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1,481 results for “data processing”
IReL Survey Data: Article Processing Charges
<p>This is the raw data from a survey carried out from 16 October to 13 December 2019 and distributed to researchers, staff and students at the nine <a href="https://irel.ie/">IReL</a> member institutions: Dublin City University, Maynooth University, National University of Ireland Galway, Royal College of Surgeons in Ireland, Trinity College Dublin, Technological University Dublin, University College Cork, University College Dublin and University of Limerick.</p> <p>Responses were anonymised at point of capture and participants were informed that "Anonymised data will be incorporated into IReL reporting for future strategic planning and may also feed into future reporting and publications on IReL activities to illustrate issues and points."</p> <p>Records 1, 2, and 170 were removed by request, originating from institutional testing.</p> <p>The preprint analysis of this survey data is available at <a href="http://10.5281/zenodo.3891073">10.5281/zenodo.3891073</a>.</p>
Data for the parameterization of radiative transfer processes in urban climate models
<p><em>Radiative Transfer</em> <em>Model</em> (RTM) is a key component in microscale building resolving urban climate models (<em>UCM</em>), which are used to simulate the flow within urban area. We use different parameterizations of RTMs in the model system <a href="https://gmd.copernicus.org/articles/13/1335/2020/gmd-13-1335-2020.html">PALM</a> version 6.0 to show how much detail modellers should include in their simulation.</p> <p>We introduce the output PALM model results for two examples: (1) A simplified urban geometry consisting of an urban crossing (UC) and (2) a realistic urban domain located at the town square Ernst-Reuter-Platz in Charlottenburg in Berlin (ER). The netCDF files contain the radiative flux received by each surface in the domains, including the shortwave (direct and diffuse) radiation as well as the longwave radiation. Also, the data set includes the 3D flow variables (<em>u</em>, <em>v</em>, <em>w</em>) and the potential temperature. The model drivers (input data) for both examples are included as well.</p> <p>The data set consists of the following model input/output data:</p> <p>1) Simplified urban domain (UC):</p> <ul> <li>Input driver for the model PALM for UC (UC_model_driver.tar.gz)</li> <li>Radiation fluxes for UC when using RTM_01: radiation for horizontal surfaces (UC_RTM_01.nc)</li> <li>Radiation fluxes for UC when using RTM_02: sky view effect (building shadows) (UC_RTM_02.nc)</li> <li>Radiation fluxes for UC when using RTM_03: vegetation interaction with SW radiation (UC_RTM_03.nc)</li> <li>Radiation fluxes for UC when using RTM_04: receiving radiation from surface emission (UC_RTM_04.nc)</li> <li>Radiation fluxes for UC when using RTM_05: vegetation interaction with LW radiation (UC_RTM_05.nc)</li> <li>Radiation fluxes for UC when using RTM_06: single reflection (UC_RTM_06.nc)</li> <li>Radiation fluxes for UC when using RTM_07: vegetation interaction with reflected radiation (UC_RTM_07.nc)</li> <li>Radiation fluxes for UC when using RTM_08: multiple reflections (UC_RTM_08.nc)</li> <li>3D data for the UC reference case which includes u,v,w,theta</li> </ul> <p>2) Realistic urban domain (ER):</p> <ul> <li>Input driver for the model PALM for ER (ER_model_driver)</li> <li>Radiation fluxes for ER when using RTM_01: radiation for horizontal surfaces (ER_RTM_01.nc)</li> <li>Radiation fluxes for ER when using RTM_02: sky view effect (building shadows) (ER_RTM_02.nc)</li> <li>Radiation fluxes for ER when using RTM_03: vegetation interaction with SW radiation (ER_RTM_03.nc)</li> <li>Radiation fluxes for ER when using RTM_04: receiving radiation from surface emission (ER_RTM_04.nc)</li> <li>Radiation fluxes for ER when using RTM_05: vegetation interaction with LW radiation (ER_RTM_05.nc)</li> <li>Radiation fluxes for ER when using RTM_06: single reflection (ER_RTM_06.nc)</li> <li>Radiation fluxes for ER when using RTM_07: vegetation interaction with reflected radiation (ER_RTM_07.nc)</li> <li>Radiation fluxes for ER when using RTM_08: multiple reflections (ER_RTM_08.nc)</li> <li>3D data for the ER reference case which includes u,v,w,theta</li> </ul> <p>For more information and analysis, please check out the relevant publication in the international journal Geoscientific Model Development: Salim et. al, Importance of radiative transfer processes in urban climate models:A study based on the PALM model system 6.0, submitted to GMD.</p>
