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6,467 results for “process”
Comprehensive Risk and Emergency Management Conceptual Design and Map (Response Process Big Picture)
<p>Comprehensive Risk and Emergency Management Conceptual Design and Map helps to have an insight about Risk and Emergency Planning and Management Process to better act.</p> <p>Response Process Big Picture</p>
Structure of small tropical islands freshwater fish and crustacean communities: a niche- or dispersal-based process?
Determining the relative importance of niche- and dispersal-based processes in the structuring of animal communities is central in ecology. Freshwater fish and crustacean communities of small tropical islands can bring new insights for understanding these processes as all their species present a pelagic larval stage which gives them important dispersal capacities. Consequently, we hypothesized that dispersal-based process maybe preponderant for structuring these communities from the regional- to the local, i.e. survey site, scales. Gradient forest analyses allowed us to model the effect of 12 environmental variables on freshwater taxa abundances in two southwestern Indian Ocean islands: Mayotte (26 taxa) and Reunion (21). A total of 153 surveys in Mayotte and 266 in Reunion were used for building the models. Despite the strong heterogeneity of environmental conditions between the two islands, the main factors structuring freshwater fish and crustacean communities in both islands were the elevation and the slope of the sites. The observed structure appeared more pronounced for predatory species than for primary consumers and omnivores. As predators generally have limited locomotor capacities, it is concluded that dispersal-based process structures these communities not only at large geographical scales but also at the intra-watershed scale, by limiting the inland penetration (or dispersion) of species in relation to their locomotor capacities. However, more knowledge concerning ecological traits and taxonomic status of many species is needed to confirm this assumption.
Genome-wide haplotype counting in diatoms S. robusta and P. tricornutum - processed datasets
<p><strong>Datasets used for genome-wide haplotype counting in <em>S. robusta</em> and <em>P. tricornutum</em> next-generation sequencing data.</strong></p> <p>For <em>S. robusta</em> and <em>P. tricornutum </em>genome-wide haplotype counting, reliable SNPs set was first identified in ILLUMINA short-read sequencing datasets and then used for counting of the number of haplotypes in the PacBio RS II and MinION long reads. The ILLUMINA and PacBio data of <em>S. robusta</em> were downloaded from <a href="https://www.ebi.ac.uk/ena/browser/view/PRJEB36614">https://www.ebi.ac.uk/ena/browser/view/PRJEB36614</a> and ILLUMINA and Minion data of <em>P. tricornutum</em> were downloaded from <a href="https://www.ebi.ac.uk/ena/browser/view/PRJNA487263">https://www.ebi.ac.uk/ena/browser/view/PRJNA487263</a>.</p> <p>Reference genome assembly for<em> S. robusta</em>: CAICTM010000001-CAICTM010004752 (European Nucleotide Archive) and</p> <p>Reference genome assembly for<em> P. tricornutum</em>: GCA_000150955.2 (European Nucleotide Archive).</p> <p>Uploaded files: </p> <p>-.bam files containing S. robusta PacBio self-corrected CCS reads aligned to reference and processed and P. tricornutum self-corrected MinION reads aligned to reference and processed: </p> <p><em>S_robusta_aligned_corrected_PacBio_reads.bam</em></p> <p><em>P_tricornutum_aligned_corrected_MinION_reads.bam</em></p> <p>-.table files with selected reliable SNPs used for haplotype counting with CHROM, POSITION, REFERENCE and ALTERNATIVE allele </p> <p><em>S_robusta_SNPs.table</em></p> <p><em>P_tricornutum_SNPs.table</em></p> <p> </p>
Parallel responses of species diversity and functional diversity to changes in patch size are driven by distinct processes
1. Do species and functional trait diversity respond similarly to deterministic and random processes? Theory predicts that the contributions of random and deterministic processes to species diversity depend on patch size. Smaller patches are more strongly influenced by random sampling effects, by having fewer individuals, as well as ecological drift, which propagates the effects of small samples through stochastic birth and death processes. These random processes decrease species richness and increase compositional differences among small patches. Larger patches are predicted to be more deterministically assembled, with greater species richness and greater predictability of composition for a particular environment. The consequences of patch size for the diversity of functional traits, however, are poorly understood. Species diversity may be a poor proxy for functional diversity due to trait redundancies among species, making it unclear how random and deterministic processes alter functional diversity within patches of differing size, and how these differences scale up to determine among-patch functional diversity. 2. We report a novel experimental study of species and functional diversity across spatial scales. We manipulated patch area in an experimental plant metacommunity and used a nested sampling design to distinguish the effects of deterministic processes, ecological drift, and sampling effects on species and functional trait diversity. 3. Our study revealed a pervasive influence of ecological drift and sampling effects on diversity, with distinct influences on functional traits and species composition within and among patches. Overall, drift and sampling effects caused a 2- to 3-fold decrease in the importance of deterministic processes in small fragments. Species and functional diversity showed similar patterns with patch size: larger patches had greater within-patch (alpha) diversity and lower among-patch (beta) diversity, consistent with theory. However, our nested sampling design revealed that sampling effects (i.e. the size of the sample area) largely determined alpha species diversity and beta functional diversity, while ecological drift had a stronger influence on alpha functional diversity and beta species diversity. 4. Synthesis. The compositions of species and functional diversity in a community are influenced by distinct processes, resulting in divergent spatial scaling of species and their traits within patches and across landscapes.
