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348 results for “Core data”
Data from: Detection of tephra layers in Antarctic sediment cores with hyperspectral imaging
Tephrochronology uses recognizable volcanic ash layers (from airborne pyroclastic deposits, or tephras) in geological strata to set unique time references for paleoenvironmental events across wide geographic areas. This involves the detection of tephra layers which sometimes are not evident to the naked eye, including the so-called cryptotephras. Tests that are expensive, time-consuming, and/or destructive are often required. Destructive testing for tephra layers of cores from difficult regions, such as Antarctica, which are useful sources of other kinds of information beyond tephras, is always undesirable. Here we propose hyperspectral imaging of cores, Self-Organizing Map (SOM) clustering of the preprocessed spectral signatures, and spatial analysis of the classified images as a convenient, fast, non-destructive method for tephra detection. We test the method in five sediment cores from three Antarctic lakes, and show its potential for detection of tephras and cryptotephras.
Data from: Opposing mechanisms drive richness patterns of core and transient bird species
Studies of biodiversity typically assume that all species are equivalent. However, some species in a community maintain viable populations in the study area, while others occur only occasionally as transient individuals. Here we show that North American bird communities can reliably be divided into core and transient species groups, and that the richness of each group is driven by different processes. The richness of core species is influenced primarily by local environmental conditions, while the richness of transient species is influenced primarily by the heterogeneity of the surrounding landscape. This demonstrates that the well-known effects of the local environment and landscape heterogeneity on overall species richness are the result of two sets of processes operating differentially on core and transient species. Models of species richness should focus on explaining two distinct patterns, those of core and transient species, rather than a single pattern for the community as a whole.
Data from: Pangenome and immuno-proteomics analysis of Acinetobacter baumannii strains revealed the core peptide vaccine targets
Background: Acinetobacter baumannii has emerged as a significant nosocomial pathogen during the last few years, exhibiting resistance to almost all major classes of antibiotics. Alternative treatment options such as vaccines tend to be most promising and cost effective approaches against this resistant pathogen. In the current study, we have explored the pan-genome of A. baumannii followed by immune-proteomics and reverse vaccinology approaches to identify potential core vaccine targets. Results: The pan-genome of all available A. baumannii strains (30 complete genomes) is estimated to contain 7,606 gene families and the core genome consists of 2,445 gene families (~32 % of the pan-genome). Phylogenetic tree, comparative genomic and proteomic analysis revealed both intra- and inter genomic similarities and evolutionary relationships. Among the conserved core genome, thirteen proteins, including P pilus assembly protein, pili assembly chaperone, AdeK, PonA, OmpA, general secretion pathway protein D, FhuE receptor, Type VI secretion system OmpA/MotB, TonB dependent siderophore receptor, general secretion pathway protein D, outer membrane protein, peptidoglycan associated lipoprotein and peptidyl-prolyl cis-trans isomerase are identified as highly antigenic. Epitope mapping of the target proteins revealed the presence of antigenic surface exposed 9-mer T-cell epitopes. Protein-protein interaction and functional annotation have shown their involvement in significant biological and molecular processes. The pipeline is validated by predicting already known immunogenic targets against Gram negative pathogen Helicobacter pylori as a positive control. Conclusion: The study, based upon combinatorial approach of pan-genomics, core genomics, proteomics and reverse vaccinology led us to find out potential vaccine candidates against A. baumannii. The comprehensive analysis of all the completely sequenced genomes revealed thirteen putative antigens which could elicit substantial immune response. The integration of computational vaccinology strategies would facilitate in tackling the rapid dissemination of resistant A.baumannii strains. The scarcity of effective antibiotics and the global expansion of sequencing data making this approach desirable in the development of effective vaccines against A. baumannii and other bacterial pathogens.
Data from: The Victoria West: earliest prepared core technology in the Acheulean at Canteen Kopje and implications for the cognitive evolution of early hominids
Prepared core technology illustrates in-depth planning and the presence of a mental template during the core reduction process. This technology is, therefore, a significant indicator in studying the evolution of abstract thought and the cognitive abilities of hominids. Here, we report on Victoria West cores excavated from the Canteen Kopje site in central South Africa, with a preliminary age estimate of approximately 1 Ma (million years ago) for these cores. Technological analysis shows that the Victoria West cores bear similarities to the 'Volumetric Concept' as defined for the Levallois, a popular and widely distributed prepared core technology from at least 200 ka (thousand years ago). Although these similarities are present, several notable differences also occur that make the Victoria West a unique and distinctive prepared core technology; these are: elongated and convergent core shapes, consistent blow directions for flake removal, a predominance of large side-struck flakes, and the use of these flakes to make Acheulean large cutting tools. This innovative core reduction strategy at Canteen Kopje extends the roots of prepared core technology to the latter part of the Early Acheulean and clearly demonstrates an increase in the cognitive abilities and complexities of hominids in this time period.