Shaft Misalignment Data for: Inter-component Phase Processing of Quasipolyharmonic Signals
<p>This dataset contains observations of vibration of test stand in three states: normal state, horizontal and vertical parallel misalignment. Full dataset is avaliable at:</p> <p>https://data.mendeley.com/datasets/pt9mjcvghd/1</p>
Composite 2D video of raw and processed video footage from an outdoor camerawork training session for qualitative data collection
<p>The video clip, in traditional 2D format, contains a short excerpt (1:43 minutes) from an outdoor camerawork training session. The raw and processed footage from the different cameras is composited in a single frame. The original composite file has 32 channels of audio so that one can switch between different microphones and combinations of microphones. This is indicated in the video clip but is not available in this file. All participants are playing particular roles in the training session, and each carries a camera. In preparation for the real data collection with a guide, one person is pretending to be a nature guide. She carries a GoPro camera on a gimbal. There is an instructor, who is carrying a single lens 360° camera on a raised extension pole with a separate ambisonic microphone. Two others are filming with a prosumer camcorder and a single lens 360° camera on a lowered extension pole respectively. And a fifth person is filming with a stereoscopic 360° camera and an independent ambisonic microphone on a monopod. In a nutshell, this is a typical team filming arrangement, in which the team needs to attentively yet silently coordinate their joint camerawork. Languages: Danish and English</p>
Analytical solution of apparent permeability of a laminated structure with cross flow in the transient flow process-data
<p>This file is the data used in the aritcle "Analytical solution of apparent permeability of a laminated structure with cross flow in the transient flow process"</p>
Data associated with the publication titled The impact of resolving sub-kilometer processes on aerosol-cloud interactions in global model simulations
<p>Datasets and scripts that are used in the journal article The impact of resolving sub-kilometer processes on aerosol-cloud interactions in global model simulations</p>
Pre-processed data for kmspd
<p>This is the pre-processed SAR data used for the paper <a href="https://arxiv.org/pdf/2008.03454.pdf">k-means on Positive Definite Matrices, and an Application to Clustering in Radar Image Sequences </a></p> <p>Code for reproducing results in the paper is available at <a href="https://github.com/frycast/kmspd">github.com/frycast/kmspd</a></p> <p>Any use of this data should attribute the author Pascal Catellazzi for his work in pre-processing.</p>
Supporting model data for paper: Measuring the impact of a new snow model using surface energy budget process relationships
<p>Supporting model data for paper: Measuring the impact of a new snow model using surface energy budget process relationships which has been submitted to the Journal of Advances in Modelling Earth Systems: https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2020MS002144</p> <p>The experiment id h3hh corresponds to simulations with the ECMWF IFS with a single layer snow model. h3eg corresponds to the experimental 5-layer snow model.</p> <p>The timeseries are made by concatenating hourly data from day2 of forecasts initialised at 00UTC each day between Dec 1st 2013 and 1 June 2014.</p>
Processed multibeam bathymetry data collected around the Ria de Aveiro, Portugal, onboard the NEREIDE research vessel.
