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Computed tomography (CT) was used to study the interaction of NMs with the plant cell tissue in vivo using Zeiss Xradia 510 system on Arabidopsis thaliana leaf. T
<p>This work was supported by the National Research Facility for Lab X-ray CT (NXCT) at the µ-VIS X-ray Imaging Centre, University of Southampton, through EPSRC grant EP/T02593X.</p>
Data from: Computational fluid dynamics confirms drag reduction associated with trilobite queuing behaviour
<p>Queuing behaviour has been documented in marine arthropods from Cambrian to modern oceans. One possible explanation of this behaviour is drag reduction, with trilobites in the following positions hypothesized to produce less drag than those leading. In this study, we evaluate the hydrodynamics of queuing behaviour in the Devonian trilobite Trimerocephalus chopini using computational fluid mechanics. Our results show that the drag forces of the trilobites following in the queue were substantially lower than those produced by the leader (75.1% lower at 2 cm s-1). Drag reduction is positively correlated with the movement speed of the trilobites, but decreases with increasing distance from the leader. Our results support the hypothesis that the queuing behaviour of trilobites was an adaptation for reducing hydrodynamic drag. This drag reduction effect compensated for the energy cost of movement, which would have been particularly advantageous during migration.</p>
Data for: Many-body thermodynamics on quantum computers via partition function zeros
<p>Partition functions are ubiquitous in physics: they are important in determining the thermodynamic properties of many-body systems, and in understanding their phase transitions. As shown by Lee and Yang, analytically continuing the partition function to the complex plane allows us to obtain its zeros and thus the entire function. Moreover, the scaling and nature of these zeros can elucidate phase transitions. Here we show how to find partition function zeros on noisy intermediate-scale trapped ion quantum computers in a scalable manner, using the XXZ spin chain model as a prototype, and observe their transition from XY-like behavior to Ising-like behavior as a function of the anisotropy. While quantum computers cannot yet scale to the thermodynamic limit, our work provides a pathway to do so as hardware improves, allowing the future calculation of critical phenomena for systems beyond classical computing limits.</p>
Fortran code to compute the spiralling North Atlantic Gyre
<p>Code to compute and plot the figures describing the North Atlantic Subtropical Gyres contribution to the AMOC. </p>
Investigating the two regimes of fibrin clot lysis: an experimental and computational approach
<p> </p> <p><strong>Investigating the two regimes of fibrin clot lysis: an experimental and computational approach</strong></p> <p>Dataset and python files (Python3) to reproduce all figures and simulations presented in the manuscript.</p> <p> </p> <p>**********************<br> * Run_simulations.py *<br> **********************</p> <p>* To run the simulations:<br> python3.8 Run_simulations.py arg1 arg2 arg3 arg4</p> <p> - arg1:<br> Directory with experimental lysis profiles<br> <br> - arg2:<br> Directory to store initial conditions of the lysis (i.e state of the system after clot formation)<br> if the directory does not exist, it is created.<br> <br> - arg3:<br> Directory to store the simulated lysis profiles<br> if the directory does not exist, it is created.</p> <p> - arg4:<br> index of the first set of clotting kinetic parameters (92 sets of parameters)</p> <p> - arg5:<br> index of the last set of clotting kinetic parameters (92 sets of parameters)</p> <p>* Example: python3.8 Run_simulations.py Raw_Data/ Init/ Results/ 0 92</p> <p><br> * Requires:<br> - module_fibrin_polymerization_Diamond_kinetics.py<br> - module_kinetics.py<br> - solid_Diamond_Anand_dict.py (dictionnary with parameters of the simulations)<br> - output_parameters_polymerization_T1000.txt (sets of clotting kinetic parameters)<br> - Mean_LAT_LYS_shell.txt (mean fraction of shells during slow and fast lysis for each experiment. Used to compute the distribution of shells for the surrogate model)</p> <p><br> ****************************************<br> * make_analysis_figures_simulations.py *<br> ****************************************</p> <p>* To reproduce the figures associated to simulation results:<br> python3.8 make_analysis_figures_simulations.py arg1 arg2 arg3 arg4</p> <p> - arg1:<br> Directory with experimental lysis profiles</p> <p> - arg2:<br> Directory with the simulated lysis profiles</p> <p> - arg3:<br> Directory with initial conditions</p> <p> - arg4:<br> Directory with the results of the sensitivity analysis</p> <p>* Example: python3.8 make_analysis_figures_simulations.py Raw_Data/ Results/ Init/ Sensitivity_Analysis/</p> <p>* PDF Figures are created in the current