiv.org/abs/2011.08825">https://arxiv.org/abs/2011.08825</a></p> <p>The folder <em>typical_input_files</em> contains typical MetalWalls input files used to perform the simulations. </p> <p>The folder <em>DATA_ASCII_FIGURES</em> contains the processed data used to plot all the figures of the paper.</p>
EEG Data for: "Learning from Label Proportions in Brain-Computer Interfaces"
<p>Data about two experiments is contained in this repository. An EEG experiment utilizing visual event-related potentials (ERPs) with N=13 healthy subjects was conducted in addition to a smaller study with N=5 subjects performing both an auditory and a visual ERP paradigm. </p> <p>The dataset is used and described in the following journal article:</p> <p><em>Hübner, D., Verhoeven, T., Schmid, K., Müller, K. R., Tangermann, M., & Kindermans, P. J. (2017). Learning from label proportions in brain-computer interfaces: online unsupervised learning with guarantees. PloS one, 12(4), e0175856.</em></p> <p><strong>Please cite the above article when using the data.</strong></p> <p>The larger data set with N=13 is different to ordinary ERP datasets in the sense that the train of stimuli to spell one character (68) is divided into repetitions of two interleaved sequences with length 8 and 18, respectively. We added '#' symbols to the spelling matrix which should never be attended by the subject and hence, are non-targets by definition. The first, shorter sequence, now highlights only ordinary characters, while the second sequence also highlights '#' -- visual blank symbols. By construction, sequence 1 has a higher target ratio than sequence 2. These known, but different target and non-target proportions are then used to reconstruct the target and non-target class means. This approach which does not need explicit class labels is termed Learning from Label Proportions (LLP). It can be used to decode brain signals without prior calibration session. More details can be found in the article.</p> <p>In another study, the above data set was used to simulate a new unsupervised mixture approach which combines the mean estimation of the unsupervised expectation-maximization algorithm by Kindermans et al. (2012, PLoS One) with the means obtained with the LLP approach. This leads to an unsupervised solution for which the performance is as good as in the supervised scenario. Please find more details in the following article:</p> <p><em>Verhoeven, T., Hübner, D., Tangermann, M., Müller, K. R., Dambre, J., & Kindermans, P. J. (2017). Improving zero-training brain-computer interfaces by mixing model estimators. Journal of neural engineering, 14(3), 036021.</em></p> <p>The following files are available:</p> <p>description.pdf: <strong>Full description of the dataset</strong><br> offline_auditory.zip: <strong>Data from the auditory offline study with N=5 subjects</strong><br> offline_visual.zip: <strong>Data from the visual offline study with N=5 subjects</strong><br> online_study_1-7.zip: <strong>Data from the online study for subjects 1-7</strong><br> online_study_8-13.zip: <strong>Data from the online study for subjects 8-13</strong><br> sequence.mat: <strong>Sequence data necessary for applying LLP to the online study. It is the same for all subjects</strong></p> <p>We will create a git repository with example code soon.</p>
Oxidation of thin films at the air-water interface of atmospheric aerosol
<p>X-ray reflectivity data (reflectivity vs Q) for the oxidation of insoluble organic material at the air-water interface. The organic material was extracted from atmospheric aerosol and sea water samples. The organic material was reacted with gas-phase ozone and aqueous phase hydroxyl radicals. The reflectivity data was collected at the Diamond Light source on I07 in May 2013 (SI8744) and April 2014 (SI9632) funded by STFC and NERC. The data supports a publication in Atmospheric Environment entitled “Are organic films from atmospheric aerosol and sea water inert to oxidation by ozone at the air-water interface?"</p>
EEG Motor Imagery Dataset from the PhD Thesis "Commande robuste d'un effecteur par une interface cerveau machine EEG asynchrone"
<p>This Dataset contains EEG recordings from 8 subjects, performing 2 task of motor imagination (right hand, feet or rest). Data have been recorded at 512Hz with 16 wet electrodes (Fpz, F7, F3, Fz, F4, F8, T7, C3, Cz, C4, T8, P7, P3, Pz, P4, P8) with a g.tec g.USBamp EEG amplifier.</p> <p>File are provided in MNE raw file format. A stimulation channel encoding the timing of the motor imagination. The start of a trial is encoded as 1, then the actual start of the motor imagination is encoded with 2 for imagination of a right hand movement, 3 for imagination of both feet movement and 4 with a rest trial.</p> <p>The duration of each trial is 3 second. There is 20 trial of each class.</p>
