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806 results for “cavities”
Data from: Comparative analysis of the shape and size of the middle ear cavity of turtles reveals no correlation with habitat ecology
<p>The middle ear of turtles differs from other reptiles in being separated into two distinct compartments. Several ideas have been proposed as to why the middle ear is compartmentalized in turtles, most suggesting a relationship with underwater hearing. Extant turtle species span fully marine to strictly terrestrial habitats, and ecomorphological hypotheses of turtle hearing predict that this should correlate with variation in the structure of the middle ear due to differences in the fluid properties of water and air. We investigate the shape and size of the air-filled middle ear cavity of 56 extant turtles using 3D data and phylogenetic comparative analysis to test for correlations between habitat preferences and the shape and size of the middle ear cavity. Only weak correlations are found between middle ear cavity size and ecology, with aquatic taxa having proportionally smaller cavity volumes. The middle ear cavity of turtles exhibits high shape diversity among species, but we found no relationship between this shape variation and ecology. Surprisingly, the estimated acoustic transformer ratio, a key functional parameter of impedance-matching ears in vertebrates, also shows no relation to habitat preferences (aquatic/terrestrial) in turtles. We suggest that middle ear cavity shape may be controlled by factors unrelated to hearing, such as the spatial demands of surrounding cranial structures. A review of the fossil record suggests that the modern turtle ear evolved during the Early to Middle Jurassic in stem turtles broadly adapted to freshwater and terrestrial settings. This, combined with our finding that evolutionary transitions between habitats caused only weak evolutionary changes in middle ear structure, suggests that tympanic hearing in turtles evolved as a compromise between subaerial and underwater hearing.</p>
Lava tree cavity at Takapuna
1.5m wide cavity thought to have been formed by lava from Pupuke volcano flowing around a kauri tree around 200,000 years ago. Near Brett Ave, Takapuna, Auckland, New Zealand. My 3D model from photos generated with photogrammetry software 3DF Zephyr v4.009 processing 12 images Source: Objaverse 1.0 / Sketchfab
Pine Island Glacier ice shelf ocean cavity self-consistent spatial discretization mesh
<p>Pine Island Glacier ice shelf ocean cavity<br> ==========================================</p> <p>An unstructured mesh spatial discretisation of the Pine Island Glacier ice shelf ocean cavity.</p> <p>This is stored in an unstructured VTU file defined by the visualisation toolkit VTK [2].</p> <p>A state PVSM file for Paraview [3] is also provided to reproduce visualisations shown in [1]. Note that Paraview requires absolute pathnames, so it may be necessary to edit file references to the VTU file in this state file.</p> <p>Files<br> -----</p> <p>- PineIslandGlacierIceShelfOceanCavity.vtu<br> - PineIslandGlacierIceShelfOceanCavity_grid_quality_analysis.pvsm</p> <p>Author<br> ------</p> <p>- Dr Adam S. Candy <a.s.candy@tudelft.nl>, <candy@cantab.net><br> - Technische Universiteit Delft<br> - Imperial College London</p> <p>References<br> ----------</p> <p>[1] Candy, A.S., 2016. A consistent approach to unstructured mesh generation for geophysical models. In review. Preprint available at https://arxiv.org/abs/1703.08491.</p> <p>[2] The Visualization Toolkit (VTK), version 5.10.1. URL: http://www.vtk.org.</p> <p>[3] Paraview, version 4.3.1. https://www.paraview.org.</p>
Filchner-Ronne ice shelf ocean cavity self-consistent spatial discretization mesh
<p>Filchner-Ronne ice shelf ocean cavity<br> =====================================</p> <p>An unstructured mesh spatial discretisation of the Filchner-Ronne ice shelf ocean cavity and the ice sheet floating above.</p> <p>This is stored in two unstructured VTU files defined by the visualisation toolkit VTK [2].</p> <p>A state PVSM file for Paraview [3] is also provided to reproduce visualisations shown in [1]. Note that Paraview requires absolute pathnames, so it may be necessary to edit file references to the VTU files in this state file.</p> <p>Files<br> -----</p> <p>- FilchnerRonneIceShelfOceanCavity.vtu<br> - FilchnerRonneIceShelfOceanCavity_ice.vtu<br> - FilchnerRonneIceShelfOceanCavity.pvsm</p> <p>Author<br> ------</p> <p>- Dr Adam S. Candy <a.s.candy@tudelft.nl>, <candy@cantab.net><br> - Technische Universiteit Delft<br> - Imperial College London</p> <p>References<br> ----------</p> <p>[1] Candy, A.S., 2016. A consistent approach to unstructured mesh generation for geophysical models. In review. Preprint available at https://arxiv.org/abs/1703.08491.</p> <p>[2] The Visualization Toolkit (VTK), version 5.10.1. URL: http://www.vtk.org.</p> <p>[3] Paraview, version 4.3.1. https://www.paraview.org.</p>
