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3,690 results for “Computing”
statistics of SST, computed by Climatology.jl, from NOAA's OISST
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Figure 6 in Cranial anatomy of the Triassic rhynchosaur Mesosuchus browni based on computed tomography, with a discussion of the vomeronasal system and its deep history in Reptilia
Figure 6. Digitally isolated skull roof bones of SAM-PK-6536 in ventral view.
Computational data for "Nano onions based on an amphiphilic Au3(pyrazolate)3 complex"
<p>Computational data for "Nano onions based on an amphiphilic Au3(pyrazolate)3 complex": data include the parameters of the CG model, input files, trajectories.</p>
scCDC: a computational method for gene-specific contamination detection and correction in single-cell and single-nucleus RNA-seq data
<p><span>In droplet-based single-cell and single-nucleus RNA-seq assays, systematic contamination of ambient RNA molecules biases the quantification of gene expression levels. Existing methods correct the contamination for all genes globally. However, specific evaluation for different contamination levels is lacking. Here, we show that DecontX and CellBender under-correct highly-contaminating genes, while SoupX and scAR over-correct lowly-/non-contaminating genes. Here, we develop scCDC as the first method to detect the contamination-causing genes and only correct expression levels of these genes, some of which are cell-type markers. Compared with existing decontamination methods, scCDC excels in decontaminating highly-contaminating genes while avoiding over-correction of other genes.</span></p>
Appendix to the paper titled: Which teamwork challenges do computing students face in a project-based learning course in research methods?
<p>Instructions on reflection reports, interview guide, and example student projects.</p>
Versatile and Robust Reservoir Computing with PWM-Driven Heterogenous R-C Circuits
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Enhance Cold Adaptation of Bidomain Amylases via High-throughput Computational Engineering
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Filming the sound: Anomaly Detection on Audio Tape Recordings using Computer Vision Algorithms
<p>This repository makes available the dataset related to the paper:</p> <p>Zafer Çınar, Alessandro Russo, Matteo Spanio, Niccolò Pretto, and Sergio Canazza, <em>Filming the Sound: Anomaly Detection on Audio Tape Recordings using Computer Vision Algorithms</em>, IAI4CH, Bozen, 2024.</p> <p>The dataset and the experiment are described in the publication above.</p> <p>This repository contains two main directories (<strong>bold</strong> indicates directory names):</p> <ul> <li><strong>video samples</strong>: the actual videos used in the paper's experiment. This folder contains four subdirectories - 3.75 ips, 7.5 ips, 15 ips, and 30 ips - each representing a different playback speed (in inches per second). Within each subdirectory are several MP4 files, recorded on an A810 Studer open reel recorder, documenting the playback of magnetic audio tapes. The files follow the naming convention “Xips (Y).mp4,” where <em>X</em> represents the tape playback speed and <em>Y</em> is a serial number identifier for each video.</li> <li><strong>irregularities</strong>: the metadata for each video with timestamp and type of irregularity. The folder includes four CSV files - 3.75.csv, 7.5.csv, 15.csv, and 30.csv - corresponding to the playback speeds of the video samples. Each CSV file provides handmade annotations for its respective videos, with three columns: <ul> <li><em>video_id</em>: name of the video file in the format “Xips (Y).mp4,” where <em>X</em> is the tape speed and <em>Y</em> is the ID number.</li> <li><em>time_label</em>: timestamp indicating the irregularity, formatted as HH:MM:SS.mls.</li> <li><em>irregularity_type</em>: category of the detected anomaly, which may be one of the following: “splice,” “shadow,” “end-of-tape,” or “annotation.”</li> </ul> </li> </ul>
Data for "Observation of the non-Hermitian skin effect and Fermi skin on a digital quantum computer"
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Facilitating Sensemaking in Computational Notebooks
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Facilitating Sensemaking in Computational Notebooks
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Data from: Inhibition behavior of mild steel by three new benzaldehyde thiosemicarbazone derivatives in 0.5 M H2SO4: Experimental and computational study
Three new benzaldehyde thiosemicarbazone derivatives namely benzaldehyde thiosemicarbazone (BST), 4-carboxyl benzaldehyde thiosemicarbazone (PBST) and 2-carboxyl benzaldehyde thiosemicarbazone (OCT) were synthesized and their inhibition effects on mild steel corrosion in 0.5 M H2SO4 solution were studied systematically using gravimetric and electrochemical measurements. Weight loss results revealed that PBST exhibited the highest inhibition efficiency of 96.6% among the investigated compounds when the concentration was 300 μM. The analysis of polarization curves indicated that the three benzaldehyde thiosemicarbazone derivatives acted as mixed type inhibitors and PBST and OCT predominantly anodic. The adsorption process of all these benzaldehyde thiosemicarbazone derivatives on Q235 steel surface in 0.5 M H2SO4 solution conformed to Langmuir adsorption isotherm. Scanning electron microscopy was conducted to show the presence of benzaldehyde thiosemicarbazone derivatives on Q235 mild steel surface. The results of theoretical calculations were in good agreement with that of experimental measurements.
