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10,561 results for “mechanics”
Analysis of Flood Mechanisms in the Delaware River Basin in a Warming Climate
<p>The dataset is used by a study focused on analyzing flood hazards in future climates and understanding the underlying mechanisms driving changes in floods across the Delaware River Basin. The dataset encompasses the following components:</p> <p>1. Historical Flood events (<em>AMF/hist/</em>): flood events for each HUC8 basin of the Delaware River Basin from water year (WY) 1980 to 2018. The flood events were simulated using the Distributed Hydrology Soil Vegetation Model (DHSVM), a process-based hydrological model. Each flood event is defined as the annual maximum daily flow within the respective water year, which spans from October 1 through September 30. The dataset is organized into two columns, where the first column represents the year, and the second column represents the discharge in cubic meters per second.</p> <p>2. Future flood events (<em>AMF/GCMs/</em>): DHSVM simulated flood events for each HUC8 basin of the Delaware River and each GCM for two distinct periods: the baseline period (WY 1970–1999) and the future period (WY 2070–2099). Future climates in the region are represented by 10 downscaled General Circulation Model (GCM) climate projections.The dataset is organized into two columns, where the first column represents the year, and the second column represents the discharge in cubic meters per second.</p> <p>3. Hydrometeorological Variables (<em>daily_states/</em>): daily-scale continuous simulations of various hydrometeorological variables for historical climate (<em>daily_states/hist) </em>and under GCM scenarios (<em>daily_states/GCMs)</em>. These data were used to analyze the generating mechanisms of each flood event within the HUC8 basins of the Delaware River Basin. The variables include soil moisture (SM), precipitation (PPT), snowfall, snow water equivalent (swq), and snowmelt (melt). These variables were derived from the simulation outputs of DHSVM and were aggregated from the grid cell levels to the HUC8 basin level by calculating daily averages over each basin.The files are stored in the .mat (Matlab data) format and consist of four dimensions, namely huc8 basins, GCMs, periods (baseline and future), and days. Specifically, the dimensions are 10x10x2x10957.</p>
Comparative transcriptomic analysis reveals coordinated mechanisms of different genotypes of common vetch in response to Al stress
<p><strong>Supplementary Table</strong></p>
Plant productivity response to inter- and intra-symbiont diversity: mechanisms, manifestations, and meta-analyses
<p>Symbiont diversity can have large effects on plant growth but the mechanisms generating this relationship remain opaque. We identify three potential mechanisms underlying symbiont diversity-plant productivity relationships: provisioning with complementary resources, differential impact of symbionts of varying quality, and interference between symbionts. We connect these mechanisms to descriptive representations of plant responses to symbiont diversity, develop analytical tests differentiating these patterns, and test them using meta-analysis. We find generally positive symbiont diversity-plant productivity relationships, with relationship strength varying with symbiont type. Inoculation with symbionts from different guilds (e.g. mycorrhizal fungi and rhizobia) yields strongly positive relationships, consistent with complementary benefits from functionally distinct symbionts. In contrast, inoculation with symbionts from the same guild yields weak relationships, with co-inoculation not consistently generating greater growth than the best individual symbiont, consistent with sampling effects. The statistical approaches we outline, along with our conceptual framework, can be used to further explore plant productivity and community responses to symbiont diversity, and we identify critical needs for additional research to explore context-dependency in these relationships.</p>
Dataset - Fast mechanical and biochemical cell wall dynamics underlie plant nutation
<p>Dataset and codes (Python and Matlab) used to produce the figures in the article "Fast mechanical and biochemical cell wall dynamics underlie plant nutation".</p>
Mechanical transmission of Dengue Virus by Aedes aegypti may influence disease transmission dynamics during outbreaks data