Lesser Woodcreepers (Xiphorhynchus fuscus) excavate nest cavities in trees
<p class="MsoNormal"><span>To understand the evolution, life-history trade-offs, and population ecology of cavity nesters, it is critical to identify the avian lineages and circumstances in which birds excavate tree cavities. Woodcreepers (Furnariidae: Dendrocolaptinae; 56 species) are considered non-excavators dependent on existing cavities. We overturn this assumption by providing definitive evidence that the Lesser Woodcreeper (<em>Xiphorhynchus fuscus</em>, 23 g) is a facultative tree-cavity excavator. From 2007 to 2022 in the Atlantic forest of Misiones, Argentina, they nested in pre-existing tree crevices (4 nests), or excavated in trunks of large-diameter trees or stumps in advanced stages of decay (mean: 58 cm diameter; range: 22–121 cm; 22 nests). Nest entrances were vertically elongated and chambers were usually pocket-like, excavated in the exterior of the trees (sapwood), with floors that curved along the trees' circumference. Excavating woodcreepers pulled out elongated, fibrous pieces of decayed wood with a spongy texture, tapping only when inside cavities. Published and online photographs of nests of <em>Xiphorhynchus</em> species suggest that excavation may be widespread in the genus. Our observations that woodcreepers tore out elongated pieces of spongy wood (rather than hammering) are consistent with the idea that their long, thin bills are more resistant to torsion and less resistant to impact compared to the stouter bills of other excavators in Passeriformes and Piciformes. Research has tended to focus on birds with chisel-shaped bills, perforating harder sapwood to create nesting chambers in the center of heartrot-infected trees (resulting in typical woodpecker cavities, with circular floors). We hypothesize that Lesser Woodcreepers have adopted an alternative strategy, selecting large trunks with soft outer wood (sapwood), stopping their excavation radially if they reach harder wood, and then expanding the nest chamber laterally. Furnariidae may offer a useful model family for understanding ecological and evolutionary factors that influence cavity excavation.</span></p>
Data for: Observing dynamical phases of BCS superconductors in a cavity QED simulator
<p>In conventional Bardeen-Cooper-Schrieffer (BCS) superconductors, electrons with opposite momenta bind into Cooper pairs due to an attractive interaction mediated by phonons in the material. While superconductivity naturally emerges at thermal equilibrium, it can also emerge out of equilibrium when the system's parameters are abruptly changed. The resulting out-of-equilibrium phases are predicted to occur in real materials and ultracold fermionic atoms but have not yet all been directly observed. Here we realise an alternate way to generate the proposed dynamical phases using cavity quantum electrodynamics (cavity QED). Our system encodes the presence or absence of a Cooper pair in a long-lived electronic transition in <sup>88</sup>Sr atoms coupled to an optical cavity and represents interactions between electrons as photon-mediated interactions through the cavity. To fully explore the phase diagram, we manipulate the ratio between the single-particle dispersion and the interactions after a quench and perform real-time tracking of subsequent dynamics of the superconducting order parameter using non-destructive measurements. We observe regimes where the order parameter decays to zero (phase I), assumes a non-equilibrium steady-state value (phase II), or exhibits persistent oscillations (phase III). This opens up exciting prospects for quantum simulation, including the potential to engineer unconventional superconductors and to probe beyond mean-field effects like the spectral form factor, and for increasing coherence time for quantum sensing.</p>
Direct laser-written optomechanical membranes in fiber Fabry-Perot cavities
<p>Data for "Direct laser-written optomechanical membranes in fiber Fabry-Perot cavities".</p>
Carole Niffenegger, Sebastian Dirren, Christian Schano, Fränzi Korner-Nievergelt (2023) Data from : Natural nest cavities in a high elevation habitat provide a more constant thermal environment than human-made nest cavities
