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10,561 results for “mechanics”
Genomic Data for "Structure of Anellovirus-like Particles Reveal a Mechanism for Immune EvasionAnellovirus-like Particles Reveal a Mechanism for Immune Evasion"
<p>All genomic data supporting the paper 'Structure of Anellovirus-like Particles Reveal a Mechanism for Immune EvasionAnellovirus-like Particles Reveal a Mechanism for Immune Evasion'. Include amino acid sequence alignment used to produce supplemental figure 6 in the manuscript.</p>
The Mechanical Performance of Permanent and Bioabsorbable Metal Stents: Supporting Data
<p>Materials including scripts, finite element models and experimental data that were created during the Phd work toward 'The Mechanical Performance of Permanent and Bioabsorbable Metal Stents' http://hdl.handle.net/10379/3744 but wasn't ultimately used in the thesis or publications.</p>
DataSet & R code used for the analysis of "Mechanisms of mobbing call recognition: Exploring featural decoding in great tits"
<p>Data and R code used in a playback experiment exploring the mechanisms of mobbing call recognition in the great tit, Parus major. Accepted in Animal Behaviour (2024). </p> <p>This experiment aimed at testing the hypothesis of simple featural interpretation in the great tit (i.e., the fact that receivers can focus on specific acoustic features rather than complete note recognition). </p> <p>The experiment is organised with two parts: first, we test the response of great tits to artificial calls that possess either none or all of the characteristics present in their own calls (and shared with other Parids), and compare their level of response to natural mobbing calls. </p> <p>As the 'complete' treatment triggered the same level fo response than the natural calls, we then create artifical calls with only one of the four features used to create our artifical mobbing calls (large frequency range, low frequency, noise and harmonics). </p> <p> </p> <p>More information can be obtained by contacting Ambre SALIS (salis.ambre87[at]gmail.com)</p>
Data for "High-temperature low-cycle fatigue and fatigue-creep behaviour of Inconel 718 superalloy: Damage and deformation mechanisms"
<p>Title of dataset: Data for "High-temperature low-cycle fatigue and fatigue-creep behaviour of Inconel 718 superalloy: Damage and deformation mechanisms"<br>Name/institution/contact information: Dr. Michal Bartošák, Czech Technical University in Prague - Faculty of Mechanical Engineering, email: michal.bartosak@fs.cvut.cz<br>Date of data collection: The data were collected from the start of 2021 to the end of 2023.<br>File name structure: The data within the folder "SEM" are images of microstructural observations of selected specimens. The data within the folder "FATIGUE_LIFE" include the fatigue lifetimes, as well as the stress and strain amplitudes at mid-life, of all investigated specimens.</p> <p>See https://doi.org/10.1016/j.ijfatigue.2024.108369 for the associated article and a detailed description of the methods.</p>
Рис. 6. Удельный вес ЭкЗемплЯров глицимериса (%, от обЩего числа раковин и створок) с механическими повреЖдениЯми на иЗученном участке. Fig. 6. Proportions of the Glycymeris yessoensis specimens with mechanical damage (of the total number of shells and valves) on the beach studied. in Shell destruction of the bivalve mollusk Glycymeris yessoensis on a beach in Possjet Bay (the Sea of Japan)
Рис. 6. Удельный вес ЭкЗемплЯров глицимериса (%, от обЩего числа раковин и створок) с механическими повреЖдениЯми на иЗученном участке. Fig. 6. Proportions of the Glycymeris yessoensis specimens with mechanical damage (of the total number of shells and valves) on the beach studied.
