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10,561 results for “mechanics”
Figure 48 in Diverse mechanisms of feeding and movement in Cyclorrhaphan larvae (Diptera)
Figure 48. Acidia cognata, preserved larva, lateral view, head to the right, length 5.7 mm.
Simple muscle-lever systems are not so simple: The need for dynamic analyses to predict lever mechanics that maximize speed
<p><span>Here we argue that quasi-static analyses are insufficient to predict the speed of an organism from its skeletal mechanics alone (i.e. lever arm mechanics). Using a musculoskeletal numerical model we specifically demonstrate that 1) a single lever morphology can produce a range of output velocities, and 2) a single output velocity can be produced by a drastically different set of lever morphologies. These two sets of simulations quantitatively demonstrate that it is incorrect to assume a one-to-one relationship between lever arm morphology and organism maximum velocity. We then use a statistical analysis to quantify what parameters are determining output velocity, and find that muscle physiology, geometry, and limb mass are all extremely important. Lastly we argue that the functional output of a simple lever is dependent on the dynamic interaction of two opposing factors: those decreasing velocity at low mechanical advantage (low torque and muscle work) and those decreasing velocity at high mechanical advantage (muscle force-velocity effects). These dynamic effects are not accounted for in static analyses and are inconsistent with a force-velocity tradeoff in lever systems.</span> <span>Therefore, we advocate for a dynamic, integrative approach that takes these factors into account when analyzing changes in skeletal levers.</span></p>
Mechanisms of male-male interference during dispersal of orchid pollen
<p>Siring success of flowering plants depends on the fates of male gametophytes, which compete for access to stigmas, stylar resources and ovules. Although rarely considered, pollen may often compete during dispersal, affecting the processes required for export to stigmas; pollen pickup, transport and deposition. We quantified dispersal interference by tracking bee dispersal of stained <em>Anacamptis morio </em>(Orchidaceae) pollen from individual donor flowers and inferred the affected dispersal mechanisms based on the fit of a process-based model. During individual trials, all recipient flowers were either emasculated, precluding interference with donor pollen, or intact, adding potentially interfering pollen to the pollinator. The presence of competing pollinaria on bees reduced pickup of additional pollinaria, doubled the overall proportion of lost donor pollen and reduced total pollen export by 27%. Interference specifically increased loss of donor pollen between successive flower visits and variation in deposition among trials, and likely also reduced pollen contact with stigmas and pollen deposition when contact occurred. Thus, by altering pollen removal, transport and deposition, male-male interference during pollen dispersal can significantly, and perhaps commonly, limit plant siring success.</p>
Data for "Elephant Genomes Reveal Insights into Differences in Disease Defense Mechanisms between Species".
<p>Data for "Elephant Genomes Reveal Insights into Differences in Disease Defense Mechanisms between Species".</p>
Interspecific social dominance networks reveal mechanisms promoting coexistence in sympatric charrs in Hokkaido, Japan
<p>1. Coexistence of species requires equalizing mechanisms that minimize fitness differences, which are balanced by stabilizing mechanisms that enhance negative intraspecific interactions versus interspecific ones. Here, we develop a simple theoretical framework that allows measuring the relative strength of intraspecific versus interspecific competition in dominance hierarchies. We use it to evaluate mechanisms promoting coexistence between congeneric charrs that compete for foraging positions, which strongly influence density-dependent growth and survival.</p> <p>2. Agonistic interactions (n = 761) among 71 Dolly Varden Salvelinus malma and whitespotted charr S. leucomaenis were measured by snorkeling in two pools in the sympatric zone of a Hokkaido stream during two summers. Interspecific dominance hierarchies, analyzed using three methods, were closely correlated with fish length but the species treated each other equally. Ranks for the most dominant fish in each pool, determined directly by knockout experiments, were also virtually identical to ranks by length.