Sunyaev-Zeldovich Effect Tomography: Processed Planck Maps and Masks
<p>This package contains two sets of products constructed and used in the Sunyaev-Zeldovich Effect Tomography project by Yi-Kuan Chiang, Ryu Makiya, Brice Ménard, and Eiichiro Komatsu.</p> <p><br> The first directory is a set of full-sky Planck HFI channel intensity maps from 100 to 353 GHz (Planck Collaboration 2016). We post-processed the maps to remove CMB fluctuations using that constructed in Bobin et al. (2016). The maps are stored using the HEALPix (Górski et al. 2005) scheme with the ring ordering of N_side = 2048. The map unit is MJy/sr.</p> <p><br> The second directory is a set of masks, including a 60% Galactic mask, a joint Planck point source mask, and a joint SDSS footprint and veto mask. The masks are in ring ordered HEALPix format of N_side = 2048.</p> <p><br> If you make use of these products, please cite the following papers:</p> <p>Chiang, Makiya, Ménard, & Komatsu, 2020, arXiv:2006.14650<br> Chiang, Makiya, Komatsu, & Ménard, 2020, arXiv:2007.01679<br> </p>
Evidence for two main domestication trajectories in Saccharomyces cerevisiae linked to distinct bread-making processes
<p>Data and code supporting the manuscript "Evidence for two main domestication trajectories in <em>Saccharomyces cerevisiae</em> linked to distinct bread-making processes" by Bigey et al. (2020)</p>
ICECAP-2 consortium processed airborne ice thickness data from the Princess Elizabeth Land, East Antarctica
<p>Airborne ice thickness data from the Princess Elizabeth Land (PEL), East Antarctica was collected in four separate seasons. During the first ICECAP2 season (2015/16), a survey acquiring exploratory ‘fan-shaped’ radial profiles to maximize range and data return on each flight was completed across the broadly unknown region of PEL. These flight lines extend from the coastal Progress Station to the interior ice-sheet divide at Ridge B. In the second and third seasons (2016/17 and 2017/18), a survey ‘grid’ was completed, targeting enhanced resolution over a proposed subglacial lake and a series of basal canyons (Jamieson et al., 2016). In the fourth season (2018/19), a few additional transects were completed to fill the largest data gaps within aircraft range. Field data acquisition was achieved using the “Snow Eagle 601” aero geophysical platform; a BT-67 airplane operated by the Polar Research Institute of China for the Chinese National Antarctic Research Expedition (CHINARE) program. The suite of instruments configured on the airplane include a phase-coherent radio-echo sounder system, operating at a central frequency of 60 MHz and a peak power of 8 kW, making it capable of penetrating deep (>3 km) ice in Antarctica. After applying coherent integration and pulse compression at a bandwidth of 15 MHz, which gave an along-track spatial sampling rate and a vertical resolution of ~10 m and ~5.6 m, respectively.</p>
A glimpse into rapid closed-system freezing processes in remoulded clay: dataset
<p>This is the data set</p>
FOP nutrient labels in Argentina: purchase intent, perception of healthiness and understanding in three processed food categories.