The Pan-Canadian Chemical Library: A Mechanism to Open Academic Chemistry to High-Throughput Virtual Screening
<h1>Pan-Canadian Chemical Library</h1> <p>This Zenodo repository contains the cheap and druglike subset of the Pan-Canadian Chemical Library (PCCL) project. For more information, visit <a href="https://pccl.thesgc.org/" rel="nofollow">https://pccl.thesgc.org</a>.</p> <h2>PCCL library</h2> <p>The PCCL library is splitted by reaction, then by number of heavy atoms. Two types of files are available in zip archives:</p> <ul> <li>The SMILES format files, with the SMILES string and their product name,</li> <li>The CSV format file, with all the information generated during their enumeration: reagents, druglike properties, etc.</li> </ul> <p>Note: Purchasability is defined according to two integers: 1 for products only composed of BB-50 reagents, and 2 for products composed of BB-40 or BB-50 reagents. Read more about the meaning of these reagents groups in the article below.</p> <h2>Citation</h2> <p>If you find the PCCL useful or if you use it, please cite our paper:</p> <p>Bedart, C. <em>et al.</em> The Pan-Canadian Chemical Library: A mechanism to open academic chemistry to high-throughput virtual screening. Scientific Data 11, (2024).<br>doi: <a title="10.1038/s41597-024-03443-5" href="https://www.nature.com/articles/s41597-024-03443-5">10.1038/s41597-024-03443-5</a></p> <p> </p> <p> </p>
Rock magnetic data from IODP Exp. 382 Sites U1537 and U1538 to support Reilly et al. "A geochemical mechanism for >10 m offsets of magnetic reversals inferred from the comparison of two Scotia Sea drill sites"
<p>Rock magnetic data from IODP Exp. 382 Sites U1537 and U1538 to support Reilly et al. "A geochemical mechanism for >10 m offsets of magnetic reversals inferred from the comparison of two Scotia Sea drill sites"</p><p>Excel Files:</p><ul><li>U1537_CubeSummary_Zenodo.xlsx : Summary of NRM, ARM, IRM, and magnetic susceptibility investigations on U1537 cube samples</li><li>U1538_CubeSummary_Zenodo.xlsx : Summary of NRM, ARM, IRM, and magnetic susceptibility investigations on U1538 cube samples</li></ul><p>Zip Files:</p><ul><li>FORC_Data.zip : First order reversal curve data files in MicroMag format for samples discussed in paper</li><li>DCD_Data.zip : DC Demagnetization curve data files for samples discussed in paper</li><li>Hysteresis_Data.zip : Hysteresis Loops for samples discussed in paper</li><li>MPMS_Data.zip : Data collected on Magnetics Property Measurement System 3, including Field Cooled/Zero Field Cooled Curves, Low Temperature Cycling of Room Temperature IRM, and AC Susceptibility</li></ul><p> </p><p>NRM = Natural Remanent Magnetization; ARM = Anhysteretic Remanent Magnetization; IRM = Isothermal Remanent Magnetization</p>
Data from: Female-biased population sex ratios caused by genetic rather than ecological mechanisms in dwarf willow (Salix herbacea L.)
