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10,561 results for “mechanics”
Dataset related to article "Glia-to-neuron transfer of miRNAs via extracellular vesicles: a new mechanism underlying inflammation-induced synaptic alterations"
<p>This record contains raw data related to article "Glia-to-neuron transfer of miRNAs via extracellular vesicles: a new mechanism underlying inflammation-induced synaptic alterations"</p> <p>Recent evidence indicates synaptic dysfunction as an early mechanism affected in neuroinflammatory diseases, such as multiple sclerosis, which are characterized by chronic microglia activation. However, the mode(s) of action of reactive microglia in causing synaptic defects are not fully understood. In this study, we show that inflammatory microglia produce extracellular vesicles (EVs) which are enriched in a set of miRNAs that regulate the expression of key synaptic proteins. Among them, miR-146a-5p, a microglia-specific miRNA not present in hippocampal neurons, controls the expression of presynaptic synaptotagmin1 (Syt1) and postsynaptic neuroligin1 (Nlg1), an adhesion protein which play a crucial role in dendritic spine formation and synaptic stability. Using a Renilla-based sensor, we provide formal proof that inflammatory EVs transfer their miR-146a-5p cargo to neuron. By western blot and immunofluorescence analysis we show that vesicular miR-146a-5p suppresses Syt1 and Nlg1 expression in receiving neurons. Microglia-to-neuron miR-146a-5p transfer and Syt1 and Nlg1 downregulation do not occur when EV-neuron contact is inhibited by cloaking vesicular phosphatidylserine residues and when neurons are exposed to EVs either depleted of miR-146a-5p, produced by pro-regenerative microglia, or storing inactive miR-146a-5p, produced by cells transfected with an anti-miR-146a-5p. Morphological analysis reveals that prolonged exposure to inflammatory EVs leads to significant decrease in dendritic spine density in hippocampal neurons in vivo and in primary culture, which is rescued in vitro by transfection of a miR-insensitive Nlg1 form. Dendritic spine loss is accompanied by a decrease in the density and strength of excitatory synapses, as indicated by reduced mEPSC frequency and amplitude. These findings link inflammatory microglia and enhanced EV production to loss of excitatory synapses, uncovering a previously unrecognized role for microglia-enriched miRNAs, released in association to EVs, in silencing of key synaptic genes.</p>
Mechanisms and drivers of belemnite body-size dynamics across the Pliensbachian-Toarcian crisis
<p>Supplementary material of the manuscript Rita et al., <em>Mechanisms and drivers of belemnite body-size dynamics across the Pliensbachian-Toarcian </em><em>crisis</em>, submited to Open Science Royal Society.</p> <p>Set of .ply files of CT scans of belemnite rostra. The first 27 files correspond to bed P925; the next 5 files correspond to P949; the next 18 correspond to P961; the next 5 correspond to P976; the next 38 specimens correspond to bed P982 and the last 35 files correspond to bed P984. The number of each file is the specimen number, as listed in the supplementary material of the article. For details on the scanning details or on the age of the specimens, please see the supplementary material of the article.</p> <p> </p> <p>The supplementary figures ("supplementary figures_ESM8.docx" file) and tables ("supplementary tables.xlsx" file) and the R script used for the statistical analysis ("supplement_rscript.docx" file) are also provided. </p> <p>For more details contact patricia.rita@fau.de.</p>
On the emergence mechanism of carrot sprites