<p><strong>Abstract</strong></p><p>Nest cavities with suitable thermal conditions can provide fitness benefits for birds through reduced thermoregulatory cost. Insulation can however vary between natural and human-made cavities. While several studies have assessed cavity temperatures, research from high elevation habitats, where environmental conditions are particularly variable, is still scarce. We compared temperature profiles of vacant natural and human-made nest cavities of white-winged snowfinches <i>Montifringilla nivalis</i>, a high elevation cavity nestling species. Human-made cavities experienced more extreme temperatures, with potential consequences for offspring viability, bringing into question their suitability as conservation measure, particularly as extreme temperature events become more frequent. </p>
Unraveling the cavity-nesting network at large spatial scales: The biogeographic role of woodpeckers as ecosystem engineers
<p><strong>Aim</strong>: Cavities are usually a limiting resource for several forest-dwelling vertebrates, with effects that propagate through ecological networks. Although diverse assemblages of primary excavators (e.g., woodpeckers) are assumed to increase cavities, other forest resources can also limit populations of primary excavators and cavity users, thus undermining the ecological role of excavators over different scales. We aim to test the biogeographical-scale relationships between primary excavators and cavity users by distinguishing the contribution of forest characteristics.</p> <p><strong>Location</strong>: Southern South America</p> <p><strong>Methods</strong>: We used species distribution models, which combine bioclimatic and remote sensing derived variables, to map the richness of vertebrates composing the cavity network of temperate and Mediterranean forests of South America. Based on a resampling procedure for ensuring spatial independence, we fitted structural equation models to estimate causal relationships between forest characteristics and cavity-user vertebrates.</p> <p><strong>Results</strong>: Secondary cavity users (obligated, habitat generalists and forest specialists) were positively and strongly influenced by the richness of primary excavators, while mammal richness was more influenced by tree richness. The richness of trees and <em>Nothofagus</em> tree species influenced positively the richness of primary excavators and secondary cavity users. Canopy height and net primary productivity affected positively secondary cavity users.</p> <p><strong>Main conclusions</strong>: Our results confirm the role of primary excavators as ecosystem engineers but highlight the importance of considering large spatial scales when analyzing cavity-nesting networks. Biogeographical patterns of tree diversity and forest structure can be important drivers of cavity-nesting networks that remain hidden when studies are conducted over fine spatial scales. </p>
Research data for "Fabrication uncertainty guided design optimization of a photonic crystal cavity by using Gaussian processes"
<h1>Data publication for the paper "Fabrication uncertainty guided design optimization of a photonic crystal cavity by using Gaussian processes"</h1> <div>Contains scripts for performing fabrication uncertainty guided design optimization, example scripts, research data (raw data), cleanup), additional information on models, convergence plots, and field exports.</div> <h2>Funding</h2> <div> <div> <div>We acknowledge funding by the German Federal Ministry of Education and Research (BMBF project siMLopt number 05M20ZAA and BMBF Forschungscampus MODAL number 05M20ZBM) as well as funding by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany's Excellence Strategy -- The Berlin Mathematics Research Center MATH+ (EXC-2046/1, project ID: 390685689). This project (20FUN05 SEQUME) has received funding from the EMPIR programme co-financed by the Participating States and from the European Union’s Horizon 2020 research and innovation programme. This project is co-financed by the European Regional Development Fund (EFRD, application no. 10184206, QD-Sense).</div> </div> </div> <p> </p> <p> </p> <p> </p> <p> </p>
Gate-Compatible Circuit QED in a Three-Dimensional Cavity Architecture
<p>This repository contains the raw data and processing code of the paper "Gate-Compatible Circuit QED in a Three-Dimensional Cavity Architecture"</p>
Dataset: Intercavity polariton slows down dynamics in strongly coupled cavities
<p>Dataset for the experimental data of article: Intercavity polariton slows down dynamics in strongly coupled cavities </p>