<strong><span>Summary</span></strong> <p class="MsoNormal"><em><span>Background</span></em><span>: Dengue virus outbreaks are increasing in number and severity worldwide. Viral transmission is assumed to require a minimum time period of viral replication within the mosquito midgut. It is unknown if alternative transmission periods not requiring replication are possible.</span></p> <p class="MsoNormal"><em><span>Methods</span></em><span>: We used a mouse model of dengue virus transmission to investigate the potential of mechanical transmission of dengue virus. We investigated minimal viral titres necessary for development of symptoms in bitten mice and used resulting parameters to inform a new model of dengue virus transmission within a susceptible population.</span></p> <p class="MsoNormal"><em><span>Findings</span></em><span>: Naïve mice bitten by mosquitoes immediately after they took partial blood meals from dengue infected mice showed symptoms of dengue virus, followed by mortality. Incorporation of mechanical transmission into mathematical models of dengue virus transmission suggests that this supplemental transmission route could result in larger outbreaks which peak sooner.</span></p> <p class="MsoNormal"><em><span>Interpretation</span></em><span>: The potential of dengue transmission routes independent of midgut viral replication has implications for vector control strategies that target mosquito lifespan and suggest the possibility of similar mechanical transmission routes in other disease-carrying mosquitoes.</span></p>
Comparative Study of Molecular Mechanics Force Fields for β-peptidic Foldamers: Folding and Self-Association
<p>Molecular dynamics simulation input files and Python scripts used for preparing the runs and analyzing the trajectories.</p>
Comparing effects of food mechanical properties on oral processing behaviors in two sympatric lemur species - Dataset
<p>Dataset for maximal random slope mixed models from manuscript "Comparing effects of food mechanical properties on oral processing behaviors in two sympatric lemur species". Column headers are described in the article and the key tab of the excel. </p>
Supporting data to Heterogeneity in spatiotemporal variability of High Mountain Asia's runoff and its underlying mechanisms
<p>This dataset includes (1) the boundary of 12 basins over the southern High Mountain Asia, (2) their climate and catchment properties, (3) significance of interannual, interdecadal and multidecadal variability of runoff and corresponding climate variables, and (4) the decomposed timeseries of runoff and its related atmospheric drivers. Please see the publication for more details.</p>
Supporting data to Heterogeneity in spatiotemporal variability of High Mountain Asia's runoff and its underlying mechanisms
<p>This dataset includes (1) the boundary of 12 basins over the southern High Mountain Asia, (2) their climate and catchment properties, (3) significance of interannual, interdecadal and multidecadal variability of runoff and corresponding climate variables, and (4) the decomposed timeseries of runoff and its related atmospheric drivers. Please see the publication for more details.</p>
Code and Datasets for "A simple mechanism for collective decision-making in the absence of payoff information"
<p>This repository contains R code and datasets used for analyses in the paper:</p> <p>"A simple mechanism for collective decision-making in the absence of payoff information"</p> <p>Published in <em>Proceedings of the National Academy of Sciences of the United States of America</em> (PNAS) in 2023</p> <p>by Daniele Carlesso, Justin M. McNab, Christopher J. Lustri, Simon Garnier, and Chris. R. Reid.</p> <pre><code>✓ Ensure that all files are in the same folder for the code to run properly. ✓ the repository also includes a summary HTML file for easier visualisation. </code></pre> <p>Datasets:</p> <pre><code>• chain_growth.csv • cumsum_df.csv • growth_data.csv • GrowthMP.csv • JL_chaingrowth.csv • joining_distance.csv • leave_10.csv • leaving_positions.csv • timespent.csv • traffic_mean.csv </code></pre> <p>Code:</p> <pre><code>• Code.Rmd </code></pre> <p>Markdown summary:</p> <pre><code>• Code.html </code></pre>
Roger Penrose Why Quantum Mechanics Is an Inconsistent Theory
<p>Roger Penrose Why Quantum Mechanics Is an Inconsistent Theory</p>
Data for: Mechanisms that can cause population decline under heavily skewed male-biased adult sex ratios