</p> <p>3. Similarly, exponential random graph modeling of the social networks provided no evidence that either species was dominant over the other. Instead, larger fish were more likely to win contests, especially over fish of the next lower ranks.</p> <p>4. These results demonstrated that the two species were nearly ecological equivalents in accessing key resources in this sympatric zone. Nearly identical growth and stable densities over 4 years further supported this inference, although Dolly Varden were a minority (29% of the assemblage), a sign of some fitness difference.</p> <p>5. Detailed foraging observations coupled with two concurrent studies revealed an effective stabilizing mechanism. Dolly Varden shifted to feeding directly from the benthos when drifting invertebrates declined, a behavior enhanced by morphological character displacement, thereby partitioning food resources and enhancing intraspecific competition while avoiding agonistic encounters with whitespotted charr.</p> <p>6. The plurality of evidence indicates that fitness differences between these ecologically equivalent species are small in this local assemblage, and balanced by resource partitioning, a modest stabilizing mechanism that promotes coexistence. The theoretical framework presented here is a useful tool to evaluate the strength of interspecific versus intraspecific competition, which combined with information on tradeoffs in ecological performance can contribute to a mechanistic understanding of species coexistence. 26-Oct-2020</p>
Input data for performing chemistry coupled PALM model system 6.0 simulations with different chemical mechanisms
<p>The data presented here comprised of input files that have been used to run chemistry coupled PALM model system 6.0 simulations for the article entitled "Development of an atmospheric chemistry model coupled to the PALM model system 6.0: Implementation and first applications". In this article we describe the implementation of an online-coupled gas-phase chemistry model in the turbulence resolving PALM model system 6.0.</p> <p>List of the input data required for performing chemistry model simulations with different chemical mechanisms is given below. A text file comprised of measured concentrations of NO, NO<sub>2</sub> and O<sub>3</sub> is also added.</p> <ol> <li>Fortran parameter (PARIN) files for four mechanisms and one meteorology-only simulation.</li> <li>Static file</li> <li>Dynamic file</li> <li>Two files (shortwave and longwave input data) for rrtmg radiation model</li> <li>Observation from two air quality stations in Berlin, Germany .</li> <li>PALM model source code revision 4450 (palm_trunk_rev-4450.tar.gz)</li> <li>PALM model source code revision 4601 (palm_trunk_rev-4601.tar.gz)</li> </ol> <p>The PALM model system 6.0 revision 4451 and 4601 (for chemistry flux profiles only) have been used for these simulations. </p>
DFT Calculated xyz and log Files in Support of "Reaction Mechanism of Pd-catalyzed "CO-free" Carbonylation Reaction Uncovered by In situ Spectroscopy: The Formyl Mechanism"
<p>Theoretically calculated xyz and log files for hydrogen, carbon monoxide, carbon dioxide, methane, methanol, methyl formate, butene, methyl pentanoate and multiple Pd-dtbpx complexes (dtbpx = 1,2-Bis(di-<em>tert</em>-butylphosphino)xylene) which catalyze the addition of HCOOMe/CO onto butene to form methyl pentanoate.</p> <p>All quantum chemical simulations were performed using the Gaussian16 software. The ground state equilibrium structures and electronic properties were obtained at the density functional (DFT) level of theory utilizing the B3LYP XC functional.The def2-SVP basis set as well as the respective core potentials were applied for all atoms. A subsequent vibrational analysis was carried out for each optimized ground state structure to verify that a minimum on the potential energy (hyper‑)surface (PES) was obtained. All calculations were performed including D3 dispersion correction with Becke-Johnson damping.</p> <p>An analogous computational setup was applied for the optimization of transition states (TSs), while an initial guess in the vicinity of the saddle point was at first obtained via the Nudged Elastic Band (NEB) method as implemented in pysisyphus with xtb.<sup> </sup>Thereafter, the TSs were obtained in Gaussian16 via the Berny algorithm, followed by a vibrational analysis to verify that a first-order saddle point on the PES was obtained.</p>
Molecular geometries and energies from quantum mechanical calculations and small molecule force field evaluations.