Data from: Limited evidence of biased offspring sex allocation in a cavity-nesting conspecific brood parasite
<p>Sex allocation theory predicts that mothers should bias investment in offspring toward the sex that yields higher fitness returns; one such bias may be a skewed offspring-sex ratio. Sex allocation is well-studied in birds with cooperative breeding systems, with theory on local resource enhancement and production of helpers at the nest, but little theoretical or empirical work has focused on birds with brood parasitic breeding systems. Wood ducks (<em>Aix sponsa</em>) are conspecific brood parasites, and rates of parasitism appear to increase with density. Because female wood ducks show high natal philopatry and nest sites are often limiting, local resource competition (LRC) theory predicts that females should overproduce male offspring—the dispersing sex—when competition (density) is high. However, the unique features of conspecific brood parasitism generate alternative predictions from other sex allocation theories, which we develop and test here. We experimentally manipulated the nesting density of female wood ducks in four populations from 2013-2016 and analyzed the resulting sex allocation of >2000 ducklings. In contrast to predictions we did not find overproduction of male offspring by females in high-density populations, females in better condition, or parasitic females; modest support for LRC was found in overproduction of only female parasitic offspring with higher nest box availability. The lack of evidence for sex ratio biases, as expected for LRC and some aspects of brood parasitism, could reflect conflicting selection pressures from nest competition and brood parasitism, or that mechanisms of adaptive sex ratio bias are not possible.</p>
05_HTMD_Cavity_Bulk: Incorporating prior knowledge in the seeds of adaptive sampling molecular dynamics simulations of ligand transport in enzymes with buried active sites
<p># Contains input, output, and restart files used for HTMD (High-throughput molecular dynamics) adaptive sampling simulations at 310K for Cavity&Bulk schemes. </p> <p># The folders are organized as:</p> <p>Input_files/ # Contains .parm7 and .rst files of 30 seed conformations obtained from equilibrations and used for adaptive sampling inputs, *run_adaptiveMD.py* : Script file executing the adaptive sampling using distance matrix considering protein C-alpha atoms and heavy atoms of DBE.<br>rep1/<br>└── adaptive_data/<br> ├── generators/ # Contains the initial generator files provided by the user<br> │ ├── ../structure.parm7<br> │ ├── ../input.ncrst<br> │ └── ...<br> ├── input/ # Contains the files needed to start all simulations of all epochs (automatically generated)<br> │ ├── ../equil1.log<br> │ ├── ../input.ncrst<br> │ └── ...<br>└──rep2/<br>...<br>...<br> </p>
04_HTMD_Cavity: Incorporating prior knowledge in the seeds of adaptive sampling molecular dynamics simulations of ligand transport in enzymes with buried active sites
<p># Contains input, output and restart files used for HTMD (High-throughput molecular dynamics) adaptive sampling simulations at 310K for Cavity schemes. </p> <p># The forders are organized as:</p> <p>Input_files/ # Contains .parm7 and .rst files of 30 seed conformations obtained from equilibrations and used for adaptive sampling inputs, **run_adaptiveMD.py** : Script file executing the adaptive sampling using distance matrix considering protein C-alpha atoms and heavy atoms of DBE.<br>rep1/<br>└── adaptive_data/<br> ├── generators/ # Contains the initial generator files provided by the user<br> │ ├── ../structure.parm7<br> │ ├── ../input.ncrst<br> │ └── ...<br> ├── input/ # Contains the files needed to start all simulations of all epochs (automatically generated)<br> │ ├── ../equil1.log<br> │ ├── ../input.ncrst<br> │ └── ...<br>└──rep2/<br>...<br>...<br> </p>
Dataset related to the publication "Procedure for automated low uncertainty assessment of empty cavity mode frequencies in Fabry-Pérot cavity based refractometry"
<p>The data set consists of; The published paper, all figures that present measurement or simulation data in .png and .fig format and the underlying data plotted in the figures in text format. The published plots were generated from the fig files. The text files were generated by reading the plotted data from the fig files. The files are named Fig_XX were XX corresponds to the figure number in the publication. The format of the text file is as follows. Before every data set there is a header consisting of; The number of the subplot where the data is plotted (Plot: XX), the number of the data set in the sub plot (DataSet: XX), and the color of the line or marker in the plot (Color: XX). The description of what each color represents can be found in the publication.</p>
