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Fig. 24 in Comparative Morphology Of The Internal Nasal Skeleton Of Adult Marsupials Based On X-Ray Computed Tomography
Fig. 24. Coronal CT images showing the presence or absence of prominent lateral expanded bulges within the shaft of the ossified nasal septum (char. 31). (A) bulges present (char. 31.0), Dromiciops gliroides, C136 (FMNH 127463), scale bar equals 1 mm; (B) bulges absent (char. 31.1), Wallabia bicolor, C386 (TMM M-4169), scale bar equals 5 mm. Abbreviations: Ecto, ectoturbinal; Endo, endoturbinal; ONS, ossified nasal septum; SER, sphenethmoid recess.
Fig. 23 in Comparative Morphology Of The Internal Nasal Skeleton Of Adult Marsupials Based On X-Ray Computed Tomography
Fig. 23. Digital renderings of the cribriform plate showing the presence or absence of a crista galli (char. 34). (A) crista galli is present (char. 34.0), Caluromys philander (AMNH 95526); (B) crista galli is absent (char. 34.1), Dendrolagus lumholtzi (AMNH 65254). Both scale bars equal 1 mm.
Fig. 13 in Comparative Morphology Of The Internal Nasal Skeleton Of Adult Marsupials Based On X-Ray Computed Tomography
Fig. 13. Coronal CT images showing the morphology of the caudodorsal portion of caudal nasoturbinal (caudal to nasoturbinal division around endoturbinal I; char. 10). (A) caudodorsal portion is unfolded (ch. 10.0), Dromiciops gliroides, C245 (FMNH 127463), scale bar equals 1 mm; (B) caudodorsal portion curls (char. 10.1), Phalanger orientalis, C250 (AMNH 157211), scale bar equals 5 mm. Abbreviations: Ecto, ectoturbinal; Endo, endoturbinal; ONS, ossified nasal septum; SER, sphenethmoid recess.
Fig. 8. Schematic diagram showing a in Comparative Morphology Of The Internal Nasal Skeleton Of Adult Marsupials Based On X-Ray Computed Tomography
Fig. 8. Schematic diagram showing a dorsal view of the paries nasi of the chondrocranium of a marsupial. Rostral is to the left. Figure modeled after Smith and Rossie (2006: fig. 8.4). Abbreviations: EC, ectoturbinal; EN, endoturbinal.
Fig. 28 in Comparative Morphology Of The Internal Nasal Skeleton Of Adult Marsupials Based On X-Ray Computed Tomography
Fig. 28. Coronal CT images showing the complexity of the rostral portion of the maxilloturbinal in marsupials (char. 1). (A) arborlike maxilloturbinal (char. 1.0), Dasyurus hallucatus, C208 (TMM M-6921); (B) simple maxilloturbinal (char. 1.1), Isoodon macrourus, C150 (TMM M-6922); (C) curled lamella (char. 1.1), Phascolarctos cinereus, C129 (TMM M-2946). All scale bars equal 5 mm. Abbreviations: Endo, endoturbinal; ONS, ossified nasal septum.
Fig. 16 in Comparative Morphology Of The Internal Nasal Skeleton Of Adult Marsupials Based On X-Ray Computed Tomography
Fig. 16. Coronal CT images showing the caudalmost extent of ventral attachment of nasoturbinal (char. 13). (A) attachment is rostral to caudal terminus of maxilloturbinal (char. 13.0), Petauroides volans, C450 (AMNH 150055); (B) attachment is at coronal level of caudal terminus of maxilloturbinal (char. 13.1), Trichosurus vulpecula, C212 (TMM M-849); (C) attachment is caudal to caudal terminus of maxilloturbinal (char. 13.2), Isoodon macrourus, C374 (TMM M-6922). All scale bars equal 5 mm. Abbreviations: Ecto, ectoturbinal; Endo, endoturbinal; ONS, ossified nasal septum; PTL, posterior transverse lamina.