directory</p> <p>* Requires:<br> - module_analyze_simulations.py<br> - module_analyze_data.py<br> - output_parameters_polymerization_T1000.txt<br> - manip_summary.txt (clot formation time, slow lysis time, fast lysis time for each experiment)<br> - Experiments_sorted.txt (experimental conditions, sorted by increasing order of concentrations)</p> <p><br> ****************************************<br> * make_analysis_figures_experiments.py *<br> ****************************************</p> <p>* To reproduce the figures associated to experimental results:<br> python3.8 make_analysis_figures_experiments.py arg1</p> <p> - arg1:<br> Directory with experimental lysis profiles</p> <p>* Example: python3.8 make_analysis_figures_experiments.py Raw_Data/</p> <p>* PDF Figures are created in the current directory</p> <p>* Requires:<br> - module_analyze_data.py<br> - Experiments.txt (contains experimental conditions)</p> <p> </p>
Data from: Computer-aided X-ray screening for tuberculosis and HIV testing among adults with cough in Malawi (the PROSPECT study): a randomized trial and cost-effectiveness analysis
<p>Suboptimal tuberculosis (TB) diagnostics and HIV contribute to the high global burden of TB. We investigated costs and yield from systematic HIV-TB screening, including computer-aided digital chest X-ray (DCXR-CAD). Suboptimal tuberculosis (TB) diagnostics and HIV contribute to the high global burden of TB. We investigated costs and yield from systematic HIV-TB screening, including computer-aided digital chest X-ray (DCXR-CAD).</p> <p>In this open, three-arm randomised trial, adults (≥18 years) with cough attending acute primary services in Malawi were randomised (1:1:1) to standard-of-care (SOC); oral HIV testing (HIV screening) and linkage to care; or HIV testing and linkage to care plus DCXR-CAD with sputum Xpert for high CAD4TBv5 scores (HIV-TB screening). Participants and study staff were not blinded to intervention allocation, but investigator blinding was maintained until final analysis. The primary outcome was time to TB treatment. Secondary outcomes included proportion with same-day TB treatment; prevalence of undiagnosed/untreated bacteriologically-confirmed TB on day 56; and undiagnosed/untreated HIV. Analysis was done on an intention to treat basis. Cost-effectiveness analysis used a health-provider perspective. Between 15/11/2018-27/11/2019, 8236 were screened for eligibility, with 473, 492, and 497 randomly allocated to SOC, HIV, and HIV-TB screening arms; 53 (11%), 52 (9%), and 47 (9%) were lost to follow-up, respectively. At 56 days, TB treatment had been started in 5 (1.1%) SOC, 8 (1.6%) HIV-screening, and 15 (3.0%) HIV-TB screening participants. Median (IQR) time to TB treatment was 11 (6.5-38), 6 (1-22) and 1 (0-3) days (hazard ratio for HIV-TB vs. SOC: 2.86, 1.04-7.87), with same-day treatment of 0/5 (0%) SOC, 1/8 (12.5%) HIV, and 6/15 (40.0%) HIV-TB screening arm TB patients (p=0.03). At day 56, 2 SOC (0.5%), 4 HIV (1.0%), and 2 HIV-TB (0.5%) participants had undiagnosed microbiologically-confirmed TB. HIV screening reduced the proportion with undiagnosed or untreated HIV from 10 (2.7%) in the SOC arm to 2 (0.5%) in the HIV-screening arm (risk ratio [RR]: 0.18, 0.04-0.83), and 1 (0.2%) in the HIV-TB screening arm (RR: 0.09, 0.01-0.71). Incremental costs were US$3.58 and US$19.92 per participant screened for HIV and HIV-TB; the probability of cost-effectiveness at a US$1200/quality-adjusted life-year (QALY) threshold were 83.9% and 0%. Main limitations were the lower than anticipated prevalence of tuberculosis and short participant follow-up period; cost and quality of life benefits of this screening approach may accrue over a longer time horizon.</p> <p>DCXR-CAD with universal HIV screening significantly increased the timeliness and completeness of HIV and TB diagnosis. If implemented at scale this has potential to rapidly and efficiently improve TB and HIV diagnosis and treatment.</p>
FIGURE 3 in COMPUTER-AIDED DRAWING SYSTEM - SUBSTITUTE FOR CAMERA LUCIDA Ekaterina A. S and Dmitry D. V
FIGURE 3: Setting a live image from the camera as the background for drawing (software used for this example are VLC media player and GIMP graphic software). Since the overlay mode image cannot be reproduced in a screenshot, we photographed the computer screen using a digital camera instead of making the combined images from incomplete screenshots: A – media player showing the image; B – screenshot taken from A and pasted to the new file in the drawing software. The overlay mode is active: part of the video frame is visible through a replica of the media player's window where it overlaps with an original window of the media player, the rest of the replica is dark but is nevertheless filled with overlay color. Both arrows point to the area filled with overlay color; C – media player is closed, the whole area filled with overlay color looks dark; D – same as C, but the media player was not in overlay mode when the screenshot was taken. There is no overlay color on the screen. See text for further explanations.