Dataset related to the publication "An Invar-based dual Fabry–Perot cavity refractometer for assessment of pressure with a pressure independent uncertainty in the sub-mPa region"
<p>The data set consists of; The published paper, all figures that present measurement or simulation data in .png and .fig format and the underlying data plotted in the figures in text format.<span> </span>The published plots were generated from the fig files. The text files were generated by reading the plotted data from the fig files. The files are named Fig_XX were XX corresponds to the figure number in the publication.<span> </span>The format of the text file is as follows. Before every data set there is a header consisting of; The number of the subplot where the data is plotted (Plot: XX), the number of the data set in the sub plot (DataSet: XX), and the color of the line or marker in the plot (Color: XX). The description of what each color represents can be found in the publication.</p>
External cavity quantum cascade laser vibrational circular dichroism spectroscopy for fast and sensitive analysis of proteins at low concentrations (Data analysis)
<p>This record contains a docker container image of the data evaluation shown in the publication "External cavity quantum cascade laser vibrational circular dichroism spectroscopy for fast and sensitive analysis of proteins at low concentrations". The evaluations can be accessed by running the container and accessing the contained Jupyter Lab via a browser. The calculations are contained in 'Eval_protein_D2O.ipynb'.</p> <p>To run the container (requires docker):</p> <p>1.download 'd2o_vcd.tar'</p> <p>2. in the command line, execute 'docker load -i d2o_vcd.tar'. This will return something like 'Loaded image: <image_name>' with image_name probably being "drhermann/vcd_d2o_00:trial_03"</p> <p>3. then 'docker run -p 8889:8889 <image_name>' replacing the brackets with the actual name of the image, such as drhermann/vcd_d2o_00:trial_03</p> <p>4.In your command line a link starting in 'http://127.0.0.1:8888/lab?token=...' will appear. Open this link in your browser to access the evaluation.</p>
Dynamics of tree-cavity occupancy: Data and code
<h3>Supplementary data and code to the paper entitled “Resource suitability drives low use of avian-excavated tree cavities: a multi-state occupancy dynamics approach”</h3> <p> </p> <p>The following list indicates the names of files included as supplementary data and code, as well as a brief description of their content. File names are given by headings in italic, followed by content description.</p> <p> </p> <p><em>CavNestMisiones.rds</em> </p> <p>Contains the data used to fit the model in file <em>MSODynModel.R</em>. It includes the following objects:</p> <p> <strong>y</strong> An array with dimensions 452x20x16 showing the observed cavity states for each of 452 cavities, a maximum of 20 visits per cavity per year, and 16 years. This array contains NAs prior to the first year of cavity registration, after cavity loss, and in any year*visit combination for which there was no data for the corresponding cavity.</p> <p><strong>origen </strong>A vector with length 452 with ‘1’ for excavated and ‘2’ for non-excavated cavities.</p> <p> </p> <p><em>MSODynModel.R</em></p> <p>Model code including preliminary data processing, JAGS code for the dynamic multi-state occupancy model, and call to JAGS to fit the model. Model code includes posterior predictive checking for goodness-of-fit.</p> <p> </p> <p><em>MSMO60k.Rdata</em></p> <p>JAGs output with MCMC samples from the posterior probability distribution of model parameters.</p> <p> </p> <p><em>SimCavs.R</em></p> <p>Code for simulating cavity use.</p> <p> </p> <p><em>SimCavsFunctions.R</em></p> <p>Functions used in <em>SimCavs.R.</em></p>
Ultrasound-Guided Trans-Uterine Cavity Core Needle Biopsy of Uterine Myometrial Tumors - Diagnostics 2022, 12(6), 1348
<p>Ultrasound-guided trans-uterine cavity core needle biopsy of myometrial tumors to differentiate sarcoma from a benign lesion. </p> <p>This is a supplementary Video to the article published in <em>Diagnostics</em> <strong>2022</strong>, <em>12</em>(6), 1348.</p> <p><a href="https://doi.org/10.3390/diagnostics12061348">https://doi.org/10.3390/diagnostics12061348</a></p>
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International Brain Laboratory public data
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OpenNeuro
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