<p>Data analysis (non-statistically significant results) and raw survey response data.</p>
Processes at the soil-root interface determine the different responses of nutrient limitation and metal toxicity in forbs and grasses to nitrogen enrichment
<ol> <li>Nutrient limitation and metal toxicity have been implicated in changes of grassland communities by nitrogen (N) deposition. Belowground processes, especially those at the soil-root interface, play important roles in determining variation in nutrient concentrations in plants. However, few studies have specifically focused on the roles of these processes in mineral-element acquisition in grassland plants in response to N enrichment.</li> <li>Here we investigated the contributions of belowground processes at the soil-root interface to the differential acquisition of phosphorus (P), calcium (Ca) and manganese (Mn) by forbs and grasses of a temperate steppe in response to N addition by combining field and glasshouse experiments.</li> <li>Nitrogen addition increased the concentrations of both leaf P ([P]) and Mn ([Mn]) and decreased leaf [Ca] of forbs, while it had little effects on leaf concentrations of these elements in grasses. Nitrogen addition led to a higher activity of acid phosphatase in the rhizosphere of forb, and greater release of protons and carboxylates from forb roots than grass roots, contributing to the differential [P], [Ca] and [Mn] in leaves of forbs and grasses. Applying oxalate to soil to simulate the release of carboxylates by N enrichment enhanced [P] and [Mn], and decreased [Ca] in the soil solution. However, addition of hydrogen-ion increased [P], [Mn] and [Ca] in the soil solution. Lime addition mitigated the N addition-induced soil acidification, while it did not abolish the stimulatory effect of short-term N addition on leaf [P] and [Mn] of forbs. Therefore, we conclude that differences in the ecophysiological processes at the soil-root interface account for changes in leaf [P], [Ca] and [Mn] under short-term N addition, and that soil acidification aggravates the responses of these elements, especially [Ca] and [Mn], to long-term N enrichment.</li> <li><span>Synthesis: Our results highlight the contribution of belowground processes, especially those at the soil-root interface, to variation in plant element concentrations between dominant forbs and grasses in the temperate steppe. These findings greatly enhance our mechanistic understanding of the effects of N deposition on grassland communities.</span></li> </ol>
Scalasca summary analysis of HemeLB_GPU application execution with 129 MPI processes on JUWELS/V100
<p>The CompBioMed HPC CoE flagship application HemeLB (prototype GPU version) was run with a (patched) arteries geometry dataset on JSC's JUWELS supercomputer, and its execution performance with 129 MPI processes on 32 dual 20-core CPU + quad V100 GPU compute nodes measured by Score-P and analysed by Scalasca (and Vampir)</p>
Scalasca summary analysis of HemeLB application execution with 13824 MPI processes on SuperMUC-NG
<p>The CompBioMed HPC CoE flagship application HemeLB was run with a 6.4 micron resolution "circle of Willis" geometry dataset on LRZ's SuperMUC-NG supercomputer, and its execution performance with 13824 MPI processes on 288 dual 24-core compute nodes measured by Score-P (including PAPI hardware counters) and analysed by Scalasca.</p>
Scalasca summary analysis of HemeLB application execution with 300000 MPI processes on SuperMUC-NG
<p>The CompBioMed HPC CoE flagship application HemeLB was run with a 6.4 micron resolution "circle of Willis" geometry dataset on LRZ's SuperMUC-NG supercomputer, and its execution performance with 300000 MPI processes on 6250 dual 24-core compute nodes measured by Score-P (including PAPI hardware counters) and analysed by Scalasca.</p> <p>Two compute nodes with poor memory performance can be distinguished by examining the PAPI_RES_STL metric for resource stall cycles.</p>
Hidden in the DNA: insights on how multiple historical processes and natural history traits shaped patterns of cryptic diversity in an Amazon leaf-litter lizard Loxopholis osvaldoi (Squamata: Gymnophthalmidae).
