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10,561 results for “mechanics”
Data from: Whole genomes reveal evolutionary relationships and mechanisms underlying gene-tree discordance in Neodiprion sawflies
<p>Rapidly evolving taxa are excellent models for understanding the mechanisms that give rise to biodiversity. However, developing an accurate historical framework for comparative analysis of such lineages remains a challenge due to ubiquitous incomplete lineage sorting and introgression. Here, we use a whole-genome alignment, multiple locus-sampling strategies, and locus-based and SNP-based species-tree methods to infer a species tree for eastern North American <em>Neodiprion</em> species, a clade of pine-feeding sawflies (Order: Hymenopteran; Family: Diprionidae). We recovered a well-supported species tree that—except for three uncertain relationships—is robust to different strategies for analyzing whole-genome data. Despite this consistency, underlying gene-tree discordance is high. To understand this discordance, we use multiple regression to model topological discordance as a function of several genomic features. We find that gene-tree discordance tends to be higher in regions of the genome that may be more prone to gene-tree estimation error, as indicated by a lower density of parsimony-informative sites, a higher density of genes, a higher average pairwise genetic distance, and gene trees with lower average bootstrap support. Also, contrary to the expectation that discordance via incomplete lineage sorting is reduced in low-recombination regions of the genome, we find a <em>negative</em> correlation between recombination rate and topological discordance. We offer potential explanations for this pattern and hypothesize that it may be unique to lineages that have diverged with gene flow. Our analysis also reveals an unexpected discordance hotspot on Chromosome 1, which contains several genes potentially involved in mitochondrial-nuclear interactions and produces a gene-tree that resembles a highly discordant mitochondrial tree. Based on these observations, we hypothesize that our genome-wide scan for topological discordance has identified a nuclear locus involved in a mito-nuclear incompatibility. Together, these results demonstrate how phylogenomic analysis coupled with high-quality, annotated genomes can generate novel hypotheses about the mechanisms that drive divergence and produce variable genealogical histories across genomes.</p>
Supplementary data for A Systematic Literature Review on the Code Smells Datasets and Validation Mechanisms
<p>The attached Microsoft Excel files contain the data and diagrams of the paper:</p> <p><strong>A systematic literature review on the code smells datasets and validation mechanisms</strong></p> <p>The article is under review in the ACM Computing Surveys.</p> <p> </p>
Multi-fidelity modelling of shark skin denticle flows: Insights into drag generation mechanisms
<p>We investigate the flow over smooth (non-ribletted) shark skin denticles in an open-channel flow using Direct Numerical Simulation (DNS) and two Reynolds Averaged Navier-Stokes (RANS) closures. Large peaks in pressure and viscous drag are observed at the denticle crown edges, where they are exposed to high-speed fluid which penetrates between individual denticles, increasing shear and turbulence. Strong lift forces lead to a positive spanwise torque acting on individual denticles, potentially encouraging bristling if the denticles were not fixed. However, DNS predicts that denticles ultimately increase drag by 58 % compared to a flat plate.</p> <p>Good predictions of drag distributions are obtained by RANS models, although an underestimation of turbulent kinetic energy production leads to an underprediction of drag. Nevertheless, RANS methods correctly predict trends in the drag data and the regions contributing most to viscous and pressure drag. Subsequently, RANS models are used to investigate the dependence of drag on the flow blockage ratio (boundary layer to roughness height ratio), finding that the drag increase due to denticles is halved when the blockage ratio δ /h is increased from 14 to 45. Our results provide an integrated understanding of the drag over non-ribletted denticles, enabling existing diverse drag data to be explained.</p>
DATASET Sound production mechanism in triggerfish (Balistidae): a synapomorphy
<p>Dataset corresponding to the article "Sound production mechanism in triggerfish (Balistidae): a synapomorphy". </p> <p>This dataset contains the sounds of three species of Balistidae : <em>Balistapus undulatus</em>, <em>Rhinecanthus aculeatus</em> and <em>Rhinecanthus rectangulus</em>.</p> <p>All the specimens are from Moorea Island (French Polynesia)<br> <em>B. undulatus</em> [standard length (SL) 10.59–15.35 cm]<br> <em>R. aculeatus</em> (SL: 12.7–17.4 cm) <br> <em>R. rectangulus</em> (SL: 8.1–15.3 cm) </p> <p>Specimens were recorded hand-held in a glass aquarium with a hydrophone HTI-96-MIN (sensitivity: −163.9dB V μPa−1; High Tech Inc., Long Beach, MS, USA) connected to a TASCAM DR-07 recorder (TEAC, Wiesbaden, Germany).<br> The sounds were digitized at 44.1 kHz (16-bit resolution).</p>