Fig. 12 in Comparative Morphology Of The Internal Nasal Skeleton Of Adult Marsupials Based On X-Ray Computed Tomography
Fig. 12. Coronal CT images showing the morphology of the caudal nasoturbinal (char. 7). (A) caudal nasoturbinal is unbranched (char. 7.0), Dromiciops gliroides, C230 (FMNH 127463); (B) caudal nasoturbinal has at least one branch (char. 7.1), Caenolestes fuliginosus, C389 (KU 124015). Both scale bars equal 1 mm. Abbreviations: Ecto, ectoturbinal; Endo, endoturbinal; ONS, ossified nasal septum.
Fig. 27 in Comparative Morphology Of The Internal Nasal Skeleton Of Adult Marsupials Based On X-Ray Computed Tomography
Fig. 27. Coronal CT images showing the morphology of the maxillary recess (char. 26). (A) caudal portion of recess is medially enclosed by posterior transverse lamina (char. 26.0), Dasyurus hallucatus, C330 (TMM M-6921), scale bar equals 5 mm; (B) uncinate process of the caudal nasoturbinal also contributes to the medial wall of the recess (char. 26.1), Monodelphis domestica, C190 (TMM M-7599), scale bar equals 1 mm. Abbreviation: Ecto, ectoturbinal; Endo, endoturbinal; ONS, ossified nasal septum; NPM, nasopharyngeal meatus; PTL, posterior transverse lamina; SER, sphenethmoid recess.
Supplementary data for the manuscript "Comparison of computational and experimental saturation vapor pressures of α-pinene + O3 oxidation products"
<p>COSMO-files of potential ozonolysis products of α-pinene for the manuscript:<br> Hyttinen, N., Pullinen, I., Nissinen, A., Schobesberger, S., Virtanen, A., and Yli-Juuti, T.: Comparison of computational and experimental saturation vapor pressures of α-pinene + O<sub>3</sub> oxidation products, Atmos. Chem. Phys. Discuss. [preprint], https://doi.org/10.5194/acp-2021-775, in review, 2021.</p>
Syntheses of aircraft noise obtained by computational methods
<p>In ANIMA WP4, where focus is put on toolset development, a benchmark on three partners’ auralization tools was performed.</p> <p>These tools are used to reproduce the sound of an aircraft flyover from either physical modelling of noise, a prediction based on measurement or a combination of both. As the chosen methodologies and the modelling hypotheses are different between partners, a benchmark was performed to assess the impact of these strategies on the produced sound synthesis.</p> <p>The realism of each auralization was evaluated through comparison to experimental recordings. For propriety reasons, only the synthesized sounds are available here, and can be compared between each other.</p> <p>Two of the three tools were further used in the WP3 task dedicated to Virtual Reality, see "<a href="https://doi.org/10.5281/zenodo.5517218">Virtual reality simulated aircraft flyovers: Influence of the landscape on the overall pleasantness of the environment</a>"</p> <p>The sounds represent three flight configurations, one landing, and two take-offs with different engine speeds. Two aircraft are considered, one single-aisle and one double-aisle aircraft. The synthesis is performed at a receiver position below the aircraft trajectory.</p> <p>For more information, please contact:</p> <ul> <li><a href="mailto:Ingrid.legriffon@onera.fr">Ingrid.legriffon@onera.fr</a> (ONERA)</li> <li><a href="mailto:isabelle.boullet@airbus.com">isabelle.boullet@airbus.com</a> (Airbus Aviation)</li> <li><a href="mailto:jean-michel.boiteux@safrangroup.com">jean-michel.boiteux@safrangroup.com</a> (Safran Aircraft Engine)</li> </ul> <p> </p>
Mirror of data from NOAA U.S. Climate Reference Network for Research Computing in Earth Science
<p>This is a mirror of data from the NOAA U.S. Climate Reference Network (https://www.ncei.noaa.gov/products/land-based-station/us-climate-reference-network).</p> <p>It was created because outbound FTP access is not allowed from some cloud-based JupyterHub setups.</p>
Supplemental material for "Computational study of the dissolution of cellulose into single chains: the role of the solvent and agitation"