<p>Biased sex ratios among reproductive individuals are common in plants, but the underlying mechanisms, as well as the evolutionary consequences, are not well understood. The classical theory of Düsing and Fisher predicts an equal primary sex ratio at seed production, based on the selective advantage of the rare sex. Biased sex ratios among reproductive plants can arise from sexual dimorphism in survival and flowering. Sex ratio biases can also be present from the seed stage; in these cases, assumptions of Düsing's and Fisher's theory, for example, random mating or demographic equilibrium, are thought to be violated.</p> <p>We investigated mechanisms leading to female-biased sex ratios in the arctic-alpine dwarf willow <em>Salix herbacea</em> L. We studied sex ratios in three natural populations over three years as well as in 29 crosses (full-sib families) under controlled conditions over four growth periods. We tested whether sex ratio was associated with habitat parameters (elevation and snowmelt time), or with germination, survival or flowering, and whether females and males differed in size or flowering that may cause observation bias.</p> <p>We detected a strong and consistent female bias, both in natural populations (sex ratio [proportion of females]: 0.71-0.82) and in our controlled experiment (overall sex ratio: 0.70-0-72). Female bias became more pronounced with increasing elevation. Our data did not support sexual dimorphism in size or flowering. Family sex ratios varied largely (from 0.25 to 1), including many female-biased families, unbiased families and two male-biased families. Families with lower germination, seedling establishment, survival or flowering did not have stronger female bias, indicating that intrinsically higher survival or flowering in females does not explain overall female bias. </p> <p>Synthesis: Our results suggest that sex ratio bias in <em>S. herbacea</em> is already present in seeds and does not arise through intrinsic differences between sexes. Candidate mechanisms that can lead to both overall female bias and variation in sex ratio among families are meiotic drive or cyto-nuclear interactions. The pioneer habit of <em>Salix</em> may lead to non-equilibrium population dynamics that allow for the long-term persistence of variable genetic sex ratio distortion systems that arise from genetic conflict.</p>
Data and original code for: Explaining the diversity of optical effects in Christmas beetles: climate, history, and mechanisms
<p><span>Beetles exhibit an extraordinary diversity of brilliant and colourful appearances. The mechanisms producing these optical effects have received some attention, but we know little about the ecological variables driving their evolution. Here we investigated environmental correlates of reflectivity and circular polarization produced by a combination of pigments and structures in optically diverse Christmas beetles (Scarabaeidae: Rutelinae). We quantified the optical properties of 261 specimens representing 46 species using spectrophotometry and calibrated photographs. Then, we examined associations between these properties and environmental variables such as temperature, humidity, and vegetation cover, controlling for body size and phylogenetic relatedness. Our results showed that larger beetles have higher reflectivity and occur in drier environments. Unexpectedly, near-infrared (NIR) reflectivity was not correlated with ecological variables. We observed no universal ecogeographical pattern for polarization but identified trade-offs with other optical properties: beetles without polarization-associated nanostructures had higher NIR reflectivity. Visible reflectivity seems less affected by nanostructures and is instead negatively correlated with the accumulation of pigments such as melanin. Our study highlights the value of a macroecological approach for testing alternative hypotheses to explain the diversity of optical effects in beetles and to understand the link between structure and function.</span></p>
Fluid Mechanics Dataset PhysPHD.
<p>The Fluid Mechanics dataset for the PhysPHD paper includes three scenarios: S1, S2 and S3. Each scenario has two numpy zip files, for training and testing.</p>
Mechanisms of coexistence: Exploring species sorting and character displacement in woody plants to alleviate belowground competition
<p>Rarely do we observe competitive exclusion within plant communities, even though plants compete for a limited pool of resources. Thus, our understanding of the mechanisms sustaining plant biodiversity might be limited. In this study, we explore two common ecological strategies, species sorting and character displacement, that promote coexistence by reducing competition. We assess the degree to which woody plants may implement these two strategies to lower belowground competition for nutrients which occurs via nutritional (mostly mycorrhizal) mutualisms. First, we compile data on plant traits and the mycorrhizal association state of woody angiosperms using a global inventory of indigenous flora. Our analysis reveals that species in locations with high mycorrhizal diversity exhibit distinct mean values in leaf area and wood density based on their mycorrhizal type, indicating species sorting. Second, we reanalyze a large dataset on leaf area to demonstrate that in areas with high mycorrhizal diversity, trees maintain divergent leaf area values, showcasing character displacement. Character displacement among plants is considered rare, making our observation significant. In summary, our study uncovers a rare occurrence of character displacement and identifies a common mechanism employed by plants to alleviate competition, shedding light on the complexities of plant coexistence in diverse ecosystems.</p>