<p>Force fields are used in a wide variety of contexts for classical molecular simulation, including studies on protein-ligand binding, membrane permeation, and thermophysical property prediction.<br> The quality of these studies relies on the quality of the force fields used to represent the systems. <br> Focusing on small molecules of fewer than 50 heavy atoms, this data compares nine force fields: GAFF, GAFF2, MMFF94, MMFF94S, OPLS3e, SMIRNOFF99Frosst, and the Open Force Field Parsley, versions 1.0, 1.1, and 1.2.<br> On a dataset comprising 22,675 molecular structures of 3,271 molecules, we analyzed force field-optimized geometries and conformer energies compared to reference quantum mechanical (QM) data.<br> <br> The data was created using scripts of the <a href="https://github.com/MobleyLab/benchmarkff/commit/fa45247aa9867f504c02eb6f62d8459a94a0a936">benchmarkff github repository</a>.</p> <p>A corresponding manuscript is submitted, a preprint is available on ChemRxiv:<br> <a href="https://doi.org/10.26434/chemrxiv.12551867.v2 ">Lim, Victoria T.; Hahn, David F.; Tresadern, Gary; Bayly, Christopher I.; Mobley, David (2020): Benchmark Assessment of Molecular Geometries and Energies from Small Molecule Force Fields. ChemRxiv. Preprint</a></p> <p>Read below or the file README.md for further information and description of the content:</p> <pre><code class="language-markdown"># README Version: 04 Nov 2020 For Python scripts that are NOT found in these directories, please check the [BenchmarkFF Github repo](https://github.com/MobleyLab/benchmarkff/tree/master/tools). ## Procedure 1. Prep OPLS3e file for analysis: standardize format by OpenEye in case of differences and convert from kJ/mol to kcal/mol. ``` cd prep python convert_extension.py -i opls3e_minimized.sd -o opls3e.sdf ``` 2. Remove mols that couldn't parameterize by ALL FFs. ``` python get_by_tag.py -i opls3e.sdf -s "SMILES QCArchive" -list trim3.txt -o trim3_full_opls3e.sdf ``` 3. Run analysis. ``` conda activate parsley # calc ddE, RMSD, and TFD distributions python compare_ffs.py -i match.in -t 'SMILES QCArchive' --plot > metrics.out # match_minima, only in 01_analysis_all and 02_analysis_all_smaller_cutoff python match_minima.py -i match.in --plot --cutoff 1.0 --readpickle # look at specific subsets, only in 01_analysis_all python color_by_moiety.py -i match.in -p metrics.pickle -s N-N.dat azetidine.dat octahydrotetracene.dat -o scatter_tfd_3_ # look at outliers,only in 01_analysis_all and 02_analysis_all_smaller_cutoff python tailed_parameters.py -i refdata_trim_overlap_full_openff_unconstrained-1.2.0.sdf -f <offxml file> --metric 'TFD' --cutoff 0.12 --tag "TFD to trim_overlap_full_qcarchive.sdf" --tag_smiles "SMILES QCArchive" > output_tfd.dat ``` ## Brief description of contents * High level: ``` . ├── 00_prep │ ├── convert_extension.py │ ├── opls3e_minimized.sd OPLS3e minimized structures from Schrodinger Maestro │ ├── opls3e.sdf standardized through OpenEye tools │ ├── opt_openff*.sdf OpenFF minimized conformations ├── 01_analysis_all compare all ffs (qm, GAFF(2), MMFF94(S), Smirnoff, OpenFF-X.X, OPLS3e) ├── 02_analysis_all_smaller_cutoff compare all ffs (qm, GAFF(2), MMFF94(S), Smirnoff, OpenFF-X.X, OPLS3e) with a smaller cutoff of .3 for match_minima ├── 03_analysis_latest_ffs compare only the latest versions of ffs (qm, GAFF2, MMFF94S, OpenFF-1.2, OPLS3e) ├── 04_analysis_openff_only compare only OpenFF ffs (qm, Smirnoff, OpenFF-X.X) └── README.md ``` * Inside an output directory: ``` YY_analysis_* various output files of above mentioned scripts, some are listed and described below: ├── bar*.png parameter coverage bar plots ├── ddE.dat relative energies data ├── fig_density_*.png scatter plots of ddE vs (RMSD or TFD) for each force field ├── match.in input file for compare_ffs.py ├── metrics.out output file for compare_ffs.py ├── metrics.pickle pickle file for compare_ffs.py -- you can read this into compare_ffs instead of rerunning the full analysis ├── refdata_*.sdf output SDF files with stored RMSD / TFD scores with reference to QM for each structure ├── relene_*.dat relative energies of matched conformers ├── ridge_dde.png compared energies plot ├── ridge_rmsd.svg compared rmsds plot ├── ridge_tfd.svg compared tfds plot ├── fig_scatter_*.png scatter plots of ddE vs (RMSD or TFD). these are noisy; I don't use these ├── trim3_*.sdf input SDF files for compare_ffs.py listed in match.in file ├── violin*.* violin plot showing ddE distributions ``` </code></pre>
Multi-omics analysis reveals the glycolipid metabolism response mechanism in the liver of Genetically Improved Farmed Tilapia (GIFT, Oreochromis niloticus) under hypoxia stress