FIGURE 2 in COMPUTER-AIDED DRAWING SYSTEM - SUBSTITUTE FOR CAMERA LUCIDA Ekaterina A. S and Dmitry D. V
FIGURE 2: Settings of VLC media player. Those important for correct and convenient work in overlay mode are indicated by arrows. This dialog can be found under the 'Tools> Preferences' menu.
FIGURE 1 in COMPUTER-AIDED DRAWING SYSTEM - SUBSTITUTE FOR CAMERA LUCIDA Ekaterina A. S and Dmitry D. V
FIGURE 1: An example of a working place with the complete drawing apparatus ready to use. C-camera, T-pen tablet
FIGURE 4 in COMPUTER-AIDED DRAWING SYSTEM - SUBSTITUTE FOR CAMERA LUCIDA Ekaterina A. S and Dmitry D. V
FIGURE 4: The procedure of setting the video camera as a source of live capture image in VLC media player: A – click 'Open capture device' under 'Media' menu; B – choose the video camera ('Video device name'), set 'Audio device name' to 'None' and set the horizontal pixel size of the video image — it must be chosen from the predefined list specific for particular video camera or, alternatively, left blank. In the latter case the video, most probably, will have the lowest possible resolution. The bottom arrow points to the command line string which is generated by VLC media player and which can be used to automate the procedure of setting the video camera parameters; this command line is not required for the method described in this paper; C – setting the live capture image as a desktop background for convenient drawing.
Fig. 4 in SNAIL - an interactive computer program for the determination of Central European freshwater gastropods
Fig. 4: Key offered by thee computer proogram SNAIL for determiningg the family oof the Lymnaeidae.
Fig. 2 in Redescription and phylogenetic position of the enigmatic Neotropical electric fish Iracema caiana Triques (Gymnotiformes: Rhamphichthyidae) using x-ray computed tomography
Fig. 2. Head of Iracema caiana, MZUSP 49205 (paratype), 345 mm SL.
X-ray computed tomography and scanning electron microscopy datasets of unidirectional and textured glass fibre composites.