<p>Input-scripts and data-files from the Cellulose article "Computational study of the dissolution of cellulose into single chains: the role of the solvent and agitation" by Bering, E., Torstensen, J., Lervik, A., Wijn, A. S.</p> <p># Content</p> <p>The folder "glycamstructures" contains the output from GLYCAM carbohydrate builder with force-field parameters, coordinates and topology of a single chain of cellulose composed of 4 cellobiose units.</p> <p>The folder "intermol" contains the output from the software Intermol were the content of "glycamstructures" is translated into the lingo of LAMMPS.</p> <p>The folder "packmol" contains input files for the software Packmol, which was used for creating coordinate-files for solvated systems of cellulose with water and cellulose with the solvent mixture. (The bash-script clean.sh fixes the formatting of the .xyz-files such that LAMMPS can read it.)</p> <p>The folder "36bundle" contains input files for creating the initial configuration of the bundle with 36 chains in a maze configuration, namely 36bundle.sh reads 1chain.xyz to make the coordinate file 36bundle.xyz. Further, nvt00.in is the initial LAMMPS script for slowly starting up this system with the NVT-ensemble, which reads system information from the LAMMPS-datafile chain.36bundle, cellulose parameters from the LAMMPS-datafile data.cellulose_nohybrid and coordinates from 36bundle.xyz. nvt01.in and nvt02.in continues sequentially, resulting in the configuration stored in the LAMMPS data-file chain.nvt02.</p> <p>The folder "36bundle_mix" continues from 36bundle by first adding the solvent mixture with coordinates from Packmol in the file 36bm.xyz and slowly starting up in the NVT-ensemble with nvt00.in, with force-field parameters in data.cellulose.in, data.water_spce.in, data.naoh.in and data.urea.in, with charges and connectivity of the solvent molecules in the files water_spce.txt, naoh.txt and urea.txt. The LAMMPS script npt00.in continues with the NPT-ensemble, which is continued with npt01.in etc., resulting in the configuration stored in the LAMMPS data-file chain.npt06. These systems can be continued with length- or force-controlled oscillatory stretching/compression with osc_length.in and osc_force.in respectively, which was used to make the configurations stored in the LAMMPS data-files chain.osc_length4 and chain.osc_force4.</p> <p>Similarly, the folder "36bundle_water" continues from 36bundle by first adding the water with coordinates from Packmol in the file 36bw.xyz and slowly starting up in the NVT-ensemble with nvt00.in, with force-field parameters in data.cellulose.in and data.water_spce.in, with charges and connectivity of the water molecules in the file water_spce.txt. Again, these systems can be continued with length- or force-controlled oscillatory stretching/compression with osc_length.in and osc_force.in respectively, which was used to make the configurations stored in the LAMMPS data-files chain.osc_length4 and chain.osc_force4.</p>
Hydrothermohaline streamfunctions computed in EC-Earth
<p>NetCDF files containing hydrothermohaline streamfunctions computed from the ESM EC-Earth. The streamfunctions have been computed for the last 10 years of a historical run (1996-2005) and the last 10 years of a RCP 8.5 scenario run (2090-2100).</p>
REMODEL. WP4. Vision-Based Perception. T4-4. Functional component detection. Data related to a paper presented at 27th International Conference on Automation and Computing (ICAC) (2022)
<p>Dataset with evaluation parameters of the paper "Real-Time Instance Segmentation of Pedestrians using Transfer Learning", DOI: <a href="https://doi.org/10.1109/ICAC55051.2022.9911121">10.1109/ICAC55051.2022.9911121</a></p>
ICITS'23 - Understanding the Success Factors of Research Software: Interviews with Brazilian Computer Science Academic Researchers