DATASET Unusual sound production mechanism in the triggerfish Rhinecanthus aculeatus (Balistidae)
<p>Dataset corresponding to the article "Unusual sound production mechanism in the triggerfish <em>Rhinecanthus aculeatus</em> (Balistidae) ". </p> <p>This dataset contains the sounds and results of morphological studies of <em>Rhinecanthus aculeatus</em></p> <p>Specimens were recorded hand-held in a glass aquarium with a hydrophone HTI-96-MIN (High Tech Inc., Long Beach, MS, USA) connected to a TASCAM DR-07 recorder (TEAC, Wiesbaden, Germany).<br> The sounds were digitized at 44.1 kHz (16-bit resolution).</p> <p>Contact: Xavier.Raick@uliege.be ; xavierraick@hotmail.com</p>
Circuit mechanisms underlying embryonic retinal waves
<p>Spontaneous activity is a hallmark of developing neural systems. In the retina, spontaneous activity comes in the form of retinal waves, comprised of three stages persisting from embryonic day 16 (E16) to eye opening at postnatal day 14 (P14). Though postnatal retinal waves have been well characterized, little is known about the spatiotemporal properties or the mechanisms mediating embryonic retinal waves, designated Stage 1 waves. Using a custom-built macroscope to record spontaneous calcium transients from whole embryonic retinas, we show that Stage 1 waves are initiated at several locations across the retina and propagate across a broad range of areas. A gap junction antagonist, meclofenamic acid, reduced the frequency and size of Stage 1 waves, nearly abolishing them. The general nAChR antagonist, hexamethonium similarly nearly abolished Stage 1 waves. Application of the α4β2 nAChR antagonist dihydro-ß-erythroidine only slightly reduced the frequency of waves but significantly reduced the number of cells that participated in waves. Thus, Stage 1 waves are mediated by a complex circuitry involving subtypes of nAChRs and gap junctions. Stage 1 waves in mice lacking the β2 subunit of the nAChRs (β2-nAChR-KO) were reduced, but in contrast to WT mice, they persisted in the hexamethonium and were completely blocked by meclofenamic acid. To assay the impact of Stage 1 waves on retinal development, we compared the spatial distribution of a subtype of retinal ganglion cells, intrinsically photosensitive retinal ganglion cells (ipRGCs), which undergo a significant amount of cell death, in WT and β2-nAChR-KO mice. We found that the developmental decrease of ipRGC density is preserved between WT and β2-nAChR-KO mice, indicating that processes regulating ipRGC distribution are not influenced by spontaneous activity.</p>
Developing elastic mechanisms: Ultrafast motion and cavitation emerge at the millimeter scale in juvenile snapping shrimp
<p>Organisms such as jumping froghopper insects and punching mantis shrimp use spring-based propulsion to achieve fast motion. Studies of elastic mechanisms primarily focus on fully developed and functional mechanisms in adult organisms. However, the ontogeny and development of these mechanisms can provide important insights into lower size limits of spring-based propulsion, the ecological or behavioral relevance of ultrafast movement, and the scaling of ultrafast movement. Here we examine the development of the spring-latch mechanism in the big claw snapping shrimp, <em>Alpheus</em> <em>heterochaelis</em> (Alpheidae). Adult snapping shrimp use an enlarged claw to produce high-speed strikes that generate cavitation bubbles. However, until now, it was unclear when the elastic mechanism emerges during development and whether juvenile snapping shrimp can generate cavitation at this size. We reared <em>A</em>. <em>heterochaelis</em> from eggs, through their larval and postlarval stages. Starting one month after hatching, the snapping shrimp snapping claw gradually developed a spring-actuated mechanism and began snapping. We used high-speed videography (300,000 frames s<sup>-1</sup>) to measure juvenile snaps. We discovered that juvenile snapping shrimp generate the highest recorded accelerations (5.8x10<sup>5</sup> ± 3.3x10<sup>5</sup> m s<sup>-2</sup>) for repeated use and underwater motion and are capable of producing cavitation at the millimeter scale. The angular velocity of snaps did not change as juveniles grew; however, juvenile snapping shrimp with larger claws produced faster linear speeds and generated larger, longer-lasting cavitation bubbles. These findings establish the development of the elastic mechanism and cavitation in snapping shrimp and provide insights into early life-history transitions in spring-actuated mechanisms.</p>