<ol> <li><span>While adult sex ratio (ASR) is a crucial component for population management, there is still a limited understanding of how its fluctuation affects population dynamics. To demonstrate mechanisms that hinder population growth under a biased ASR, we examined changes in reproductive success with ASR using a decapod crustacean exposed to female-selective harvesting. </span></li> <li> <span>We examined the effect of ASR on the spawning</span><span> success </span><span>of females. A laboratory experiment showed that the number of eggs carried by females decreased as the proportion of males in the mating groups increased. Although the same result was not observed in data collected over 25 years in the wild, the negative effect of ASR was suggested when success in carrying eggs was considered as a spawning success. These results indicate that a surplus of males results in females failing to carry eggs, probably due to sexual coercion, and</span> <span>the negative effect of ASR can be detected at the population level only when the bias increases because failure in spawning success occurs in part of population.</span> </li> <li><span>We experimentally examined how male-biased sex ratios affected the maintenance of genetic diversity in a population. The diversity of paternity in a clutch increased with the number of candidate fathers. However, over 50% of a clutch was fertilised by a single male regardless of the sex ratio, and the degree of diversity was less than half of the highest diversity expected in each mating group. </span></li> <li><span>We also experimentally examined the mating ability of males during the breeding season. The experiment showed that multiple mating by males could not compensate for the risk that their genotypes would be lost when multiple males competed for one female. These results suggest that a male-biased ASR could trigger a decline of genetic diversity in a population.</span></li> <li><span>We show that ASR skewed by female-selective harvesting decreases reproductive success not only of males that have few mating opportunities but also of females. We discuss that we may still underestimate the significance of ASR on population persistence due to the difficulty of revealing the effect of ASR.</span></li> </ol>
The weaken-fill-repair model for cell budding: Linking cell wall biosynthesis with mechanics
<p>The interplay between cellular mechanics and other biochemical processes leading to the cell cycle is poorly understood. Here, we propose a quantitative model of the mechanism of cell budding, particularly for Saccharomyces cerevisiae, as a ''weaken-fill-repair'' process. This model links Newtonian mechanics over the cell wall with biochemical processes that change the mechanical properties of the wall. Our model shows that: (1) The oscillatory behavior in the size of the mother compartment during cell division, as observed experimentally, is an inevitable consequence of the budding mechanism; (2) The asymmetry of cell division is necessary for the daughter cell to maintain mechanical stiffness; (3) Although different aspects of a cell are strictly constrained and intricately interconnected, the budding process is governed by a single reduced parameter that, when at an appropriate value, can automatically achieve homeostasis. Our quantitative model of the evolution of cell walls and their impact on cell division could provide valuable insights into cell morphology from a system perspective. This knowledge could be instrumental in developing effective antimicrobial treatments against microorganisms with cell walls and even in building synthetic cells.</p>
Migration of mechanical perturbations estimated by seismic coda wave interferometry during the 2018 pre-eruptive period at Kīlauea volcano, Hawaii : Noise Cross-correlation Functions, Seismic catalog, and GNSS data
<p>ARCHIVE_NCFs_KILAUEA_2018.zip : Compress folder with (1) the daily noise cross-correlation functions (in MSEED format) of the station pairs used in the paper and (2) the one hour noise cross-correlation functions (in H5 format) of the station pairs used in the figure 9 of the paper.</p> <p>Code_Data_HVO.ipynb : Code to download the seismic data, available on IRIS, used in this paper.</p> <p>GPS_data_AHUP.zip : Compress folder with the daily GPS data of the station AHUP used in the paper [Year, Month, Day, Day_of_the_year, Second_of_the_day, East_comp(mm), North_comp(mm), Vertical_comp(mm), Sig_East_comp, Sig_North_comp, Sig_Vertical_comp].</p> <p>Radial_tilt_UWD.txt : Daily radial tilt measurement of the tiltmeter UWD [Year, Month, Day, Radial_tilt(µrad)].</p> <p>Seismic_stations_Kilauea.txt : Name code and location of the seismic stations used in the paper [Station_code, Longitude, Latitude].</p> <p>Seismicity_Catalog_Kilauea_2018_USGS.txt : Seismic catalog from USGS used in the paper [Date_Time, Latitude, Longitude, Depth, Magnitude].</p>
The Collective Burst Mechanism in Liquid Water