<p>Artifacts used for data collection and analysis of the article accepted for publication in ICITS'23.</p> <p>Mourão, E., Trevisan, D., Viterbo, J. (2022).Understanding the Success Factors of Research Software: Interviews with Brazilian Computer Science Academic Researchers. In: ICITS'23 - 6th International Conference on Information Technology & Systems. Advances in Intelligent Systems and Computing, Springer, Cham.</p>
3D Data from "New look at Concavicaris woodfordi (Euarthropoda: Pancrustacea?) using micro-computed tomography"
<p>It includes the tomograms (CT-scan), the segmentation project (Mimics) the 3D rendered data (STL) of the holotype of <em>Concavicaris woodfordi</em> (USNM PAL 112025).</p> <p><strong>Tomograms</strong>. The specimen was micro-CT scanned using the North Star Imaging µCT scanner housed at Vanderbilt University (Tennessee, USA). 1377 two-dimensional images were obtained with a voxel size of 46 µm at a voltage of 115 kV and current of 10 µA; the volume was reconstructed using EFX-CT (North Star Imaging, Minnesota, USA).</p> <p><strong>Segmentation. </strong>Rotation (178°), cropping and conversion to 8-bit were applied to every slice prior to segmentation. Manual and semi-automatic segmentation were done using Mimics 24.0 Research Edition (Materialise). The results of the segmentation were exported as STL files. 3D rendering and processing was done using Meshlab 2021.05 (GNU GPL 3.0)</p>
Trapalyzer: A computer program for quantitative analyses in fluorescent live-imaging studies of Neutrophil Extracellular Trap formation.
<p>This data set contains a set of fluorescent microscopy images of a co-culture of neutrophil cells and E. coli bacteria used to study the Neutrophil Extracellular Trap (NET) formation stimulated by bacteria. </p> <p>NETs and live cells were visualized with a double fluorescent staining of DNA using Hoechst 33342 and SYTOX Green. </p> <p><strong>Reagents.</strong></p> <p>Roswell Park Memorial Institute (RPMI) 1640 medium, HEPES, SYTOX<sup>TM</sup> Green, and Hoechst 33342 were purchased from Thermo Fisher Scientific (Waltham, USA). LB broth was purchased from Sigma Aldrich (St Louis, MO, USA).</p> <p><strong>Preparation of blood neutrophils.</strong></p> <p>Neutrophils were obtained from peripheral blood of one healthy blood donor. Blood sample was purchased at Local Blood Donation Centre and according to local regulations, the blood donor enabled blood donation center to sell their blood samples for scientific purposes and the consent of bioethical committee was not required. Blood was collected into a citrate tube and processed within 2 hours from collection. Neutrophils were isolated using density gradient centrifugation followed by polyvinyl alcohol sedimentation, exactly as described in [1]. Isolated neutrophils were suspended in RPMI 1640 medium with 10 mM HEPES (RH). </p> <p><strong>Preparation of bacteria.</strong></p> <p><em>Escherichia coli</em> (American Type Culture Collection(ATCC) 25922 strain) were grown overnight in LB broth with shaking. In the morning, an aliquot of bacterial culture was taken, diluted 100 x in a fresh LB medium and grown for subsequent 2-3 hours. Subsequently, bacterial cultures were washed and resuspended in RH medium.</p> <p><strong>Co-culture of neutrophils with bacteria</strong><br> Neutrophils were seeded into the wells of 48-well plates at the density of 2 ⨉ 10<sup>4</sup> cells/well and allowed to settle for 30 minutes at 37°C, 5% CO2. Subsequently, <em>E. coli</em> was added into the appropriate wells at the multiplicity of infection of 4 or 1 (<em>E.coli</em>: neutrophil). Neutrophils incubated without bacteria were used as a control group. A technical duplicate for each condition was prepared. <br> For each intended timepoint (t=0, 60, 90, 120, 180 minutes), a separate 48 well plate was prepared. The plates were centrifuged for 5 minutes at 250 g to allow the contact of bacteria with neutrophils. The plates were incubated at 37°C, 5\% CO2 for a specified time and then the samples were stained with SYTOX<sup>TM</sup> Green (100 nM) and Hoechst 33342 (1.25 μM) for 10 minutes. Four images of each well were taken with Leica DMi8 fluorescent microscope equipped with a 10× magnification objective (Leica, Wetzlar, Germany). Overall, 120 images have been obtained.