<p>A Kongsberg EM 2040 C multibeam echo sounder transducer installed on the scientific vessel NEREIDE, was used to collect multibeam bathymetry data during graduation activities and equipment testing. This particular dataset was collected around the Ria de Aveiro, Portugal during March, 2020.</p> <p>The range of opening angles of the EM 2040 C multibeam varies between 60 and 65 degrees. The positioning system used was supported by the Real Time Kinematic (RTK) technique with the transmission of differential data in Ultra High Frequency (UHF) mode.</p> <p>The data is calibrated and corrected for the surface sound velocity. The processing of hydrographic data was performed using specific algorithms for hydrography - Combined Uncertainty and Bathymetric Estimator (CUBE). In its processing, data was referenced to the hydrographic Zero of Portugal and projected in the WGS84-UTM29N coordinate system.</p>
The spatial landscape of lung pathology during COVID-19 progression - processed IMC data
<p>Recent studies have provided insights into the pathology and immune response to coronavirus disease 2019 (COVID-19). However thorough interrogation of the interplay between infected cells and the immune system at sites of infection is lacking. We use high parameter imaging mass cytometry9 targeting the expression of 36 proteins, to investigate at single cell resolution, the cellular composition and spatial architecture of human acute lung injury including SARS-CoV-2. This spatially resolved, single-cell data unravels the disordered structure of the infected and injured lung alongside the distribution of extensive immune infiltration. Neutrophil and macrophage infiltration are hallmarks of bacterial pneumonia and COVID-19, respectively. We provide evidence that SARS-CoV-2 infects predominantly alveolar epithelial cells and induces a localized hyper-inflammatory cell state associated with lung damage. By leveraging the temporal range of COVID-19 severe fatal disease in relation to the time of symptom onset, we observe increased macrophage extravasation, mesenchymal cells, and fibroblasts abundance concomitant with increased proximity between these cell types as the disease progresses, possibly as an attempt to repair the damaged lung tissue. This spatially resolved single-cell data allowed us to develop a biologically interpretable landscape of lung pathology from a structural, immunological and clinical standpoint. This spatial single-cell landscape enabled the pathophysiological characterization of the human lung from its macroscopic presentation to the single-cell, providing an important basis for the understanding of COVID-19, and lung pathology in general.</p>
Code and processed data accompanying "Widespread haploid-biased gene expression enables sperm-level natural selection"
<p>Code and processed data required to reproduce the analysis in "Widespread haploid-biased gene expression enables sperm-level natural selection".</p>
Dataset accompanying article: On Linear and Circular Approach to GPS Data Processing: Analyses of the Horizontal Positioning Deviations Based on the Adriatic Region IGS Observables
<p>The dataset accompanies journal article: On Linear and Circular Approach to GPS Data Processing: Analyses of the Horizontal Positioning Deviations Based on the Adriatic Region IGS Observables published on 21 January 2021 in Data. </p> <p>SINEX, RINEX, position solution files, logs used for positional accuracy and deviation distribution of IGS observables and additional figures with results are included. Dataset covers period from 10th to 20th of March 2017. </p> <p>IGS SINEX combined weekly station position/velocity solutions were retrieved from the online archives of the Crustal Dynamics Data Information System (CDDIS), NASA Goddard Space Flight Center, Greenbelt, MD, USA, available at: ftp://cddis.nasa.gov/gnss/products/. Please note that from from October 31, 2020 anonymous ftp service has been discontinued. Access with examples is available via HTTPS or ftp-ssl from <a href="https://cddis.nasa.gov/Data_and_Derived_Products/CDDIS_Archive_Access.html">CDDIS Archive</a></p> <p>RINEX observation and navigation files were retrieved from IGS repository available at: ftp://igs.ign.fr/pub/igs/data/</p> <p>Position solution files were determined with <a href="https://github.com/tomojitakasu/RTKLIB_bin/">RTKLIB</a>: An Open Source Program Package for GNSS Positioning, version 2.4.3 b33 available</p> <p>Please cite respective sources accordingly.</p> <p> </p>
Data from: Beyond a single patch: local and regional processes explain diversity patterns in a seagrass epifaunal metacommunity
<p>Ecological communities are jointly structured by dispersal, density-independent responses to environmental conditions and density-dependent biotic interactions. Metacommunity ecology provides a framework for understanding how these processes combine to determine community seagrass meadows along the British Columbia coast, we tested the hypothesis that eelgrass (<i>Zostera marina</i> L.) epifaunal invertebrate assemblages are influenced by local environmental conditions, but that high dispersal rates at larger spatial scales dampen effects of environmental differences. We used hierarchical joint species distribution modelling to understand the contribution of environmental conditions, spatial distance between meadows, and species co-occurrences to epifaunal invertebrate abundance and distribution across the region. We found that patterns of taxonomic compositional similarity among meadows were inconsistent with dispersal limitation, and meadows in the same region were often no more similar to each other than meadows over 1000 km away. Abiotic environmental conditions (temperature, dissolved oxygen) explained a small fraction of variation in taxonomic abundances patterns across the region. We found novel co-occurrence patterns among taxa that could not be explained by shared responses to environmental gradients, suggesting the possibility that interspecific interactions influence seagrass invertebrate abundance and distribution. Our results suggest that biodiversity and ecosystem functions provided by seagrass meadows reflect ecological processes occurring both within meadows and across seascapes, and that management of eelgrass habitat for biodiversity may be most effective when both local and regional processes are considered.</p>