<p><span><b>Background: </b>Dissolved oxygen (DO) in the water is a vital abiotic factor in aquatic animal farming. A hypoxic environment affects the growth, metabolism, and immune system of fish. Glycolipid metabolism is a vital energy pathway under acute hypoxic stress, and it plays a significant role in the adaptation of fish to stressful environments. In this study, we used multi-omics integrative analyses to explore the mechanisms of hypoxia adaptation in Genetically Improved Farmed Tilapia (GIFT, <i>Oreochromis niloticus</i>). </span></p> <p><span><b>Results:</b><b> </b>The 96 h median lethal hypoxia (96h-LH50) for GIFT was determined by linear interpolation. We established control (DO: 5 mg/L) groups (CG) and hypoxic stress (96h-LH50) groups (HG) and extracted liver tissues for high-throughput transcriptome and metabolome sequencing. A total of 581 differentially expressed (DE) genes and 1250 DE metabolites were detected between CG and HG, and were annotated using tools at the KEGG database. We verified the transcript levels of eight DE genes by quantitative real-time PCR.</span></p> <p><span><b>Conclusions: </b>Analyses of essential glycolipid metabolism pathways of GIFT under hypoxia stress showed that, after 96 h of hypoxia stress, lipid metabolism became the primary metabolic pathway in GIFT. Our findings reveal the changes in metabolites and gene expression that occur under hypoxia stress, and shed light on the regulatory pathways that function under such conditions. Ultimately, this information will be useful to devise strategies to decrease the damage caused by hypoxia stress in farmed fish.</span></p>
In-house 3-D printed aligners: effect of in vivo ageing on mechanical properties
<p>Dataset for all analyses in the paper.</p>
Effect of Strain Amplitude on Static and Dynamic Mechanical Properties of Tight Sedimentary Rocks: An Experimental Study
<p>We perform increasing-amplitude triaxial unload cycling tests on three tight sedimentary rocks to investigate the strain-dependent mechanical properties. </p>
Both hypoxia and hypobaria impair baroreflex sensitivity but through different mechanisms
<p><strong>database using hypobaric hypoxia, normobaric hypoxia and hypobaric normoxia on pilot trainee</strong></p>
COVID-CDR: An integrative resource for network-based investigation of COVID-19 combinatorial drug repositioning and mechanism of action
<p>Repurposing of the existing medications has become the mainstream focus of anti-COVID-19 drug discovery as it offers rapid and cost-effective solutions for therapeutic development. However, a great effort is still required to enhance the efficacy of repurposing therapeutic options through combination therapy, in which promising drugs with varying mechanisms of action are administered together. Nonetheless, our ability to identify and validate effective combinations is limited due to the vast number of possible drug pairs. Yet, there is no <span>available resource that</span> <span>can systematically guide to identify or choose the effective individual drugs or best possible synergistic drug combinations for the treatment of SARS-CoV</span>-<span>2 infection.</span> To address this resource gap<span>, we </span>developed <span>a web-based platform that displays the network-based mechanism of action of drug combinations, thus simultaneously </span>providing <span>a visual of the cellular interactome involved in modes of action of the chosen drugs. The platform allows the freedom to </span>select <span>two or more drug combinations and provides the options to investigate the network-based efficacy of drug combinations and understand the similarity score, primary indications, and pairwise synergistic scores on different cell-lines. In a nutshell, the platform (accessible via </span><a href="http://vafaeelab.com/COVID19_repositioning.html"><span>http://vafaeelab.com/COVID19_repositioning.html</span></a><span>) is the first of its type, which provides a systematic approach for pre-clinical investigation of combination therapy for treating COVID-19 at the fingertips of the clinicians or researchers.</span></p>
Analytical model of delay mechanism calculations
<p>The first excel file provides the code based on the analytical equations of Gaume and Puzrin (2020) to evaluate the delay for slab avalanche release and produce the figures of the paper. The second file provides the deflection curves obtained based on MPM simulations (Figure 5).</p>
The extensibility of the plantar fascia influences the windlass mechanism during human running
<p>The arch of the human foot is unique among hominins as it is compliant at ground-contact but sufficiently stiff to enable push-off. These behaviours are partly facilitated by the ligamentous plantar fascia whose role is central to two mechanisms. The ideal windlass mechanism assumes that the plantar fascia has a nearly constant length to directly couple toe dorsiflexion with a change in arch shape. However, the plantar fascia also stretches and then shortens throughout gait as the arch-spring stores and releases elastic energy. We aimed to understand how the extensible plantar fascia could behave as an ideal windlass when it has been shown to strain throughout gait, potentially compromising the one-to-one coupling between toe arc length and arch length. We measured foot bone motion and plantar fascia elongation using high-speed x-ray during running. We discovered that toe plantarflexion delays plantar fascia stretching at foot-strike, which likely modifies the distribution of the load through other arch tissues. Through a pure windlass effect in propulsion, a quasi-isometric plantar fascia's shortening is delayed to later in stance. The plantar fascia then shortens concurrently to the windlass mechanism, likely enhancing arch recoil at push-off.</p>