Aim: To investigate cryptic diversity and diversification timing in the putatively low-dispersal Amazonian leaf-litter lizard Loxopholis osvaldoi, and to ask how geography (rivers, isolation by distance, IBD), ecological drivers (isolation by environment, IBE) and historical factors (climatic refugia) explain intraspecific genetic variation. Location: Central Amazonia, Brazil. Taxon: Squamata; Gymnophthalmidae; Loxopholis osvaldoi. Methods: We sequenced two mitochondrial and two nuclear markers in 157 individuals. Phylogeographic structure and the occurrence of independent evolving lineages where explored through phylogenetic and coalescent analyses. A species tree and divergence dates of lineages were inferred with BEAST, employing multiple DNA substitution rates. The potential genetic impacts of geographic distance among localities, the environment, and the position of localities in relation to main rivers were tested by Redundancy Analysis (RDA). Results: We detected 11 independently evolving and largely divergent intraspecific lineages. Lineage distribution patterns are complex and do not match any conspicuous barrier to gene flow, except for the Amazon River. Most lineages appear to have originated in the lower Miocene and Pliocene, in disagreement with the Pleistocene refuge hypothesis. IBD, IBE, and rivers appear to have acted in concert establishing and maintaining genetic structure. However, when controlling for other explanatory variables, IBD explains significantly more variation than rivers, IBE, or historical factors. Main conclusions: Our results strongly suggest that L. osvaldoi is a species complex. Future taxonomic work should use an integrative approach to explore whether morphological variation is present and congruent with the genetic data. While the use of a sensitive dating analysis allowed us to better describe the diversification history of L. osvaldoi, the lack of a spatial model of Neogene river dynamics prevents the test of specific, more informative river barrier hypotheses. The data suggest that non-linear correlation analyses (e.g. RDA) should be preferred to detect factors that affect phylogeographic patterns in the Amazon, instead of linear multiple regressions (e.g. Mantel tests). Given the high level of cryptic diversity detected within this and other Amazonian species, we caution against hypothesis tests based solely on the distribution of nominal taxa, which can provide a rather incomplete view of the processes behind Amazonian diversity.
Data from: Gender diversity of editorial boards and gender differences in the peer review process at six journals of ecology and evolution.
<p>Despite substantial progress for women in science, women remain underrepresented in many aspects of the scholarly publication process. We examined how the gender diversity of editors and reviewers changed over time for six journals in ecology and evolution (2003-2015 for four journals, 2007-2015 or 2009-2015 for the other two), and how several aspects of the peer review process differed between female and male editors and reviewers. We found that, for five of the six journals, women were either absent or very poorly represented as handling editors at the beginning of our dataset. The representation of women among handling editors increased gradually and consistently, with women making up 29% of the handling editors (averaged across journals) in 2015, similar to the representation of women as last authors on ecology papers (23% in 2015) but lower than the proportion of women among all authors (31%) and among members of the societies that own the journals (37-40%). The proportion of women among reviewers has also gradually but consistently increased over time, reaching 27% by 2015. Female editors invited more female reviewers than did male editors, and this difference increased with age of the editor. Men and women who were invited to review did not differ in whether they responded to the review invitation, but, of those that responded, women were slightly more likely to agree to review. In contrast, women were less likely than men to accept invitations to serve on journal editorial boards. Our analyses indicate that there has been progress in the representation of women as reviewers and editors in ecology and evolutionary biology, but women are still underrepresented among the gatekeepers of scholarly publishing relative to their representation among researchers.</p>
Data from: Measured perceptual nonlinearities show how ON-OFF asymmetric processing improves motion estimation in natural scenes
Animals detect motion using a variety of visual cues that reflect regularities in the natural world. Experiments in animals across phyla have shown that motion percepts incorporate both pairwise and triplet spatiotemporal correlations that could theoretically benefit motion computation. However, it remains unclear how visual systems assemble these cues to build accurate motion estimates. Here we use comprehensive measurements of fruit fly motion perception to show how flies combine local pairwise and triplet correlations to reduce variability in motion estimates across natural scenes. By generating synthetic images with statistics controlled by maximum entropy distributions, we showed that the observed improvement occurs only when light-dark asymmetries mimic natural ones. Thus, fly behavior suggests that asymmetric ON-OFF processing is tuned to the particular statistics of natural scenes. Since all animals encounter the world's light-dark asymmetries, many visual systems are likely to use asymmetric ON-OFF processing to improve motion estimation.