Data from: Towards an interactive, process‐based approach to understanding range shifts: developmental and environmental dependencies matter
Many species are undergoing distributional changes in response to climate change. However, wide variability in range shifting rates has been observed across taxa, and even among closely-related species. Attempts to link climate-mediated range shifts to traits has often produced weak or conflicting results. Here we investigate interactive effects of developmental processes and environmental stress on the expression of traits relevant to range shifts. We use an individual-based modelling approach to assess how different developmental strategies affect range shift rates under a range of environmental conditions. We find that under stressful conditions, such as at the margins of the species' fundamental niche, investment in prolonged development leads to the greatest rates of range shifting, especially when longer time in development leads to of improved fecundity and dispersal-related traits. However, under benign conditions, and when traits are less developmentally plastic, shorter development times are preferred for rapid range shifts, because higher generational frequency increases the number of individual dispersal events occurring over time. Our results suggest that the ability of a species to range shift depends not only on their dispersal and colonisation characteristics but also how these characteristics interact with developmental strategies. Benefits of any trait always depended on the environmental and developmental sensitivity of life history trait combinations, and the environmental conditions under which the range shift takes place. Without considering environmental and developmental sources of variation in the expression of traits relevant to range shifts, there is little hope of developing a general understanding of intrinsic drivers of range shift potential
Data from: Perceived duration of brief visual events is mediated by timing mechanisms at the global stages of visual processing
There is a growing body of evidence pointing to the existence of modality-specific timing mechanisms for encoding sub-second durations. For example, the duration compression effect describes how prior adaptation to a dynamic visual stimulus results in participants underestimating the duration of a sub-second test stimulus when it is presented at the adapted location. There is substantial evidence for the existence of both cortical and pre-cortical visual timing mechanisms; however, little is known about where in the processing hierarchy the cortical mechanisms are likely to be located. We carried out a series of experiments to determine whether or not timing mechanisms are to be found at the global processing level. We had participants adapt to random dot patterns that varied in their motion coherence, thus allowing us to probe the visual system at the level of motion integration. Our first experiment revealed a positive linear relationship between the motion coherence level of the adaptor stimulus and duration compression magnitude. However, increasing the motion coherence level in a stimulus also results in an increase in global speed. To test whether duration compression effects were driven by global speed or global motion, we repeated the experiment, but kept global speed fixed while varying motion coherence levels. The duration compression persisted, but the linear relationship with motion coherence was absent, suggesting that the effect was driven by adapting global speed mechanisms. Our results support previous claims that visual timing mechanisms persist at the level of global processing.
Data from: The influence of geomorphic processes on plant distribution and abundance as reflected in plant tolerance curves
Ecologists describe plant distribution using direct gradient analysis, by which a tolerance curve of species abundance is described along an environmental gradient (any environmental variable that affects plant distribution). Soil moisture is generally the gradient in low relief areas that explains the most variation. Traditional direct gradient analyses have used terrain structure (i.e. transects up or down hillslopes) as a correlate to soil moisture. Here we use a numerical tectonic and geomorphic process-based landscape development model to create two landscapes with different geomorphic characteristics (i) to demonstrate the influence of geomorphic processes on soil moisture patterns and plant distribution and (ii) to evaluate the effectiveness of transects in describing moisture gradients and tolerance curves on landscapes dominated by creep or overland flow. We use a topographic index to approximate the distribution of soil moisture as it is determined by the shape of these different landscapes. Transects are placed on hillslopes in each model landscape and used to construct tolerance curves. Results show that transect methods that use the distance from the channel to the ridgeline as an approximation of soil moisture create variable tolerance curves for the same plant both within a single landscape and between different landscapes. The reason for these differences is that transects do not take into account the 3-dimensional landscape form that explains water movement. Landscapes have regions of convexity and flow path divergence and regions of concavity and flow path convergence which, along with hillslope length, determine contributing area. In addition, hillslope curvature results in varying capacities to retain water. However, when the topographic index is used instead of hillslope transect position, tolerance curves from the same and different landscapes reflect the differences the topographic structure has on soil moisture. We thus show that traditional methods of direct gradient analysis are not always adequate as they do not tend to consider that soil moisture depends on hillslope length, curvature, and slope. Furthermore, we show that within and between landscapes there are differences in spatial distributions of soil moisture that are reflections of the geomorphic processes that created them.