Butterflies fly using efficient propulsive clap mechanism owing to flexible wings
<p class="Teaser">Butterflies look like no other flying animal, with unusually short, broad and large wings relative to their body size. <span>Previous studies have suggested butterflies use several unsteady aerodynamic mechanisms</span> <span>to </span>boost force <span>produc</span>tion with <span>upstroke wing</span> <span>clap </span>being a prominent feature<span>.</span> When the wings clap together at the end of upstroke the air between the wings is pressed out, creating a jet, pushing the animal in the opposite direction. <span>Although </span>viewed, for the last 50 years, <span>as a </span>crucial <span>mechanism</span> in insect flight<span>, quantitative </span>aerodynamic <span>measurements of the clap in freely flying animals are lacking</span>. Using quantitative flow measurements behind freely flying butterflies during take-off and a mechanical clapper, we provide aerodynamic performance estimates for the wing clap. We show that flexible butterfly wings, forming a cupped shape during the upstroke and clap, thrust the butterfly forwards, while the downstroke is used for weight support. We further show that flexible wings dramatically increase the useful impulse (+22%) and efficiency (+28%) of the clap compared to rigid wings. Combined, our results suggest butterflies evolved a highly effective clap, which provides a mechanistic hypothesis for their unique wing morphology. Furthermore, our findings could aid the design of manmade flapping drones, boosting propulsive performance.</p>
Data for article: Crack Identification in Necked Double Shear Lugs by means of the Electro-Mechanical Impedance Method
<p>Data to preproduce results presented in the article:<br> Title: <strong>Crack Identification in Necked Double Shear Lugs by means of the Electro-Mechanical Impedance Method</strong><br> Authors: Markus Winklberger *, Christoph Kralovec, Christoph Humer, Peter Heftberger, Martin Schagerl<br> *Correspondence: markus.winklberger@jku.at<br> Journal: Sensors<br> Section: Physical Sensors<br> Special Issue: Piezoelectric Transducers Based Structural Health Monitoring</p> <p>Data saved in csv-files with ";" delimiter.</p>
leonardlab/Source Data for "Elucidation and refinement of synthetic receptor mechanisms"
<p>This source data accompanies the manuscript "Elucidation and refinement of synthetic receptor mechanisms".</p>
Using demographic model selection to untangle allopatric divergence and diversification mechanisms in the Rheum palmatum complex in the Eastern Asiatic Region
<p>Allopatric divergence is often initiated by geological uplift and restriction to sky-islands, climate oscillations, or river capture. However, it can be difficult to establish which mechanism was the most likely to generate the current phylogeographic structure of a species. Recently, genomic data in conjunction with a model testing framework have been applied to address this issue in animals. To test whether such an approach is also likely to be successful in plants we used population genomic data of the <i>Rheum palmatum</i> complex from the Eastern Asiatic Region, in conjunction with biogeographical reconstruction and demographic model selection to identify the potential mechanism(s) which have led to the current level of divergence. Our results indicate that the <i>R. palmatum</i> complex originated in the central Hengduan Mts. and possibly in regions further to the east, and then dispersed westward and eastward resulting in genetically distinct lineages. Populations are likely to have diverged in refugia during climate oscillations followed by subsequent expansion and secondary contact. However, model simulations within the western lineage of the <i>R. palmatum</i> complex cannot reject a restriction to sky-islands as a possible mechanism of diversification due to the genetically ambiguous position of one population. This highlights that genetically mixed populations might introduce ambiguity regarding the best diversification model in some cases. Although it might be possible to resolve this ambiguity using other data, sometimes this could prove to be difficult in complex biogeographic areas.</p>
Mechanical Engineering: An International Journal ( MEIJ)
<pre>Mechanical Engineering: An International Journal is a peer-reviewed, open access journal that addresses the impacts and challenges of Mechanical Engineering. The journal documents practical and theoretical results which make a fundamental contribution for the development of Mechanical Engineering.</pre>
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.