Part-by-part interface-based search and automatic reassembly of CAD models for database expansion and model reuse
<p>This dataset contains the generated cad assembly from three differents strategy from the article "Part-by-part interface-based search and automatic reassembly of CAD models for database expansion and model reuse".<br> In ReplacePart strategy, each assembly is available in .FCStd format which has the kinematic constraints in the A2+ workbench. A .STEP format of the assembly as well as a PNG screen of the assembly is also available. For the two other strategies, juste STEP files are availables.</p>
For the people by the people: citizen science web interface for real-time monitoring of tick risk areas in Finland
<p>Ticks and tick-borne diseases (TBDs) form a significant and growing threat to human health and well-being in Europe, with increasing numbers of tick-borne encephalitis (TBE) and Lyme borreliosis cases being reported during the past few decades. Increasing knowledge of tick risk areas and seasonal activity remains the primary method for preventing TBDs. Crowdsourcing provides the best alternative for rapidly obtaining data on tick occurrence on a national level.</p> <p>In order to produce and share up-to-date data about tick risk areas in Finland, an online platform, Punkkilive (www.punkkilive.fi/en), was launched in April 2021. On the website, users can submit and browse tick observations, report tick numbers and hosts, and upload pictures of ticks.</p> <p>Here, we looked at trends in the crowdsourced data from 2021, assessed the effect of local tick species on seasonality of observations, and examined sampling bias in the data.</p> <p>The high number of tick observations (n=78 837) highlights that there was demand for such a service. Approximately 97% of 5573 uploaded pictures represented ticks. Seasonal patterns of tick observations varied across Finland, highlighting variability in the risk associated with the two human-biting tick species <em>Ixodes ricinus</em> and <em>I. persulcatus</em>, the latter having a shorter, unimodal activity peak in late spring–early summer. Tick numbers were low and the proportion of new sightings was high in northern Finland, as may be expected near the latitudinal distribution limits of both species. While the number of inhabitants generally explained the number of tick observations well, geographically weighted regression models also identified areas that deviated from this general pattern.</p> <p>This study offers a prime example of how crowdsourcing can be applied to track vectors of zoonotic diseases, to the benefit of both researchers and the public. Areas with more or fewer observations than predicted based on number of inhabitants were revealed, wherein more specific analyses may reveal factors contributing to lower or higher risk levels that may be used in increasing awareness. We hope that the success of Punkkilive serves to highlight the usefulness of citizen science in the prevention of vector-borne diseases.</p>
Nearly complete structure of DT57C bacteriophage reveals unusual architecture of head-to-tail interface and lateral tail fibers
<p><strong>Supplementary materials for "Nearly complete structure of DT57C bacteriophage reveals unusual architecture of head-to-tail interface and lateral tail fibers", Ayala et al.</strong></p><p>The dataset contains the molecular dynamics trajectories for three systems: TTMP tail protein ring along with the adjacent outermost LtfA-LtfC ring (1) and the HCP ring with (2) or without (3) the TCP ring. Each simulation was run in triplicate.</p>
Dataset for "Mo-Si alloys studied by atomistic computer simulations using a novel machine-learning interatomic potential: Thermodynamics and interface phenomena"
<p>This dataset was used to fit a general purpose machine-learning interatomic potential for Mo-Si alloys based on the Atomic Cluster Expansion (ACE) formalism. It supports the paper "Mo-Si alloys studied by atomistic computer simulations using a novel machine-learning interatomic potential: Thermodynamics and interface phenomena".</p>
The structure of a tetrameric septin complex reveals a hydrophobic element essential for NC-interface integrity