<p>This dataset includes the input and output files for the paper: On the emergence mechanism of carrot sprites.</p> <p>Intput files:</p> <p># <strong>Plasma-chemistry, diffusion and mobility coefficients</strong></p> <p>sprite_chemistry_basic.txt</p> <p># <strong>Configuration files</strong></p> <p>sprite_3d_simp.cfg</p> <p>m_user.f90</p> <p>Output files:</p> <p>sprite_3d_*.silo</p>
Text-fig. 1. A. Location of the sites of Capo di Fiume, Palena and Pollenzo near Alba. B. Capo di Fiume stratigraphic section. Facies of coastal-transitional marine associations – a. Freshwater marsh and tidal creeks interval, b. Swamp interval, c1–c4. Facies of eustarine bay associations, d1–d6. Facies of open shelf marine associations. Symbols: "black star" – fossiliferous horizon with plant material studied here, 1. mottled grey to dark-brown marls and clayey marls, 2. fissile dark-grey marls and shaly marls, 3. limestones, 4. marly limestones and limey marls, 5. bio-lithoclastic calcarenites, 6. lime conglomerate, 7. massive muddy deposit produced by mass-flow mechanism, 8. diatomitic marls, 9. "terra rossa" soil (modified after Carnevale et al. 2011). in Feather Palm Foliage From The Messinian Of Italy (Capo Di Fiume, Palena And Pollenzo Near Alba) Within The Framework Of Northern Mediterranean Late Miocene Flora
Text-fig. 1. A. Location of the sites of Capo di Fiume, Palena and Pollenzo near Alba. B. Capo di Fiume stratigraphic section. Facies of coastal-transitional marine associations – a. Freshwater marsh and tidal creeks interval, b. Swamp interval, c1–c4. Facies of eustarine bay associations, d1–d6. Facies of open shelf marine associations. Symbols: "black star" – fossiliferous horizon with plant material studied here, 1. mottled grey to dark-brown marls and clayey marls, 2. fissile dark-grey marls and shaly marls, 3. limestones, 4. marly limestones and limey marls, 5. bio-lithoclastic calcarenites, 6. lime conglomerate, 7. massive muddy deposit produced by mass-flow mechanism, 8. diatomitic marls, 9. "terra rossa" soil (modified after Carnevale et al. 2011).
Fig. 3 in Adaptations, life-history traits and ecological mechanisms of parasites to survive extremes and environmental unpredictability in the face of climate change
Fig. 3. Flow chart outlining factors that can influence the response of parasites to climate change.
Image segmentation masks for curved arrows on molecular images from chemical reaction mechanism images
<p>The dataset presented herein is designed as a ground truth for image segmentation tasks focused on noise extraction in Optical Chemical Structure Recognition (OCSR) processes. It comprises 73 manually extracted and annotated images from real reaction mechanism images, along with 5320 synthetic molecular images generated using RDKit, each featuring computer-drawn curved arrows on random locations on the molecular image pertinent to their respective tasks. Curved arrows are prevalent in chemical reaction mechanism images and significantly impact the accuracy of molecular identity recognition. This dataset aims to enhance OCSR tasks by enabling the pretreatment of molecular images to remove noise, thereby improving molecular recognition accuracy.</p>
Fig. 1 in Understanding effects of floral products on bee parasites: Mechanisms, synergism, and ecological complexity
Fig. 1. Floral products may reduce bee disease via multiple mechanisms, including both direct and host-mediated effects; the influence of these effects on populationlevel parasite prevalence and host-parasite population dynamics will depend on environmental context. Numbers in diagram refer to corresponding sections of the text where topics are discussed.