Dataset for "Engineering defect clustering in diamond-based materials for technological applications via quantum mechanical descriptors"
<p>The unique set of extreme physical properties makes diamond an ideal candidate for applications in the energy industry such as in high-power and high-frequency electronics as well as in electrochemistry and photovoltaics. Furthermore, dopant-vacancy complexes in diamond can be exploited for further development of quantum computers, single-photon emitters, high-precision magnetic field sensing and nanophotonic devices. While certain dopant-vacancy complexes are well-studied, studies of other dopant/vacancy clusters are focused mostly on defect detection while investigations on how to tune their electronic and optical properties for specific applications is mostly omitted. To this aim, we attempted to reveal coupled structural-electronic features and their effect on the band gap of such defects through first principle calculations. We investigated four different defect types: a) dopant-vacancy complexes (X-V), b) two dopants as nearest neighbours (X-X), c) two dopants separated by one carbon atom (X-C-X) and d) two dopants separated by a vacancy (X-V-X). For each of these configurations, we considered Al, B, N, P and Si as dopant atoms. This dataset contains input files needed to reproduce every ground state geometry used in our study.</p>
Reverse social contagion as a mechanism for regulating mass behaviors in highly integrated social systems
<h1>Reverse social contagion as a mechanism for regulating mass behaviors in highly integrated social systems</h1> <p>This repository houses supporting data for “Reverse social contagion as a mechanism for regulating mass behaviors in highly integrated social systems”. It contains three archives consisting of multiple files storing inter-individual interactions, trajectory data for multiple colonies of desert harvester ants (Pogonomyrmex californicus), and the code necessary to reproduce the study results. The behavioral data sets were obtained from 30s videos filmed at 15fps. </p> <h2>Description of the data and file structure</h2> <h3>Supplementary_Archive_1.zip</h3> <p>This collection of CSV files contains the antennal contact interactions among individual workers from colonies. Each file name represents the colony code and the data contained in each file belongs to a single colony. Each file contains three columns: The first (1) column represents the tag of an individual observed, the second (2) column represents the tag of the individual it interacted with, and the third (3) column represents the frame of the video at which the interaction occurred.</p> <h3>Supplementary_Archive_2.zip</h3> <p>This group of mdf files contains the trajectory data for each individual of a harvester ant colony. The files were generated using the ImageJ plugin MTrackJ. Each file contains the data of one colony and the filename represents the code of said colony. The data contained in this file is organized in rows and columns. The first row indicates the MTrackJ software version used to generate the file. The second row indicates the displaying preferences for the MTrackJ software. The third and fourth rows indicate the number of assemblies and clusters, respectively. However, this can be safely ignored as the colony was treated as a whole. The rows starting with ‘Track’ indicate the tag of the individual observed followed by its identifying number “Track 1” belongs to individual 1, “Track 2” belongs to individual 2, “Track 3 to individual 3, and so forth. The lines that start with ‘Point’ after each ‘Track’ represent the point in space in the video for each individual in a given frame. The second column after ‘Point’ simply refers to the point ID in the frame “e.g. Point 1”. The third and fourth columns represent the ‘x’ and ‘y’ coordinates in the video frame. The fourth, fifth, and sixth columns represent the dimensions of an image stack. In this case, the fourth and sixth columns are fixed to 1 and the fifth column represents the frame at which the point is taken. Each point is captured in 5-frame increments.</p> <h2>Code/Software</h2> <h3>Supplementary_Archive_3.zip</h3> <p>This archive contains the code necessary to reproduce the results of the study in the form of a Mathematica notebook. It also contains a folder with the trajectory data for each individual of a harvester ant colony, in a simplified format from that available in Supplementary_Archive_2.zip. Each CSV file in this folder corresponds to a different colony. It has four columns, respectively representing the identifying number of the individual observed, the frame number at which the observation, and the ‘x’ and ‘y’ coordinates, in that order. Finally, a XLSX file contains the number of individuals in each colony (first column), the metabolic rate of the colony (second column), and the identifying number of the colony (third column; numbers followed by the letter 's' correspond to size-reduced colonies). </p>
Figure 4 in Clonal mechanisms that matter in Agave fourcroydes and A. sisalana invasions in drylands: implications for their management
Figure 4. Mean and standard deviation of rooting rates of Agave fourcroydes and A. sisalana bulbils under experimental plots (greenhouse and natural conditions). Different letters indicate statistical differences (p-values <0.001) between planting conditions for Fisher's exact tests. The lower case letters correspond to the comparisons in the experiment under natural conditions, and the upper case letters refer to those in the greenhouse experiment.