Data from: Inferring the origin of populations introduced from a genetically structured native range by approximate Bayesian computation: case study of the invasive ladybird Harmonia axyridis
Correct identification of the source population of an invasive species is a prerequisite for testing hypotheses concerning the factors responsible for biological invasions. The native area of invasive species may be large, poorly known and/or genetically structured. Because the actual source population may not have been sampled, studies based on molecular markers may generate incorrect conclusions about the origin of introduced populations. In this study, we characterized the genetic structure of the invasive ladybird Harmonia axyridis in its native area using various population genetic statistics and methods. We found that H. axyridis native area most likely consisted of two geographically distinct genetic clusters located in eastern and western Asia. We then performed approximate Bayesian computation (ABC) analyses on controlled simulated microsatellite data sets to evaluate: (i) the risk of selecting incorrect introduction scenarios, including admixture between sources, when the populations of the native area are genetically structured and sampling is incomplete, (ii) the ability of ABC analysis to minimize such risks by explicitly including unsampled populations in the scenarios compared. Finally, we performed additional ABC analyses on real microsatellite data sets to retrace the origin of biocontrol and invasive populations of H. axyridis, taking into account the possibility that the structured native area may have been incompletely sampled. We found that the invasive population in eastern North America, which has served as the bridgehead for worldwide invasion by H. axyridis, was probably formed by an admixture between the eastern and western native clusters. This admixture may have facilitated adaptation of the bridgehead population.
Data from: Investigating the impact of feedback update interval on the efficacy of restorative brain–computer interfaces
Restorative brain–computer interfaces (BCIs) have been proposed to enhance stroke rehabilitation. Restorative BCIs are able to close the sensorimotor loop by rewarding motor imagery (MI) with sensory feedback. Despite the promising results from early studies, reaching clinically significant outcomes in a timely fashion is yet to be achieved. This lack of efficacy may be due to suboptimal feedback provision. To the best of our knowledge, the optimal feedback update interval (FUI) during MI remains unexplored. There is evidence that sensory feedback disinhibits the motor cortex. Thus, in this study, we explore how shorter than usual FUIs affect behavioural and neurophysiological measures following BCI training for stroke patients using a single-case proof-of-principle study design. The action research arm test was used as the primary behavioural measure and showed a clinically significant increase (36%) over the course of training. The neurophysiological measures including motor evoked potentials and maximum voluntary contraction showed distinctive changes in early and late phases of BCI training. Thus, this preliminary study may pave the way for running larger studies to further investigate the effect of FUI magnitude on the efficacy of restorative BCIs. It may also elucidate the role of early and late phases of motor learning along the course of BCI training.
Data from: Computational biomechanical analyses demonstrate similar shell-crushing abilities in modern and ancient arthropods
The biology of the extant American horseshoe crab, Limulus polyphemus, is well documented—including its dietary habits, particularly the ability to crush shell with its gnathobasic walking appendages—but virtually nothing is known about the feeding biomechanics of this iconic arthropod. This species is also considered the archetypal functional analogue for a range of extinct groups that have gnathobasic appendages, including eurypterids, trilobites, and some of the earliest arthropods, especially Sidneyia inexpectans from the middle Cambrian (508 million-year-old) Burgess Shale of Canada. Exceptionally-preserved specimens of S. inexpectans show intriguing evidence suggestive of durophagous (shell-crushing) tendencies—including thick gnathobasic spine cuticle and shelly gut contents—but this feeding mode has never been substantiated using advanced computational techniques, such as Finite Element Analysis (FEA). Here we present a unique application of 3D FEA by modelling the feeding mechanics of L. polyphemus and S. inexpectans, representing the first such analysis of a modern horseshoe crab, or indeed any fossil arthropod. Results show that mechanical performance of the feeding appendages in both arthropods is remarkably similar, confirming that S. inexpectans was a durophagous predator. This biomechanical solution to processing shelled prey therefore has a history extending over 500 million years, almost dating back to the first appearance of shell-bearing animals themselves. The arrival of durophagous predators such as S. inexpectans during the early phase of animal evolution undoubtedly fuelled the Cambrian 'arms race' that encompasses the rapid increase in diversity and abundance of biomineralised prey species.