Dataset for publication Sikora P., El-Khayatt A.M., Saudi H.A., Liard M., Lootens D., Chung S.-Y., Woliński P., Abd Elrahman M. Rheological, mechanical, microstructural and radiation shielding properties of cement pastes containing magnetite (Fe3O4) nanoparticles. International Journal of Concrete Structures and Materials (2023), 17, 7
<p>Open dataset for publication Sikora P., El-Khayatt A.M., Saudi H.A., Liard M., Lootens D., Chung S.-Y., Woliński P., Abd Elrahman M. Rheological, mechanical, microstructural and radiation shielding properties of cement pastes containing magnetite (Fe3O4) nanoparticles. International Journal of Concrete Structures and Materials (2023), 17, 7. https://doi.org/10.1186/s40069-022-00568-y</p> <p>File 1 - X-ray diffractogram and particle size distribution (laser granulometry) data - *.opju (Origin)<br> File 2 - Rheological test results - *.opju (Origin)<br> File 5 - Mechanical peformance (early strength - ultrasounds and compressive strength) and density test results - *.opju (Origin)<br> File 4 - Mercury intrusion porosimetry test data - *.opju (Origin)</p>
Reverberant Magnetic Resonance Elastographic Using a single Mechanical Driver
<p>Reverberant elastography provides fast and robust estimates of shear modulus. However, reverberant elastography uses multiple mechanical drivers, hampering clinical utility. In this work, we hypothesize that a single mechanical driver can generate reverberant shear fields in constrained organs such as the brain. To corroborate this hypothesis, we imaged the brain of a healthy volunteer; and two constrained phantoms containing spherical inclusions with diameters ranging from 4-18 mm. As a secondary goal, we assessed the feasibility of recovering shear modulus from a single component of the reverberant wave field. Viable reverberant and subzone elastograms were produced only when obtained at 50 and 100 Hz in phantoms. Different levels of reverberance were exhibited in different displacement components (70-82% for phantoms and 87-93% for the clinical case); however, wavefields obtained when imaging at 50 Hz and 100 Hz were not significantly different (p>0.05). Errors incurred in reverberant elastograms varied from 5% to 65% when imaging at 50 Hz and 2% to 55% when imaging at 100 Hz. Errors incurred in subzone elastograms ranged from 4% to 18% at 50 Hz and 5% and 50% at 100 Hz. The contrast-to-noise ratio of reverberant elastograms ranged from 20 dB to 44 dB compared to 25 dB to 31 dB in subzone elastograms. The accuracy of the elastograms acquired from the phantom containing internal shear wave reflectors did not differ noticeably. The global brain stiffness estimated from reverberant and subzone elastograms was 2.36 ± 0.95 kPa and 2.5 ± 1.1 kPa, respectively, when imaging at 50 Hz, and 2.56 ± 0.828 kPa and 2.89 ± 1.3 kPa respectively, when imaging at 70 Hz. The phantom study revealed that performance varied depending on the component of displacement used to compute reverberant elastograms; however, the clinical study demonstrated similar performance of reverberant and subzone elastograms</p>
Data from: Assessing the mechanisms and impacts of shrub invasion in forests: A meta-analysis
<ol> <li>The encroachment of invasive shrubs in forest understories can have detrimental effects on native plant recruitment. As a result, removal of invasive species is a common practice although long-lasting success is rare. In order to effectively conserve and manage invaded forests, it is crucial to understand the mechanisms that drive shrub invasion, i.e., high propagule pressure, low native resistance, and exploitation of empty niches.</li> <li>To gain a deeper understanding of the invasion process in forest ecosystems we conducted a meta-analysis of the work done in this topic. We collected data on invasive species and native community performance and on the abiotic conditions of forest understories under low and high levels of shrub invasion. We analyzed data from 124 articles that yielded 377 unique observations.</li> <li>Our results revealed that while invader performance did not vary by the mechanism of invasion, the impact on the native community was significantly detrimental when invasion occurred via low biotic resistance, and only marginally significant via propagule pressure. Invasive species performance was associated with increases in light availability, but not with other resources (soil water, or nutrients). When assessing impact on native performance as a function of invasive performance, results were again only significant under the low biotic resistance mechanism. Lastly, impacts were stronger when invasion took place by a single invader.</li> <li> <em>Synthesis and applications</em>: Taken together, these results suggest that restoration efforts should focus on (i) increasing the presence of strong native competitors or functionally diverse native communities, (ii) decreasing sources of invasive shrub propagules while keeping the canopies closed when invasion occurs via high propagule pressure, (iii) avoiding management techniques that degrade or diminish canopy cover, and (iv) prioritizing management of forest understories dominated by particularly impactful invasive shrubs.</li> </ol>