Figure 3 in Clonal mechanisms that matter in Agave fourcroydes and A. sisalana invasions in drylands: implications for their management
Figure 3. Box-and-whisker plots for total aerial bulbil and basal shoot production per reproductive individual registered in Agave fourcroydes and A. sisalana. Box represents median and 25th and 75th percentile levels, crosses are the means, and whiskers are the ranges. N = 30 for each species. Non-parametric Mann-Whitney U tests showed no significant differences between species (U = 403.5 and 449.0, and p-values = 0.492 and 0.986 for bulbil and basal shoot production, respectively). U = U statistic.
Figure 2 in Clonal mechanisms that matter in Agave fourcroydes and A. sisalana invasions in drylands: implications for their management
Figure 2. Flowering, aerial bulbil, and shoot from rhizomes phenology of Agave fourcroydes (AF) and A. sisalana (AS) in the study zone. Wilcoxon signed-rank tests showed no statistical differences between species in any variable. Mean % floral buds: W = 29.0, p-value = 0.141; Mean % flowers: W = 2.0, p-value = 0.789; Mean % bulbils: W = 49.0, p-value = 0.834; Mean % fallen bulbils: W = 13.0, p-value = 0.083; Mean % new shoots from rhizomes: W = 16.0, p-value = 0.834. W = Wilcoxon statistic.
Figure 1 in Clonal mechanisms that matter in Agave fourcroydes and A. sisalana invasions in drylands: implications for their management
Figure 1. Diagram of a rosette of Agave fourcroydes or A. sisalana showing their clonal ramet types. BS: basal shoots, born directly from the rosette; RS: shoots from rhizomes, and aerial bulbils from floral scapes.
Dataset for: Adapting Explainable Machine Learning to Study Mechanical Properties of Two-Dimensional Hybrid Halide Perovskites
<p>This archive contains the in plane and out of plane Young's moduli (complete with respective VASP in and outputs) for 154 n=1 and 30 n>1 2D hybrid organic and inorganic perovskites. The data was used in the publication "Adapting Explainable Machine Learning to Study Mechanical Properties of Two-Dimensional Hybrid Halide Perovskites".</p> <p>Computational settings for the calculations were:</p> <p>Perdew-Burke-Ernzerhof (PBE) exchange-correlation with Tkatchenko-Scheffler (TS) van der Waals (vdW) corrections<br>Projector augmented-wave (PAW) method for the description of interactions between core and valence electrons.<br>A plane wave cutoff energy of 520 eV<br>A Γ-centered Monkhorst-Pack k-point mesh with a grid spacing of 2π × 0.040 Å−1 <br>Geometry optimizations were performed until energy and residual forces fell below 10−6 eV and 0.001 eV/ Å, respectively. <br><br></p>
Accompanying data for the paper "Accounting for the mechanical response of the cell membrane during the uptake of random nanoparticles"
<h2>Contributions</h2> <ul> <li><strong>Iaquinta Sarah</strong> did contribute to the first draft edition, the development of the theoretical background of the algorithms and their implementation</li> <li><strong>Khazaie Sharam</strong> did contribute to the revision and edition of the draft, and to the development of the theoretical background of the algorithms</li> <li><strong>Jacquemin Frédéric</strong> did contribute to the project management and to the revision of the article.</li> <li><strong>Fréour Sylvain</strong> did contribute to the project management and to the revision of the article.</li> </ul> <h2>Funding sources</h2> <p>i-Site NExT : Grant/Award Number: ANR-16-IDEX-0007, Région Pays de la Loire and CNRS (French National Centre for Scientific Research).