<p>The septins of the yeast <i>Saccharomyces cerevisiae</i> assemble into hetero-octameric rods by alternating interactions between neighboring G-domains or N- and C-termini, respectively. These rods polymerize end to end into apolar filaments, forming a ring beneath the prospective new bud that expands during the cell cycle into an hourglass structure. The hourglass finally splits during cytokinesis into a double ring. Understanding these transitions as well as the plasticity of the higher order assemblies requires a detailed knowledge of the underlying structures.Here we present the first X-ray crystal structure of a tetrameric Shs1-Cdc12-Cdc3-Cdc10 complex at a resolution of 3.2 Å. Close inspection of the NC-interfaces of this and other septin structures reveals a conserved contact motif that is essential for NC-interface integrity of yeast and human septins <i>in</i> <i>vivo</i> and <i>in vitro</i>. Using the tetrameric structure as a template allowed AlphaFold-Multimer to propose a model of the octameric septin rod. </p>
Quasi-free-standing AA-stacked bilayer graphene induced by calcium intercalation of the graphene-silicon carbide interface
<p>APRES datasets and LEED images for "Quasi-free-standing AA-stacked bilayer graphene induced by calcium intercalation of<br>the graphene-silicon carbide interface" publication.</p>
Dataset for "Cascading effects of mammal host community composition on tick vector occurrence at the urban human-wildlife interface"
<p>Dataset for the following paper:</p> <p><strong>Cascading effects of mammal host community composition on tick vector occurrence at the urban human-wildlife interface</strong></p> <p>Jonathan Bastard *, Nichar Gregory *, Maria Pilar Fernandez, Michaela Mincone, Olivia Card, Sara Kross, Maria Diuk-Wasser</p> <p>* These authors contributed equally.</p>
Data set related to the manuscript "Dynamics and energetics of ion adsorption at the interface between a pure ionic liquid and carbon electrodes"
<p>Text files with data for plotting figures in the quoted manuscript. Example input files for simulations.</p>
A Taxonomy classifying UI components in desktop interfaces
<p><strong>Taxonomy</strong></p> <p>This publication presents a structured taxonomy for desktop User Interface (UI) Components. The development methodology foundation is extensively detailed in [1]. This taxonomy categorizes UI components into hierarchical levels of abstraction, as described in [2]: <em>System, Application, UI Group, </em>and <em>UI Element</em>.</p> <p>The taxonomy is presented in a table format, organized into the following columns:</p> <ul> <li><strong>UI Component Type</strong>: Identifies the specific UI Component being described, with examples including Icons, Taskbars, etc.</li> <li><strong>Level</strong>: Specifies the component's hierarchical position by identifying the level of abstraction to which it belongs.</li> <li><strong>Detected by</strong>: Lists the model employed to detect a particular type of UI Component, based on a multi-modal approach for detecting UI Hierarchies from desktop screenshots, as discussed in [1], where M1, M2, M3, M4 and M5 are described.</li> <li><strong>Description</strong>: Provides an explanation of the criteria for classifying a specific UI Component type.</li> </ul> <p>This taxonomy facilitates a deeper understanding and navigation of the complexities inherent in desktop UIs.</p> <p><strong>References</strong></p> <p> 1. A. Martínez-Rojas, A. Rodríguez-Ruíz, J.G. Enríquez, and A. Jiménez-Ramírez (2024, September). What’s Behind the Screen? Unveiling UI Hierarchies in Process-Related UI logs. In <em>International Conference on Business Process Management</em>. Cham: Springer International Publishing.</p> <p> 2. Abb, L., Rehse, J.R.: A reference data model for process-related user interaction logs. In: International<br>Conference on Business Process Management. pp. 57–74. Springer (2022)</p>
Localised Thermal Emission from Topological Interfaces
<p>Dataset and simulation files for the manuscript "Localised Thermal Emission from Topological Interfaces".</p>
Rapid, DNA-induced interface swapping by DNA gyrase
<p>DNA gyrase, a ubiquitous bacterial enzyme, is a type IIA topoisomerase formed by heterotetramerisation of 2 GyrA subunits and 2 GyrB subunits, to form the active complex. GyrA is usually found as a dimer in solution, whereas GyrB can exist as a monomer. DNA gyrase is able to loop DNA around the C-terminal domains (CTDs) of GyrA and pass one DNA duplex through a transient double-strand break (DSB) established in another duplex. This results in the conversion of a positive loop into a negative one, thereby introducing negative supercoiling into the bacterial genome, an activity essential for DNA replication and transcription. The strong protein interface in the GyrA dimer must be broken to allow passage of the transported DNA segment and it is generally assumed that the interface is usually stable and only opens when DNA is transported, to prevent the introduction of deleterious DSBs in the genome. In this paper we show that DNA gyrase can exchange its DNA-cleaving interfaces between two active heterotetramers. This