Mechanical data in support of "Permeability Partitioning through the Brittle-to-Ductile Transition and its Implications for Supercritical Geothermal Reservoirs"
<p>This folder contains 4 files with the nechanicakl data produced during the study titled "Mechanical data in support of "Permeability Partitioning through the Brittle-to-Ductile Transition and its Implications for Supercritical Geothermal Reservoirs". Each file correspond to an experiment ran at a different temperature:</p> <p>LG200C.txt: Lanhelin Granite, T = 200C, strain rate 10-6, Initial length = 42.32 mm</p> <p>LG400C.txt: Lanhelin Granite, T = 400C, strain rate 10-6, Initial length = 41.68 mm</p> <p>LG600C.txt: Lanhelin Granite, T = 600C, strain rate 10-6, Initial length = 41.78 mm</p> <p>LG800C.txt: Lanhelin Granite, T = 800C, strain rate 10-6, Initial length = 41.77 mm</p> <p>All data files contain the following columns: time (s), confining pressure (bar), displacement (mm), vertical load (kN), temperature (C), upstream pore pressure (bar), downstream porepressure (bar).</p> <p> </p>
Source Data for the paper: "Quantum-classical simulations reveal the photoisomerization mechanism of a prototypical first-generation molecular motor"
<p>This dataset contains the raw data for the results shown in the paper.</p> <p>For each figure of the paper (main text), one directory with data file(s) is provided.</p>
Research data supporting "Mechanical properties of semi-regular lattices"
<p>Research data supporting "Mechanical properties of semi-regular lattices" published in Materials & Design in 2022. This dataset includes:</p> <ul> <li>Processed data plotted in Figure 11 (Fig11.xlsx).</li> <li>Processed data plotted in Figure 19 (Fig19.xlsx).</li> <li>Finite element models used to compute the elastic and shear moduli of each semi-regular lattice. These can be opened with the commercial software Abaqus CAE version 2023 (periodic_boundary_model.cae).</li> </ul>
Kinetic Insights into Glycerol Electrooxidation on Nickel: Current-Dependent Product Distribution and Reaction Mechanism
<p>## FILE DESCRIPTION<br>--------------<br>### Figure 1<br>- Fig1a.txt : Cyclic voltammetry of a Ni-based electrode in 0.1 M LiOH and 50 mM glycerol, measured at 5 mV s^-1. <br>- Fig1b.txt : IS spectra obtained at 1.50 V vs RHE in 0.1 M LiOH and 0.1 M LiOH + 50 mM glycerol.<br>- Fig1c.txt : Chronopotentiometric curves at 1 mA cm^-2, 3 mA cm^-2, 5 mA cm^-2 during 2 hours in 0.1 M LiOH + 50 mM glycerol.</p> <p>### Figure 2<br>- Fig2a.txt : Faradaic Efficiencies for Glycerol oxidation electrolysis at 1 mA cm^-2.<br>- Fig2b.txt : Faradaic Efficiencies for Glycerol oxidation electrolysis at 3 mA cm^-2.<br>- Fig2c.txt : Faradaic Efficiencies for Glycerol oxidation electrolysis at 5 mA cm^-2.<br>- Fig2d.txt : Faradaic Efficiencies for Glycerol oxidation electrolysis at 10 mA cm^-2.<br>- Fig2e.txt : Concentration of reaction products vs. time plots during glycerol oxidation (50 mM) in 0.1 M LiOH at 1 mA cm^-2.<br>- Fig2f.txt : Concentration of reaction products vs. time plots during glycerol oxidation (50 mM) in 0.1 M LiOH at 3 mA cm^-2.<br>- Fig2g.txt : Concentration of reaction products vs. time plots during glycerol oxidation (50 mM) in 0.1 M LiOH at 5 mA cm^-2.<br>- Fig2h.txt : Concentration of reaction products vs. time plots during glycerol oxidation (50 mM) in 0.1 M LiOH at 10 mA cm^-2.</p> <p>### Figure 3<br>- Fig3a.txt : Rate constant comparison at varying current densities applied for the formation of formate, glycolate, glycerate, tartronate and oxalate with its error bar.</p> <p>### Figure 4<br>- Fig4a.txt : Differential optical density (m∆O.D) taken at the maximum absorption peak as a function of potential applied in a solution of 0.1 M LiOH and LiOH 0.1 M + 50 mM glycerol in different regions (capacitive, NiOOH formation and GEOR and OER).<br>- Fig4b.txt : Rate law plot for glycerol and LiOH considering current density as a function of the normalized differential absorption (m∆O.D).</p> <p>### Figure S3<br>- FigS3.txt : X-ray diffraction (XRD) analysis </p> <p><br>### Figure S4<br>- FigS4a.txt : Cyclic Voltammetries in different electrolytes.