</p> <h2>Data structure and information</h2> <ul> <li>code - <code>np_uptake source and data directory</code> <ul> <li>workflow - <code>scripts to reproduce figures</code></li> <li>np_uptake - <code>source code producing results and figures</code> <ul> <li>figures - <code>utility module to produce figures</code></li> <li>model - <code>see detailed description below</code></li> <li>metamodel_implementation - <code>see detailed description below</code></li> <li>sensitivity_analysis - <code>see detailed description below</code></li> </ul> </li> </ul> </li> </ul> <h3>Detailed description</h3> <h4>Abstract</h4> <p>In order to improve the efficiency of the delivery of cancer treatments to cancer cells, the cellular uptake of nanoparticles (NPs), used as drug delivery systems, is numerically investigated through a mechanical approach. The objective is to optimize the NP's mechanical and geometrical properties to enhance their entry into cancer cells while avoiding benign ones. In previous studies, these properties are modeled as constant during the process of cellular uptake. However, recent observations of the displacement of the membrane's constituents towards the region in the cell membrane where the uptake of the NPs takes place show that the mechanical properties of the membrane vary during this process. Reason for writing The important contribution of adhesion to the wrapping process is already well documented in literature. It is therefore crucial to model this parameter properly as the conclusions made with a constant adhesion model may not be accurate compared to reality. Methodology Based on the existing knowledge on the reaction of membrane constituents to interaction with NPs, a 3-parameter sigmoidal function, accounting for the delay, amplitude, and speed of the reaction, has been used to model the evolution of adhesion. A variance-based sensitivity analysis has then been performed in order to quantify the influence of these parameters on the outputs of the model. Results It was found that the introduction of a variable adhesion tends to alter the predictions of endocytosis of NPs. The contribution of the amplitude and delay is respectively 0.32 and 0.43 times as important as that of the NP's aspect ratio, which is the prominent parameter. The influence of the slope of the transition is the least important parameter and does not appear to contribute to endocytosis. Implications Hence, models of the cellular uptake of NPs should use a variable, instead of constant, adhesion in order a representative as possible of the behavior of the cell membrane. The predictions are different from those obtained using a model with constant adhesion.</p> <h4>Code</h4> <p>This repository is divided into 4 folders:</p> <ul> <li> <p><em>model</em>: contains the code used to compute the total variation of energy of the interface between a circular NP and a membrane by accounting for the mechanical accommodation of the latter. This folder also contains the routine to determine the final wrapping phase of the system.</p> </li> <li> <p><em>metamodel_implementation</em>: contains a script to check for the representativeness of the dataset used to create a metamodel, a script to create Kriging and PCE metamodels using the Openturns opensource library, and a routine to validate the metamodel that has just been created;</p> </li> <li> <p><em>sensitivity_analysis</em>: contains a script that allows to create samples based on the Kriging metamodels that have been created and exported as .pkl files in the metamodel folder. These samples are then used to the apply sensitivity algorithms. The user can choose among the various sensitivity algorithms provided by Openturns. For PCE metamodels, a routine is implemented to directly get the Sobol indices from the coefficients of the PCE metamodel. The indices can be plotted through plot routines;</p> </li> <li> <p><em>figures</em>: contains a utils script to display the graphs and save them as PNG files with consistency.</p> </li> </ul>
Figure 7 in Mechanism of northern pike invasion in the Columbia River Basin
Figure 7. Heat map showing probability of assignment for 77 individuals sampled from Lake Roosevelt to each population sampled in this study. Potential source populations within the Clark Fork River basin, Coeur d'Alene River basin and recently invaded areas are listed in an upstream to downstream order. While many individuals show an elevated assignment probability to Medicine-Cave Lakes (Coeur d'Alene River basin), 71 of the 77 fish had the highest probability of assignment to populations in the recently invaded waterbodies.
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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.