so-called interface "swapping" or "exchange" (IS) can occur within a few minutes in solution. We also show that bending of DNA by gyrase is essential for cleavage but not for DNA bindingper seand favors IS. interface swapping is also favored by DNA wrapping and an excess of GyrB. We suggest that proximity, promoted by GyrB oligomerization and binding and wrapping along a length of DNA, between two heterotetramers favors rapid interface exchange. This exchange does not require ATP, can occur in the presence of fluoroquinolones, and raises the possibility of non-homologous recombination solely through gyrase activity. The ability of gyrase to undergo interface swapping also explains how gyrase heterodimers, containing a single active-site tyrosine, can carry out double-strand passage reactions and therefore suggests an alternative explanation to the recently proposed "swivelling" mechanism for DNA gyrase (Gubaev, Weidlich, and Klostermeier 2016).</p>
Dataset for research paper entitled Adaptive Phase or Variant Formation at the Austenite/Twinned Martensite Interface in Modulated Ni–Mn–Ga Martensite
<p><span>The dataset contains the experimental result concerning in-situ synchrotron and SEM/EBSD measurements as a function of temperature. The list of files is listed below:</span></p> <p><span>The dataset is composed of both the raw and processed data:</span></p> <p><strong><span>X-ray phase analysis</span></strong><span> - performed with a synchrotron radiation energy 87.1 KeV.</span></p> <ul> <li><span>Origin file 1 - Diffraction experiments made on NiMnGa single crystals below and above Ms temperature</span></li> <li><span>2D Diffraction pattern for 10M 10M’ Mt, and A structures.</span></li> </ul> <p><strong><span>TEM experiments</span></strong><span> - </span><span>Microstructural observations were carried out by ThermoFisher Scientific TitanThemis Cs corrected 200 kV scanning /transmission electron microscope (S/TEM) equipped with SuperX </span><a title="Learn more about EDX from ScienceDirect's AI-generated Topic Pages" href="https://www.sciencedirect.com/topics/materials-science/energy-dispersive-x-ray-spectroscopy"><span>EDX</span></a><span> detector system. Thin foil for analysis was prepared by </span><span>TEM observations were prepared with a TenuPol-5 double jet electropolisher using an electrolyte of nitric acid (70%) and methanol (30%) at -25 °C.</span></p> <p><span>· </span><span>File 1 set of HRTEM images showing modulation boundaries</span></p> <p><span>· </span><span>File 2 set of HRTEM images showing a/b boundaries</span></p> <p><strong><span>SEM/EBSD</span></strong><span> - </span><span>FEI Quanta 3D FEG SEM equipped with a TSL system and a Murano heating stage. To analyze the lattice parameter changes, a c</span><span>rystallographic analysis of lattice metric (CALM) was used. This method does not need a standard for indexing or lattice constant determination. The lattice metric (lattice parameters) was derived through the reconstruction of the experimental EBSD pattern. In the first step, centers of Kikuchi band traces were detected from the EBSD diffraction pattern. Then, using information about the diffraction projection center, 20 to 100 independent reflectors were reconstructed in the reciprocal space. The final step involves a search for primitive lattice vectors which are fulfilling translational symmetry conditions for all reflectors. Reconstructed vectors are recomputed to the higher symmetry lattices with a relative error lower than 0.1%</span><span>Thermogravimetric curves obtained for the decomposition of powder after synthesis at 500 rpm.</span></p> <ul> <li><span>Origin file 2 Relation between a/c lattice parameters</span></li> <li><span>Origin file 3 Relation between a/c lattice parameters</span></li> <li><span>SEM/BSE pictures showing austenite twinned/martensite interface</span></li> <li><span>Video 1 shows in-situ SEM/BSE with martensitic transformation and </span><span>one planar austenite/twinned martensite interface during cooling</span></li> <li><span>Video 2 shows set of Kikuchi pattern across Austenite martensite phase indicating elastic nature of the martensitic transformation</span></li> </ul>
Dynamics of Centipede Locomotion Revealed by Large-Scale Traction Force Microscopy (J. Roy Soc INTERFACE, to be published, march 2024)