</p> <p> </p> <p><strong>2019_04_24--ecoli_neu_tiff_channel_merged.zip:</strong> Images in .tif format, each containing 5 channels: channel 1 for SYTOX Green fluorescent stain (green fluorescence), channel 2 for Hoechst 33342 fluorescent stain (blue fluorescence), and three channels for transmission light encoded in RGB values. </p> <p> </p> <p><strong>2019_04_24--ecoli_neu_tiff_raw_exported.zip:</strong> Images split by different light sources: transmission light (_ch00.tif), SYTOX Green fluorescence (_ch01.tif), Hoechst 33342 fluorescence (_ch02.tif).</p> <p> </p> <p>[1] Bystrzycka W, Moskalik A, Sieczkowska S, Manda-Handzlik A, Demkow U, Ciepiela O. The effect of clindamycin and amoxicillin on neutrophil extracellular trap (NET) release. <em>Cent Eur J Immunol</em>. 2016;41(1):1-5. doi:10.5114/ceji.2016.58811</p>
historical_spanish_PhD_computer_scientist
<p>Dataset with historical data of all Spanish mathematicians whose doctoral thesis specialised in computer science. It contains data from 1981 to 11 / 2022 and has the following 10 columns:</p> <p><br> - author <br> - year of publication<br> - university<br> - country<br> - title of the thesis<br> - subjet<br> - number of mentors<br> - name of mentors<br> - number of students<br> - name of students</p>
Computational Chromatography: A Machine Learning Strategy for Demixing Individual Chemical Components in Complex Mixtures
<p>This repository contains data for "Computational Chromatography: A Machine Learning Strategy for Demixing Individual Chemical Components in Complex Mixtures". </p>
X-ray computed microtomographic (XRCT) images of a fault core that slipped during the 1726 San Andreas faultzone earthquake
<p>Uploaded are x-ray computed microtomographic (XRCT) images used to examine solid-fluid interactions within one of the near-surface fault cores that slipped during a circa (ca.) 1726 San Andreas Fault zone earthquake. The study site is 16 km northwest of Bombay Beach, California (33.45873, -115.8560), and our sample, collected at a depth of 1.2 m below sea level, is from a trench that exposes deposits of ancient Lake Cahuilla. The ca. 1726 earthquake occurred during a highstand of ancient Lake Cahuilla; our study site was ~55 m below the lake's surface at the time. Crustal deformation caused by the ca. 1726 earthquake has been documented for at least 85 km along the southernmost San Andreas fault zone, which has been used, alongside other observations, to constrain the earthquake's size to a magnitude 7.2 or larger with offsets on the order of ~3 m. Since the ca. 1726 earthquake, creep and triggered slip have occurred along the section of the fault we study, with estimates of ~3 mm/yr of motion over the last ~160 years.</p> <p>We acquire XRCT images at the Advanced Light Source, Lawrence Berkeley National Lab, on beamline 8.3.2. Imaging uses a 50 mm LuAG scintillator, PCO Edge camera, and 1X Nikon lens. We image with white light x-rays, 13 ms exposure times, and 2625 projections through 180-degree continuous sample rotations. This produces 1280 two-dimensional image slices with voxels' linear dimensions of 3.24 microns. We reconstruct images and perform ring removal, center of rotation optimizations, and outlier removal using TomoPy. We name the sample FT_50_4_ZZZZ, where ZZZZ represents the image slice number; increasing numbers represent increasing distance into the outcrop.</p>
ScienceDex guides
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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.