<p>3D x-ray tomography and 2D scanning electron microscopy (SEM) data behind the publications: </p> <p>Salling, F.B, Jeppesen, N., Sonne, M.R., Hattel, J.H., Mikkelsen, L.P. Individual Fibre Inclination Segmentation from X-ray Computed Tomography using Principal Component Analysis, <em>Journal of Composite Materials</em>, <strong>56</strong>, 83-98, <a href="https://doi.org/10.1177%2F00219983211052741">https://doi.org/10.1177/00219983211052741</a>, 2022.</p> <p>to where the reference should be given if used. </p> <p>Details on the data-set is given in the supplementary document found together with the data</p> <p>The data-files is given for the two material case called Mock and UD. For each material case, the data is given as:</p> <ul> <li>.txm-files: 3D reconstructed x-ray scan files <ul> <li>FoV 2mm binning 2 (analyzed in the paper)</li> <li>FoV 4mm binning 1 (additional data-set)</li> </ul> </li> <li>2Dtif.zip-files: 2D tif-stack version of the 3D reconstructed data-set</li> <li>.tif-files: stitched SEM scanning file used for fiber volume fraction determination</li> <li>.hdr-files: meta-data ASCII file behind the SEM scan</li> <li>tif.zip-files: The individual images behind the stitched SEM scanning file</li> <li>fig-files: digital form of the fibre trajectories colored according to their individual mean inclination used in figure xx in reference yy</li> <li>m-files: Matlab-script for calculating the fibre volume fraction (Vf) from the SEM image</li> <li>mat-files: Mat-file with the segmented part in the SEM image used for the Vf calculation</li> </ul>
Effects of a Vibro-Tactile P300 Based Brain-Computer Interface on the Coma Recovery Scale-Revised in Patients With Disorders of Consciousness
<p>Persons diagnosed with disorders of consciousness (DOC) typically suffer from motor and cognitive disabilities. Recent research has shown that non-invasive brain-computer interface (BCI) technology could help assess these patients’ cognitive functions and command following abilities. 20 DOC patients participated in the study and performed 10 vibro-tactile P300 BCI sessions over 10 days with 8–12 runs each day. Vibrotactile tactors were placed on the each patient’s left and right wrists and one foot. Patients were instructed, via earbuds, to concentrate and silently count vibrotactile pulses on either their left or right wrist that presented a target stimulus and to ignore the others. Changes of the BCI classification accuracy were investigated over the 10 days. In addition, the Coma Recovery Scale-Revised (CRS-R) score was measured before and after the 10 vibro-tactile P300 sessions. In the first run, 10 patients had a classification accuracy above chance level (>12.5%). In the best run, every patient reached an accuracy ≥60%. The grand average accuracy in the first session for all patients was 40%. In the best session, the grand average accuracy was 88% and the median accuracy across all sessions was 21%. The CRS-R scores compared before and after 10 VT3 sessions for all 20 patients, are showing significant improvement (<em>p</em> = 0.024). Twelve of the twenty patients showed an improvement of 1 to 7 points in the CRS-R score after the VT3 BCI sessions (mean: 2.6). Six patients did not show a change of the CRS-R and two patients showed a decline in the score by 1 point. Every patient achieved at least 60% accuracy at least once, which indicates successful command following. This shows the importance of repeated measures when DOC patients are assessed. The improvement of the CRS-R score after the 10 VT3 sessions is an important issue for future experiments to test the possible therapeutic applications of vibro-tactile and related BCIs with a larger patient group.</p>
Computing Necessary Conditions for Near-Optimality in Capacity Expansion Planning Problems - Dataset
<p>This dataset contains the inputs used to compute the results presented in the submission titled "Computing Necessary Conditions for Near-Optimalityin Capacity Expansion Planning Problems".</p> <p>The dataset contains a first folder with the inputs of the model, a second folder with the outputs of the model and a file describing the content of the input folder as well as the techno-economic assumptions and sources used for the submission.</p>
A Systematic Mapping of the Classification of Open Educational Resources for Computer Science Education in Digital Sources (Data)
<p>Data from a Systematic Mapping of the classification of Open Educational Resources for Computer Science Education.</p> <p>Content:</p> <ul> <li>Studies selected</li> <li>Digital sources used to classify Open Educational Resources for Computer Science Education</li> <li>Computer Science domains explored by Open Educational Resources</li> <li>Approaches for the classification of Open Educational Resources for Computer Science Education</li> </ul>
In materia reservoir computing with a fully memristive architecture based on self-organizing nanowire networks - Dataset
<p>This is the dataset of "<em>In materia</em> reservoir computing with a fully memristive architecture based on self-organizing nanowire networks"</p>
Evaluating computational approaches for comparison of protein expression across cancer indications
<p>########################################################################################################<br># CPTAC PAN cancer imputed and normalized data <br>########################################################################################################<br># R Code snippet<br>iBAQ = readRDS("/your path/iBAQ.rds")<br>table(iBAQ$normalized)<br># CN No QN QN riBAQ Smooth QN <br># 17435640 17435640 17435640 17435640 17435640 <br>library(dplyr)<br>full.qn <- iBAQ %>% filter(normalized=="QN")<br>OV <- full.qn %>% filter(Indication=="OV")%>% filter(Tissue=="Tumor")<br>OV_4genes <- OV[OV$Gene%in% c("CDH6", "FOLR1", "ERBB2", "TACSTD2"),]</p>
A computational workflow for cell line profiling by Imaging Mass Cytometry.