<p>data and matlab code from paper "Dynamics of Centipede Locomotion Revealed by Large-Scale Traction Force Microscopy" (paper submitted to J. Roy Soc INTERFACE, to be published, march 2024)</p> <p><strong><span>Dynamics of Centipede Locomotion Revealed by Large-Scale Traction Force Microscopy</span></strong></p> <p><span> </span><span>J.P. Rieu</span><sup><span>1, *</span></sup><span>, H. Delanoë-Ayari</span><sup><span>1</span></sup><span>, C. Barentin</span><sup><span>1</span></sup><span>, T. Nakagaki</span><sup><span>2</span></sup><span> and S. Kuroda</span><sup><span>3</span></sup><sup><span> ,*</span></sup></p> <p><sup><span>1</span></sup><span> </span><span>Institut Lumière Matière, University of Lyon, Université Claude Bernard Lyon 1, CNRS, F-69622, Villeurbanne, France</span></p> <p><sup><span>2</span></sup><span> Research Institute for Electronic Science, Hokkaido University, N20W10 Kita-ku, Sapporo Hokkaido 001-0020, Japan</span></p> <p><sup><span>3 </span></sup><span>Faculty of Software and Information Technology, Aomori University, Koubata 2-3-1, Aomori, 030-0943, Japan</span></p> <p><span>* Authors for correspondence:<span> </span>Jean-Paul Rieu (e-mail: jean-paul.rieu@univ-lyon1.fr) and Shigeru Kuroda (shigeru-kuroda@aomori-u.ac.jp)</span></p> <p> </p> <p><strong><span>Abstract</span></strong></p> <p><span>We present a novel approach to traction force microscopy (TFM) for studying the locomotion of 10cm-long walking centipedes on soft substrates.</span><span> Leveraging the </span><span>remarkable</span><span> elasticity and ductility of kudzu starch gels, we utilize them as a deformable gel substrate, providing resilience against the centipedes' sharp leg tips. </span><span>Through optimizing fiducial marker size and density and fine-tuning imaging conditions, we enhance measurement accuracy. Our TFM investigation reveals traction forces along the centipede's longitudinal axis that effectively counterbalance inertial forces within the 0-10mN range, providing the first report of non-vanishing inertia forces in TFM studies. Interestingly, we observe waves of forces propagating from the head to the tail of the centipede, corresponding to its locomotion speed. Furthermore, we discover a characteristic cycle of leg clusters engaging with the substrate: forward force (friction) upon leg tip contact, backward force (traction) as the leg pulls the substrate while stationary, and subsequent forward force as the leg tip detaches to reposition itself in the anterior direction. </span><span>This work </span><span>opens perspectives for TFM applications in ethology, tribology, and robotics</span><span>.</span></p>
Observation of strong backscattering in valley-Hall photonic topological interface modes
<p><span>Dataset required to reproduce the figures in the main text and supplementary information of: Rosiek, C.A., Arregui, G., Vladimirova, A. <em><span>et al.</span></em> Observation of strong backscattering in valley-Hall photonic topological interface modes. <em><span>Nature Photonics</span></em> <strong><span>17</span></strong>, 386–392 (2023).</span></p> <p><span>Execution of scripts to generate the figures tested on Windows with Matlab 2020b or newer. COMSOL models generated and solved on version 6.0. Unzip folder to access all files.</span></p> <p><span>Scripts are named according to the associated figures of the main manuscript:</span></p> <p><span> - fig1_transmittances.m generates the graphs of Fig. 1.</span></p> <p><span> - fig2_pti_dispersion.m generates the graphs of Fig. 2.</span></p> <p><span> - fig3etc_main_analysis.m (which calls subroutine fig3etc_main_analysis_sub.m) generates graphs of Fig. 3 and 4 as well as Supplementary Figures S6 and S11.</span></p> <p><span> - </span><span>fig5c_fffits.m and fig5d_ffmap.m generates plots of Fig. 5c and d, respectively. fig5_load_images.m performs preprocessing required to run fig5c_fffits.m and fig5d_ffmap.m from the raw data alone.</span></p> <p><span> - fig_s10_w1_loss_analysis.m generates the graphs of Fig. S10.</span></p> <p><span>Note that the data analysis also makes use of data derived from COMSOL simulations. The COMSOL MPH simulation files are contained within the subfolders of contrib.</span></p> <p><span>Contact chanro@dtu.dk for any inquiry on the contents.</span></p> <p> </p>
Adaptive sampling-based structural prediction reveals opening of a GABAA receptor through the αβ interface
<p>These are the simulation of an open state of α1β2<span>γ</span><span>2 GABAA receptor. There are five replicates, each for 200 ns, saved with every ns freequency. The prot_masses.pdb is the desenstized starting state model and the .dcd files are simualtion frames of the open state. </span></p>
retinomics.org - a web interface and data repo
<p>The retinomics portal is a web interface to explore the effect that different biological factors have on the morphology of the retina.</p> <p>A variety of <em>omics</em> are included in this project including genomics, metabolomics, phenomics, other traits.</p>
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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.