Data for publication "Lipid oxidation controls peptide self-assembly near membranes through a surface attraction mechanism"
<p>The data provided refer to our published article:</p> <p>T. John,* S. Piantavigna, T. J. A. Dealey, B. Abel, H. J. Risselada, L. L. Martin*, Lipid oxidation controls peptide self-assembly near<br>membranes through a surface attraction mechanism, Chem. Sci. 14 (2023), 3730-3741. <a href="https://doi.org/10.1039/d3sc00159h">https://doi.org/10.1039/d3sc00159h</a>.</p>
Molecular origin of the two-step mechanism of gellan aggregation
<p>Data presented in the article entitled <strong>Molecular origin of the two-step mechanism of gellan aggregation</strong>.</p>
Dataset for: Temperature sensitivity of carbon concentrating mechanisms in the diatom Phaeodactylum tricornutum
<p><span>Marine diatoms are key primary producers across diverse habitats in the global ocean. Diatoms rely on a biophysical carbon concentrating mechanism (CCM) to supply high concentrations of CO<sub>2</sub> around their carboxylating enzyme, RuBisCO. The necessity and energetic cost of the CCM are likely to be highly sensitive to temperature, as temperature impacts </span><span>CO<sub>2</sub></span><span> concentration, diffusivity, and the kinetics of CCM components. Here, we used membrane inlet mass spectrometry (MIMS) and modeling to capture temperature regulation of the CCM in the diatom <em>Phaeodactylum</em> <em>tricornutum</em> (<em>Pt</em>). We found that enhanced carbon fixation rates by <em>Pt</em> at elevated temperatures were accompanied by increased CCM activity capable of maintaining RuBisCO close to CO2 saturation but that the mechanism varied. At 10 and 18 °C, diffusion of </span><span>CO<sub>2</sub></span><span> into the cell, driven by <em>Pt</em>'s 'chloroplast pump' was the major inorganic carbon source. However, at 18 °C, upregulation of the chloroplast pump enhanced (while retaining the proportion of) both diffusive </span><span>CO<sub>2</sub></span><span> and active </span><span>HCO<sub>3</sub></span><sup><span>-</span></sup><span> uptake into the cytosol, and significantly increased chloroplast </span><span>HCO<sub>3</sub></span><sup><span>-</span></sup><span> concentrations. In contrast, at 25 °C, compared to 18 °C, the chloroplast pump had only a slight increase in activity. While diffusive uptake of </span><span>CO<sub>2</sub></span><span> into the cell remained constant, active </span><span>HCO<sub>3</sub></span><sup><span>-</span></sup><span> uptake across the cell membrane increased resulting in <em>Pt</em> depending equally on both </span><span>CO<sub>2</sub></span><span> and HCO<sub>3</sub></span><sup><span>-</span></sup><span> as inorganic carbon sources. Despite changes in the CCM, the overall rate of active carbon transport remained double that of carbon fixation across all temperatures tested. The implication of the energetic cost of the <em>Pt</em> CCM in response to increasing temperatures was discussed.</span></p>
Data from: Temperature-dependent mechanical behavior of aluminum AM structures generated via multi-layer friction surfacing
<p>This dataset contains the data for the publication " Temperature-dependent mechanical behavior of aluminum AM structures generated via multi-layer friction surfacing "</p>
Data set for article "Selective deuteration as a tool for resolving autoxidation mechanisms in a-pinene ozonolysis"
<p>The data set for publication "Selective deuteration as a tool for resolving autoxidation mechanisms in a-pinene ozonolysis" (preprint https://doi.org/10.5194/egusphere-2022-1131). Contains raw data files for the CI-orbitrap mass spectrometer (.raw files), preprocessed files used in data analysis and creating the figures in the publication, and measurement diaries for the experiments.</p>
Various seasonal pattern and mechanisms of soil nitrogen transformation along elevations in the Hengduan Mountains
<p><span>Soil nitrogen (N) transformation, a key microbial process in global N cycling, is thought to alter soil N availability and subsequently regulate ecosystem functioning. In particular, the gross rates of N transformation can provide a deeper understanding of internal N dynamics and mechanisms, but questions of whether gross N transformation processes and their underlying drivers change with seasons and elevations remain large uncertain.</span></p> <p><span>Based on field collection along an elevational gradient and laboratory incubation experiments, we investigated the seasonal processes of soil N mineralization and nitrification with 15N isotope dilution technique, and also explored the potential mechanisms involved in the Hengduan Mountains.