A process proposal on how to move from data requirements to semantic data in the context of the MDA
<p>This work proposes a process for the identification of the requirements associated with the data, along with and a set of transformations in Model Driven Architecture (MDA) context, in order to obtain a semantically annotated dataset, as a result of the unification and alignment of the data in the context of its initial domain. Our proposal identifies four phases (from CIM to code), in which is describe the artifacts and transformations required to progress to the next phase: a target domain model is first obtained from the data requirements, after which the ontological schema and the ontology is generated from the previous model. A domain-specific language (DSL), also proposed in this work, is then used to obtain the semantic data model (the DSL code), which generates the final semantic dataset. We have validated the proposal by studying two cases: one with data from the public transport domain and the other with data concerning those affected by the COVID-19 pandemic.</p>
Detection and Estimation of Inundation and Associated Risks Using Traffic and Monitoring Cameras and Image Processing Under Extreme Flooding Conditions
<p>The main objective of this project is to develop an inundation detection and evaluation framework using images from traffic monitoring cameras and reliable flood monitoring under extreme precipitation conditions. This study presents a comparative assessment of image enhancement and segmentation techniques to automatically identify the flash flooding from the low-resolution images taken by traffic-monitoring cameras. Due to inaccurate equipment in severe weather conditions (e.g., raindrops or light refraction on camera lenses), low-resolution images are subject to noises that degrade the quality of information. De-noising procedures are carried out for the enhancement of images by removing different types of noises. After the de-noising, image segmentation is implemented to detect the inundation from the images automatically. In addition, the detection of the inundation using the image segmentation with and without de-noising techniques are compared. The results indicate that among de-noising methods, the Bayes shrink with the thresholding discrete wavelet transform shows the most reliable result. For the image segmentation, the Bayesian segmentation is superior to the others. The results demonstrate that the proposed image enhancement and segmentation methods can be effectively used to identify the inundation from low-resolution images taken in severe weather conditions. A new Bayesian filtering method will be devised and applied to estimate the inundation from low-resolution images that will allow traffic engineers to take preventive or proactive actions to improve the safety of drivers and protect and preserve the transportation infrastructure. This new observation with improved accuracy will enhance our understanding of dynamic urban flooding by filling an information gap in the locations where conventional observations have limitations.</p>
Process Not Product: How the Open Life Science Mentoring Program Creates Open Science Ambassadors
<p><strong>Episode Summary</strong></p> <p>In this episode we talk to Yo Yehudi and Malvika Sharan, two of the co-founders and organisers of the Open Life Science training and mentoring program. We discuss why mentorship and community are so important in encouraging open science, what makes the program unique, and what the future for Open Life Science. </p> <p><strong>Episode Links</strong></p> <ul> <li><a href="https://openlifesci.org/">Open Life Science</a></li> <li><a href="https://about.me/malvikasharan">Malvika Sharan</a> <ul> <li><a href="https://twitter.com/MalvikaSharan">Twitter</a></li> </ul> </li> <li><a href="https://yo-yehudi.com/">Yo Yehudi</a> <ul> <li><a href="https://twitter.com/yoyehudi">Twitter</a></li> </ul> </li> </ul>
An iterative process for efficient optimisation of parameters in geoscientific models: a demonstration using the Parallel Ice Sheet Model (PISM) version 0.7.3
<p>Physical processes within geoscientific models are sometimes described by simplified schemes known as parameterisations. The values of the parameters within these schemes can be poorly constrained by theory or observation. Uncertainty in the parameter values translates into uncertainty in the outputs of the models. Proper quantification of the uncertainty in model predictions therefore requires a systematic approach for sampling parameter space. In this study, we develop a simple and efficient approach to identify regions of multi-dimensional parameter space that are consistent with observations. Using the Parallel Ice Sheet Model to simulate the present-day state of the Antarctic Ice Sheet, we find that co-dependencies between parameters preclude the identification of a single optimal set of parameter values. Approaches such as large ensemble modelling are therefore required in order to generate model predictions that incorporate proper quantification of the uncertainty arising from the parameterisation of physical processes.</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.