</p> <p>### Figure S5<br>- FigS5a.txt : Faradaic Efficiencies for Glycerol oxidation electrolysis at 1.53 V vs RHE.<br>- FigS5b.txt : Faradaic Efficiencies for Glycerol oxidation electrolysis at 1.62 V vs RHE.<br>- FigS5c.txt : Faradaic Efficiencies for Glycerol oxidation electrolysis at 1.78 V vs RHE.</p> <p>### Figure S6<br>- FigS6a.txt : pH measurement near to the surface of the electrode and in the bulk of the solution every five minutes at 1 mA cm^-2.<br>- FigS6b.txt : pH measurement near to the surface of the electrode and in the bulk of the solution every five minutes at 3 mA cm^-2.<br>- FigS6c.txt : pH measurement near to the surface of the electrode and in the bulk of the solution every five minutes at 5 mA cm^-2.</p> <p>### Figure S7<br>- FigS7a.txt : UV-Vis absorbance spectra as a function of applied potentials in 0.1 M LiOH.<br>- FigS7b.txt : Chronoamperometry measurement without glycerol.<br>- FigS7c.txt : UV-Vis absorbance spectra as a function of applied potentials in 0.1 M LiOH + 50 mM glycerol.<br>- FigS8d.txt : Chronoamperometry measurement with glycerol.</p> <p>### Figure S8<br>- FigS8a.txt : Differential UV-Vis spectra of pre-catalytic (species formed in capacitive and NiOOH formation region) in 0.1 M LiOH.<br>- FigS8b.txt : Differential UV-Vis spectra of catalytic species (formed in OER and GEOR region) in 0.1 M LiOH.<br>- FigS8c.txt : Differential UV-Vis spectra of pre-catalytic species in 0.1 M LiOH + 50 mM glycerol. <br>- FigS8d.txt : Differential UV-Vis spectra of catalytic species in 0.1 M LiOH + 50 mM glycerol.<br>- FigS8e.txt : Steady state J-V curve with the onset for OER (Oxygen Evolution Reaction) and GEOR (Glycerol Electrooxidation Reaction) indicated.</p> <p>### Figure S9<br>- FigS9.txt : Rate law plot for glycerol and LiOH considering current density (j) as a function of the normalized differential absorption (m∆O.D).</p>
Mechanical Measurements of IntI1 Synaptic Complex Stability
<p>These data sets are associated with the publication "<em>The recombination efficiency of the bacterial integron depends on the mechanical stability of the synaptic complex</em>" Preprint available here: https://doi.org/10.1101/2024.04.09.588808</p> <p>Single-molecule force spectroscopy data of various IntI1 variants forming complexes with different attC-stite variants.</p> <p>ZIP files contain h5 data recoreded on a LUMICKS C-Trap device.</p> <ul> <li>IntI1wt.zip contains force spectroscopy data (indivdual h5 traces) of IntI1wt with aadA7bs attC sites</li> <li>IntI1Y312F-Alanine.zip contains force spectroscopy data (indivdual h5 traces) of IntI1Y312F-double Alanine mutant with aadA7bs attC sites</li> <li>IntI1Y312F-mEGFP.zip contains correlative force spectroscopy and confocal imaging data (h5 files) of IntI1Y312F-mEGFP binding and moving on single-stranded DNA</li> <li>IntI1Y312F-Truncated.zip contains force spectroscopy data (indivdual h5 traces) of IntI1Y312F-C-terminal truncation with aadA7bs attC sites</li> <li>IntI1Y312F_aadA7-bs.zip contains force spectroscopy data (indivdual h5 traces) of IntI1Y312F with aadA7bs attC sites</li> <li>IntI1Y312F_aadA7-ts.zip contains force spectroscopy data (indivdual h5 traces) of IntI1Y312F with aadA7ts attC sites</li> <li>IntI1Y312F_aadA7bs-L2.zip contains force spectroscopy data (indivdual h5 traces) of IntI1Y312F with aadA7bs-L2 hybrid attC sites</li> <li>IntI1Y312F_aadA7bs-VCRwt.zip contains force spectroscopy data (indivdual h5 traces) of IntI1Y312F with aadA7bs-VCRwt hybrid attC sites</li> <li>IntI1Y312F_L2.zip contains force spectroscopy data (indivdual h5 traces) of IntI1Y312F with L2 attC sites</li> <li>IntI1Y312F_VCRwt.zip contains force spectroscopy data (indivdual h5 traces) of IntI1Y312F with VCRwt attC sites</li> <li>IntI1Y312F_VCRinv.zip contains force spectroscopy data (indivdual h5 traces) of IntI1Y312F with VCRinv attC sites</li> </ul> <p>README.txt contains information about how to read the individual h5 files with e.g. a Python script.</p>