<p>This dataset contains essential data for reproducing results in the Paper</p> <p>"The Collective Burst Mechanism in Liquid Water".</p> <p>These are the files</p> <p>Nature_data_original.zip</p> <p>original_dp_space_1.mat (Dipole time series)</p> <p>original_hh_space_1.mat (HH vector time series)</p> <p> </p> <p>Nature_data_original.zip contains files </p> <p>the defect_*.mat which are time series of the defects for 1019 molecule used in the simulation.</p> <p>each number corresponds to 500ps of the full 2ns trajectory.</p> <p> </p> <p>The files gd_angle_vs_time_time_dp*.mat/gd_angle_vs_time_time_hh*.mat/ report on jumps detected in </p> <p>each of the 500ps blocks of the full 2ns trajectory </p> <p>Also contained is the code used for generating the data. See the Readme.txt file for more information</p> <p> </p> <p> </p> <p> </p> <p> </p> <p> </p>
Mapping the epigenomic landscape of human monocytes following innate immune activation reveals context-specific mechanisms driving endotoxin tolerance
<p><strong>Processed datasets for publication at <em>BMC Genomics</em>.</strong></p> <p>We exposed human primary monocytes from healthy donors (n=6) to interferon-γ or differing combinations of endotoxin (lipopolysaccharide), including acute response (2hr LPS; LPS2) and two models of endotoxin tolerance: repeated stimulations (6+6hr; LPS6:6) and prolonged exposure to endotoxin (24hr LPS; LPS24). Another subset of monocytes was left untreated (naïve; UT). We performed total RNA-seq and ATAC-seq for monocytes across these treatment conditions.</p> <p>The following processed datasets include the raw and normalised count data for each gene or ATAC peak, and the bedGraph and bigWig format for genome-wide signal data. [ bigWig files for RNA-seq (monocytes_*_mean.bw); bigWig files for ATAC-seq (Monocyte_ATAC_*_mean_normalised.by.1/size.factor.bw); bedgraph files for eRNA visualization (*RPKM_FR.bedgraph.gz); raw and normalised count files for ATAC-seq and RNA-seq data (Monocyte.featureCounts_RNAseq.txt.gz; Monocyte_filtered_log2.normalized_RNAseq_counts.txt.gz; Meta.file.txt.gz; Monocyte_raw.counts_ATACseq.txt.gz.).]</p> <p><strong>Data curator:</strong></p> <p>Ping Zhang</p> <p> </p>
Data from: Active-feedback quantum control of an integrated, low-frequency mechanical resonator
<p>Source data for Figures.</p>
Data from: Transcriptome analysis reveals the mechanism underlying rapid changes in the early phase brain of bi-directional sex change in Trimma okinawae
<p>Teleost fish exhibit remarkable sexual plasticity and display divergent developmental systems including hermaphroditism. One of the more fascinating model systems of sexual plasticity is socially controlled sex change, which is often observed in coral reef fish. The Okinawa rubble goby, <em>Trimma okinawae</em>, is a bi-directional sex change fish that can rapidly change its sex in both directions depending on social circumstances. Although behavioral and neuro-endocrinal sex change occurs within an hour and is believed to trigger gonadal changes, the underlying mechanisms remain poorly understood. In this study, we conducted a de novo transcriptome analysis of the <em>T. okinawae</em> brain and identified genes that were differentially expressed between the sexes and genes that were immediately controlled by social stimulation causing a sex change. We found that a larger number of genes are regulated during the male-to-female transition compared with a change from female to male. Several genes showed concordant expression shifts regardless of the sex change direction. Furthermore, some were associated with histone modification in nerve cells and regulated in the same direction. Overall, we identified genes that regulate the rapid behavioral and neuroendocrinal control of sex change and provide insight into the mechanism of sexual plasticity in teleost fish.</p>
Expulsion mechanism of the substrate-translocating subunit in ECF transporters
<p>Data for coarse-grained molecular dynamics simulations (final snapshots, cleaned trajectories, starting structure/simulation parameters) described in "Expulsion mechanism of the substrate-translocating subunit in ECF transporters".</p>
Data set for "Neural mechanisms underlying uninstructed orofacial movements during reward-based learning tasks"
<p>Data set for Li, Nakano, et al. (2023) Neural mechanisms underlying uninstructed orofacial movements during reward-based learning behaviors. Current Biology, https://doi.org/10.1016/j.cub.2023.07.013</p> <p><br> The file "Li_Nakano_et_al_detaset.zip" (~45.4 GB) is a compressed version of the "Li_Nakano_et_al_detaset" folder. The uncompressed folder (~76.4 GB) houses the data and some analytical codes used in the study. Upon extraction, the folder reveals two subfolders, "Raw data" and "Source data," and a 'README' text file providing further instructions or information.</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.