</span></p> <p><span>Unimodal soil gross/net mineralization rates were higher in the wet season (61.32 mg kg<sup>-1</sup> d<sup>-1</sup>; 1.01 mg kg<sup>-1</sup> d<sup>-1</sup>; respectively) than in the dry season (10.88 mg kg<sup>-1</sup> d<sup>-1</sup>; 0.55 mg kg<sup>-1</sup> d<sup>-1</sup>; respectively) (P < 0.001), with a peak at medium elevation. Soil gross/net nitrification rates were lower in the wet season (1.43 mg kg<sup>-1</sup> d<sup>-1</sup>; -0.017 mg kg<sup>-1</sup> d<sup>-1</sup>) than in the dry season (2.49 mg kg<sup>-1</sup> d<sup>-1</sup>; 0.004 mg kg<sup>-1</sup> d<sup>-1</sup>; respectively) (P < 0.001), which increased with increasing elevation. The results detected the dominant drivers of the gross transformation rates, specifically microbial attributes occupied crucial roles in controlling the gross mineralization/nitrification</span> <span>in the wet season, and soil physicochemical properties were dominant controllers on the gross mineralization/nitrification</span> <span>during the dry season.</span></p> <p><span>This study revealed the divergent patterns and drivers of N transformation, suggesting that seasonal N cycling should no longer be overlooked if we are to predict N biogeochemical cycles in response to environmental change accurately.</span></p>
Data and codes for "A squeezed mechanical oscillator with milli-second quantum decoherence"
<p>Here you find the raw data files and processing Python scripts for plots presented in "A squeezed mechanical oscillator with milli-second quantum decoherence" Amir Youssefi, et.al. Nature Physics 2023</p>
Deep learning models challenge the prevailing assumption that face-like effects for objects of expertise support domain-general mechanisms
<p>The question of whether perceptual expertise is mediated by general-expert or domain-specific processing mechanisms has been debated for decades. Because humans are experts in face recognition, face-like neural and cognitive effects for objects of expertise were considered to support for the general-expertise hypothesis. Conversely, stronger effects for faces than objects of expertise were considered to support the domain-specific hypothesis. However, the effects of domain, experience, and level of categorization, are confounded in human studies, which may lead to erroneous inferences. To overcome these limitations, we used computational models of perceptual expertise and tested different domains (objects, faces, birds) and levels of categorization (basic, sub-ordinate, individual) in isolation, matched for amount of experience. Like humans, the models generated a larger inversion effect for faces than for objects. Importantly, a face-like inversion effect was found for individual-based categorization of non-faces (birds) but only in a network specialized for that domain. Thus, contrary to prevalent assumptions, face-like effects in objects of expertise may originate from domain-specific rather than domain-general processing mechanisms. More generally, we show how deep learning algorithms can be used to isolate the effects of factors that are inherently confounded in the natural environment of biological organisms.</p>
Point clouds data "Waterfall height sets the mechanism and rate of upstream retreat"
<p>Point clouds data on the erosion shape of waterfalls in our experiment in the paper "Waterfall height sets the mechanism and rate of upstream retreat".</p>
Disentangling mechanical and sensory modules in the radiation of Noctilionoid bats
<p>The vertebrate cranium is a complex anatomical structure with diverse mechanical and sensory functions. Shifts between modularity and integration in both sets of functions, especially mechanical function, have been implicated in adaptive diversification. However, how mechanical and sensory systems and functions have coevolved and how their interrelationship contributes to phenotypic disparity remains largely unexplored. To examine the modularity, integration, and evolutionary rates of sensory and mechanical structures within the head, we analyzed hard and soft tissue scans from ecologically diverse bats from the superfamily Noctilionoidea, which range from generalized insectivores to derived frugivores and nectarivores. We identified eight cranial regions as distinct modules — five associated with bite force and three linked to the olfactory, visual, and auditory systems, respectively — whose interrelationships differ between Neotropical leaf-nosed bats (Family Phyllostomidae) and other noctilionoids. Our analyses suggest that the peak rates of sensory module evolution predate those of mechanical modules. This finding is consistent with transitions to new diets first involving changes in the detection of novel food items, followed by adaptations to process them. We propose the coevolution of structures influencing bite force, olfaction, vision, and hearing constituted a structural opportunity that allowed the phyllostomid ancestor to take advantage of existing ecological opportunity and the group to become a classic example of adaptive radiation.</p>
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.