Data, Code & Supplementary Material for "Notes' order as a mechanism to recognize unknown calls: an experiment with artificial mobbing calls"
<p>Data set and R code used to analyse the output of a field experiment. This experiment tested the response of great tits and blue tits to either conspecific mobbing calls, artificial calls with their own call order, or artificial calls with a different call order. </p>
Supporting Information for Accelerating Combustion Mechanism Discovery with Automated Uncertainty, Sensitivity, Thermodynamics, and Kinetics Calculations
<p>Supplementary material to accompany the manuscript "Accelerating Combustion Mechanism Discovery with Automated Uncertainty, Sensitivity, Thermodynamics, and Kinetics Calculations" by Sevy Harris and Richard H West.</p> <ul> <li>The software (mostly Python scripts) is in autoscience_workflow.zip. </li> <li>DFT results (Gaussian log files, Arkane input files, Arkane output files) for all species and reactions are in dft.zip</li> <li>RMG-built detailed kinetic models are in mechanisms.zip </li> <li>Additional plots and results (as described in the manuscript) are in supporting_information.pdf</li> </ul>
Physiological mechanisms and life history trade-offs shape in-tissue correlations of an essential micronutrient
<p>The Matlab code and dataset for the manuscript "Physiological mechanisms and life history trade-offs shape in-tissue correlations of an essential micronutrient". The dataset is packed in the ZIP archive 'Dataset_EjsmondTodisco_etal.zip' with variable description in the Matlab code file EjsmondTodisco_etal.m. To run the program, place the files EjsmondTodisco_etal.m and Fun_PlotResults.m in a catalog. The results are stored in two catalogs: 'ThReabsorptionAndSecretion' - modeling the rate of thiamine loss with processes of active reabsorption and secretion; and 'ThReabsorptionOnly' - modeling the rate of thiamine loss with the process of active reabsorption only. The ThReabsorptionAndSecretion catalog contains data for three life history types: iteroparity (baseline model), semelparity, and determinate growth (constant mass of somatic tissues in adults). For details see the manuscript by Ejsmond, Todisco et al.</p>
Accompanying dataset for the paper "Mesh Density and Geodesic Tortuosity in Planar Triangular Tesselations Devoted to Fracture Mechanics"
<h2>Contributions</h2> <ul> <li>Author #1 is the major contributor to the paper writing. Author #1 has created most of the Figures in the paper and has provided all the results concerning the geodesic tortuosity of planar triangular meshes.</li> <li>Author #2 and Author #3 have provided the results concerning the density of planar triangular meshes.</li> </ul> <h2>Funding sources</h2> <ul> <li>This work was funded by the French Institute for Radiation Protection and Nuclear Safety (IRSN) and the University of Montpellier, France.</li> </ul> <h2>Data structure and information</h2> <p>All the results and figures presented in the paper have been obtained with a python script available in the <code>workflows</code> folder. </p> <p>Data files processed by that script are provided in the <code>data</code> folder. The pickle files <code>t_{nb}.pkl</code> inside the <code>data/pkl</code> folder contain lists of tortuosity values computed on a <code>gmsh</code> mesh for several paths containing various number of edges (<code>nb</code>).</p> <p><code>pkl</code>files are produced via a function call to <code>main.py:comp_real_tortuosities(nb)</code></p> <h2>Data structure and information</h2> <ul> <li><code>workflows/</code> - folder containing plotting scripts<ul> <li><code>reproduce.sh</code> - bash script launching python and compressing figures</li> <li><code>main.py</code> - python script for figure creation.</li> <li><code>/utils</code> - folder containing additional python scripts for figures creation</li> <li><code>/figures</code> - folder containing the figures produced by the python script</li> </ul> </li> <li><code>data/</code> - data folder<ul> <li><code>gmsh</code> - folder containing mesh in gmsh information</li> <li><code>pkl</code> - folder containing the pickled vectors "t_{nb}.pkl".