Data from: Computational and experimental characterization of dVHL establish a Drosophila model of VHL syndrome
The von Hippel-Lindau (VHL) cancer syndrome is associated with mutations in the VHL gene. The pVHL protein is involved in response to changes in oxygen availability as part of an E3-ligase that targets the Hypoxia-Inducible Factor for degradation. pVHL has a molten globule configuration with marginal thermodynamic stability. The cancer-associated mutations further destabilize it. The Drosophila homolog, dVHL, has relatively low sequence similarity to pVHL, and is also involved in regulating HIF1-α. Using in silico, in vitro and in vivo approaches we demonstrate high similarity between the structure and function of dVHL and pVHL. These proteins have a similar fold, secondary and tertiary structures, as well as thermodynamic stability. Key functional residues in dVHL are evolutionary conserved. This structural homology underlies functional similarity of both proteins, evident by their ability to bind their reciprocal partner proteins, and by the observation that transgenic pVHL can fully maintain normal dVHL-HIF1-α downstream pathways in flies. This novel transgenic Drosophila model is thus useful for studying the VHL syndrome, and for testing drug candidates to treat it.
Data from: How little data is enough? Phase-diagram analysis of sparsity-regularized X-ray computed tomography
We introduce phase-diagram analysis, a standard tool in compressed sensing (CS), to the X-ray computed tomography (CT) community as a systematic method for determining how few projections suffice for accurate sparsity-regularized reconstruction. In CS, a phase diagram is a convenient way to study and express certain theoretical relations between sparsity and sufficient sampling. We adapt phase-diagram analysis for empirical use in X-ray CT for which the same theoretical results do not hold. We demonstrate in three case studies the potential of phase-diagram analysis for providing quantitative answers to questions of undersampling. First, we demonstrate that there are cases where X-ray CT empirically performs comparably with a near-optimal CS strategy, namely taking measurements with Gaussian sensing matrices. Second, we show that, in contrast to what might have been anticipated, taking randomized CT measurements does not lead to improved performance compared with standard structured sampling patterns. Finally, we show preliminary results of how well phase-diagram analysis can predict the sufficient number of projections for accurately reconstructing a large-scale image of a given sparsity by means of total-variation regularization.
Data from: A probabilistic metric for the validation of computational models
A new validation metric is proposed that combines the use of a threshold based on the uncertainty in the measurement data with a normalised relative error, and that is robust in the presence of large variations in the data. The outcome from the metric is the probability that a model's predictions are representative of the real world based on the specific conditions and confidence level pertaining to the experiment from which the measurements were acquired. Relative error metrics are traditionally designed for use with series of data values but orthogonal decomposition has been employed to reduce the dimensionality of data matrices to feature vectors so that the metric can be applied to fields of data. Three previously published case studies are employed to demonstrate the efficacy of this quantitative approach to the validation process in the discipline of structural analysis, for which historical data was available; however, the concept could be applied to a wide range of disciplines and sectors where modelling and simulation plays a pivotal role.
Data from: Letting the "cat" out of the bag: pouch young development of the extinct Tasmanian tiger revealed by X-ray computed tomography
The Tasmanian tiger or thylacine (Thylacinus cynocephalus) was an iconic Australian marsupial predator that was hunted to extinction in the early 1900s. Despite sharing striking similarities with canids, they failed to evolve many of the specialized anatomical features that characterize carnivorous placental mammals. These evolutionary limitations are thought to arise from functional constraints associated with the marsupial mode of reproduction, in which otherwise highly altricial young use their well-developed forelimbs to climb to the pouch and mouth to suckle. Here we present the first 3D digital developmental series of the thylacine throughout its pouch life using X-ray computed tomography on all known ethanol-preserved specimens. Based on detailed skeletal measurements, we refine the species growth curve to improve age estimates for the specimens. Comparison of allometric growth trends in the appendicular skeleton (fore- and hindlimbs) with that of other placental and marsupial mammals revealed that despite their unique adult morphologies, thylacines retained a generalized early marsupial ontogeny. Our approach also revealed mislabelled specimens that possessed large epipubic bones (vestigial in thylacine) and differing vertebral numbers. All of our generated CT models are publicly available, preserving their developmental morphology and providing a novel digital resource for future studies of this unique marsupial.
Data from: Computational 3D histological phenotyping of whole zebrafish by X-ray histotomography
Organismal phenotypes frequently involve multiple organ systems. Histology is a powerful way to detect cellular and tissue phenotypes, but is largely descriptive and subjective. To determine how synchrotron-based X-ray micro-tomography (micro-CT) can yield 3-dimensional whole-organism images suitable for quantitative histological phenotyping, we scanned whole zebrafish, a small vertebrate model with diverse tissues, at ~1 micron voxel resolutions. Using micro-CT optimized for cellular characterization (histo-tomography), brain nuclei can be computationally segmented and assigned to brain regions. Shape and volume can be computed for populations of nuclei, motor neurons and red blood cells. Computed cell density revealed striking individual phenotypic variation. Unlike histology, histo-tomography allows the detection of phenotypes that require millimeter scale context in multiple planes. We expect the computational and visual insights into 3D tissue architecture provided by histo-tomography to be useful for reference atlases, hypothesis generation, comprehensive organismal screens, and diagnostics.
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.