<p>Imaging Mass Cytometry Data as 32-bit single TIFF with computational analysis from the manuscript: <strong>A computational workflow for cell line profiling by Imaging Mass Cytometry.</strong></p> <p><strong><span lang="EN-US">Breast cancer cell lines SKBR3 MCF7 HCC1143 IMC data and CellProfiler pipelines.zip</span></strong></p> <p><strong><span lang="EN-US">Elongated cell lines HeLa SKOV3 BJ IMC data and CellProfiler pipelines.zip:</span></strong></p> <p><strong><span lang="EN-US">Small cell lines A431 HT29 BxPC3 IMC data and CellProfiler pipelines.zip</span></strong></p> <p><strong><span lang="EN-US">U937 PMA-differentiated cells IMC data and CellProfiler pipeline.zip</span></strong></p> <p><strong><span lang="EN-US">A431 Cisplatin Study IMC data and CellProfiler pipeline.zip</span></strong></p> <p><span lang="EN-US">Contains 1 folder per cell line or drug treatment of single TIFF 32-bit markers exported from MCD/txt files (including Xe131 channel) and their respective cpproj. pipeline file for IMC Cell Line Profiler workstream reproducible analysis</span></p> <p><strong><span lang="EN-US">IMC Cell Line Profiler high dimensional and correlation analysis R scripts.zip</span></strong></p> <p><span lang="EN-US">Contains three adaptable R scripts for high dimensional analysis, correlation analysis and combination of both scripts for Machine Learning classified datasets.</span></p> <p><strong><span lang="EN-US">Breast cancer cell lines nuclear state classification by CellProfiler Analyst MLs.zip</span></strong></p> <p><span lang="EN-US">Contains SQLite databases, properties files, training datasets, nuclear classes visual rendering, and classifier model files with outputs for two machine learning classifiers (Random Forest and Fast Gentle Boosting) per breast cancer cell line for CellProfiler Analyst workflow reproducibility.</span></p> <p><strong><span lang="EN-US">A431 Cisplatin Study IMC data nuclear state classification by CellProfiler Analyst MLs.zip</span></strong></p> <p><span lang="EN-US">Contains SQLite databases, properties files, training datasets, classifier model with outputs for Fast Gentle Boosting and Random Forest per treatment for CellProfiler Analyst workflow reproducibility.</span></p> <p><strong><span lang="EN-US">IMC Cell Line Profiler pseudo-color images with Ki-67 marker Cytoplasm marker and Cell-ID nuclei (Fig2 Fig3), visual nuclei and whole-cell segmentation contours rendered images (Fig4).</span></strong></p> <p><strong><span lang="EN-US">Non-compensated and compensated multiTIFF 32-bit cells lines with Cellprofiler masks SCE objects and FCS files and Datatables.zip</span></strong></p> <p>Contains publicly available compensation matrix (<a href="https://zenodo.org/records/7575859">https://zenodo.org/records/7575859</a>) , R compensation script (<strong>Compensation IMC data with CATALYST.R)</strong>, compensated and non-compensated multiTIFF stacks 32-bit per cell line experiment, exported CellProfiler 16-bit masks per cell line dataset, R single cell experiment script (<strong>Conversion IMC data to Single Cell Experiments Objects and FCS.R)</strong> with inputs and outputs (fcs files, sce files, panel files, metadata files),R<strong> </strong>conversion single cell experiment to datatable script<strong> (Conversion SCE to Datatable and analysis.R)</strong>.</p> <p><strong><span lang="EN-US">Step-by-step guide to assist users with the IMC Cell Line Profiler computational workflow.</span></strong></p>
PyGBe-LSPR—Computational nanoplasmonics for biosensing applications (problem datasets)
<p>Problem folders including all the input files necessary to reproduce the computations in the paper PyGBe-LSPR—Computational nanoplasmonics for biosensing applications. </p>
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.