Data from: Awake fMRI reveals a specialized region in dog temporal cortex for face processing
Recent behavioral evidence suggests that dogs, like humans and monkeys, are capable of visual face recognition. But do dogs also exhibit specialized cortical face regions similar to humans and monkeys? Using functional magnetic resonance imaging (fMRI) in six dogs trained to remain motionless during scanning without restraint or sedation, we found a region in the canine temporal lobe that responded significantly more to movies of human faces than to movies of everyday objects. Next, using a new stimulus set to investigate face selectivity in this predefined candidate dog face area, we found that this region responded similarly to images of human faces and dog faces, yet significantly more to both human and dog faces than to images of objects. Such face selectivity was not found in dog primary visual cortex. Taken together, these findings: (1) provide the first evidence for a face-selective region in the temporal cortex of dogs, which cannot be explained by simple low-level visual feature extraction; (2) reveal that neural machinery dedicated to face processing is not unique to primates; and (3) may help explain dogs' exquisite sensitivity to human social cues.
Data from: Social learners require process information to outperform individual learners
Humans exhibit a rich and complex material culture with no equivalent in animals. Also, social learning, a crucial requirement for culture, is particularly developed in humans and provides a means to accumulate knowledge over time and to develop advanced technologies. However, the type of social learning required for the evolution of this complex material culture is still debated. Here, using a complex and opaque virtual task, the efficiency of individual learning and two types of social learning (product-copying and process-copying) were compared. We found that (1) individuals from process-copying groups outperformed individuals from product-copying groups or individual learners, whereas access to product information was not a sufficient condition for providing an advantage to social learners compared to individual learners; (2) social learning did not seem to affect the exploration of the fitness landscape; (3) social learning led to strong within-group convergence and also to between-group convergence and (4) individuals used widely variable social learning strategies. The implications of these results for cumulative culture evolution are discussed.
Data from: Evolutionary patterns and processes: lessons from ancient DNA
Ever since its emergence in 1984, the field of ancient DNA has struggled to overcome the challenges related to the decay of DNA molecules in the fossil record. With the recent development of high-throughput DNA sequencing technologies and molecular techniques tailored to ultra-damaged templates, it has now come of age, merging together approaches in phylogenomics, population genomics, epigenomics, and metagenomics. Leveraging on complete temporal sample series, ancient DNA provides direct access to the most important dimension in evolution—time, allowing a wealth of fundamental evolutionary processes to be addressed at unprecedented resolution. This review taps into the most recent findings in ancient DNA research to present analyses of ancient genomic and metagenomic data.
Data from: Inference of evolutionary jumps in large phylogenies using Lévy processes
While it is now widely accepted that the rate of phenotypic evolution may not necessarily be constant across large phylogenies, the frequency and phylogenetic position of periods of rapid evolution remain unclear. In his highly influential view of evolution, G. G. Simpson supposed that such evolutionary jumps occur when organisms transition into so called new adaptive zones, for instance after dispersal into a new geographic area, after rapid climatic changes, or following the appearance of an evolutionary novelty. Only recently, large, accurate and well calibrated phylogenies have become available that allow testing this hypothesis directly, yet inferring evolutionary jumps remains computationally very challenging. Here, we develop a computationally highly efficient algorithm to accurately infer the rate and strength of evolutionary jumps as well as their phylogenetic location. Following previous work we model evolutionary jumps as a compound process, but introduce a novel approach to sample jump configurations that does not require matrix inversions and thus naturally scales to large trees. We then make use of this development to infer evolutionary jumps in Anolis lizards and Loriinii parrots where we find strong signal for such jumps at the basis of clades that transitioned into new adaptive zones, just as postulated by Simpson's hypothesis.
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.