</li> </ul> </li> </ul> <h2>Paper Description</h2> <p>In fracture mechanics, the mesh sensitivity is a key issue. It is particularly true concerning cohesive volumetric finite element methods in which the crack path and the overall behavior are respectively influenced by the mesh topology and the mesh density. Poisson-Delaunay tessellations parameters, including the edge length distributions, were widely studied in the literature but very few works concern the mesh density and topology in Delaunay type meshes suitable for finite element simulations, which is of crucial interest for practical use.Starting from previous results concerning Poisson-Delaunay tessellations and studying in detail the Lloyd relaxation algorithm, we propose estimates for the probability density functions of the edge length and triangle top angles sets. These estimates depend both on the intensity of the underlying point process and on an efficiency index associated to the global quality of the mesh. The global and local accuracies of these estimates are checked for various standard mesh generators. Finally the mesh density and geodesic tortuosity are estimated for standard random or structured triangular meshes typically used in finite element simulations.These results provide practical formulas to estimate bias introduced by the mesh density and topology onthe results of cohesive-volumetric finite element simulations.</p>
Supporting data and code for: Myzus persicae resistance to neonicotinoids - unravelling the contribution of different mechanisms to phenotype
<p>This is the first release of the final data and code for the article accepted for publication in <em>Pest Management Science</em> journal. It contains the necessary scripts to produce most of the analyses and figures of the manuscript. All the necessary data can be found in the 'data' folder.</p>
Data for the conference poster "TiAl6V4 bistable mechanism produced by Laser Powder Bed Fusion"
<p>The dataset contains raw data for conference poster "TiAl6V4 bistable mechanism produced by Laser Powder Bed Fusion" presented at the 9th Metal Additive Manufacturing Conference.</p>
Raw data for Role of molecular damage in crack initiation mechanisms of tough elastomers, PNAS 2024 Vol. 121 e2410515121
<p>This the raw data for figures 1-5 of the paper. the images and the data sets in csv format</p>
Revisiting lactococcal abortive infection-like antiphage systems: Diversity, structures and mechanisms
<p><em><span>Lactococcus</span></em><span> spp. are cornerstone species in the production of fermented dairy products such as cheese. However, the non-sterile dairy environment exposes these bacteria to phage infection, leading to potential environmental and economic losses. To counteract such phage threats, bacteria have evolved multiple defence mechanisms, including abortive infection (Abi) systems, of which many of the first (AbiA to AbiZ) were discovered in <em>Lactococcus</em>. Recent discoveries have expanded the list of Abi-like systems experimentally confirmed in <em>Lactococcus</em> species. In this review, we examine and revisit the antiphage activity spectrum, the interference with the phage lytic cycle, and the emergence of phage escape mutants associated with these systems. Since many of these systems were identified before the development of advanced functional and structural prediction tools, their domains and mechanisms have largely remained unexplored. Here, we group certain Abi-like systems based on structural superimposition and use predicted domain information to hypothesize their potential mechanisms. Additionally, we discuss established mechanisms for some Abi-like systems. Our findings confirm that the co-evolution of <em>Lactococcus</em> species with their phages, driven by their extensive application in dairy fermentation, has led to the selection of a diverse array of phage defence mechanisms.</span></p>
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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.