Data from: Genome-wide assessment of population structure and genetic diversity and development of a core germplasm set for sweet potato based on specific length amplified fragment (SLAF) sequencing
Sweet potato, Ipomoea batatas (L.) Lam., is an important food crop that is cultivated worldwide. However, no genome-wide assessment of the genetic diversity of sweet potato has been reported to date. In the present study, the population structure and genetic diversity of 197 sweet potato accessions most of which were from China were assessed using 62,363 SNPs. A model-based structure analysis divided the accessions into three groups: group 1, group 2 and group 3. The genetic relationships among the accessions were evaluated using a phylogenetic tree, which clustered all the accessions into three major groups. A principal component analysis (PCA) showed that the accessions were distributed according to their population structure. The mean genetic distance among accessions ranged from 0.290 for group 1 to 0.311 for group 3, and the mean polymorphic information content (PIC) ranged from 0.232 for group 1 to 0.251 for group 3. The mean minor allele frequency (MAF) ranged from 0.207 for group 1 to 0.222 for group 3. Analysis of molecular variance (AMOVA) showed that the maximum diversity was within accessions (89.569%). Using CoreHunter software, a core set of 39 accessions was obtained, which accounted for approximately 19.8% of the total collection. The core germplasm set of sweet potato developed will be a valuable resource for future sweet potato improvement strategies.
Data from: The importance of core habitat for a threatened species in changing landscapes
1. Habitat loss, fragmentation and alteration of the landscape matrix are interdependent processes, collectively responsible for most recent species extinctions. Thus, determining the extent to which these landscape processes affect animals is critical for conservation. However, researchers have often assumed that interdependent effects are independently related to animals' responses, underestimating the importance of one or several landscape processes in driving species declines. 2. We demonstrate how to disentangle the interdependent effects of habitat area, fragmentation, and edge context on population size by assessing abundance of a rapidly-declining grassland songbird species (Grasshopper Sparrow, Ammodramus savannarum) in eastern Kansas (USA). We conducted > 7,000 point-count bird surveys at > 2,000 sites over two breeding seasons, then modelled the direct, interactive, and indirect effects of landscape factors on abundance within spatial scales (200-, 400-, 800-, 1600-m radii) relevant to our focal species' dispersal behavior. 3. Sparrow abundance correlated most strongly with landscape structure within 400-m radii, increasing non-linearly with grassland area and decreasing with the proportion of grassland near cropland or woody edges. Sparrows' negative response to cropland edges was mostly an added, indirect consequence of reduced grassland area, whereas sparrows' stronger negative response to woody edges was not attributable to variation in grassland area. Fragmentation and edge context mattered most in landscapes comprising ~ 50–80% grassland. 4. Synthesis and applications. Abundance of a threatened grassland songbird was influenced more by core grassland area (a function of total grassland area, fragmentation, and edge context) than total grassland area per se. Moreover, a local extinction threshold of ~ 50% grassland indicated that small amounts of habitat were unsuitable for our focal species regardless of habitat configuration or matrix type. Local extinction thresholds in response to habitat area provide clear baseline targets for land managers; above those thresholds, configuration and the matrix can be modified to increase abundance of edge-sensitive animals. Conflicting evidence in the literature regarding the importance of fragmentation and matrix features could be partially explained by species-level traits, or methodological issues such as defining landscapes at ecologically-arbitrary spatial scales, assessing landscape quality using species richness, and ignoring interactive and indirect effects.
Data from: Colonisation dynamics during range expansion is poorly predicted by dispersal in the core range
The potential ranges of many species are shifting due to changing ecological conditions. Where populations become patchy towards the range edge, the realised distribution emerges from colonisation-persistence dynamics. Therefore, a greater understanding of the drivers of these processes, and the spatial scales over which they operate, presents an opportunity to improve predictions of species range expansion under environmental change. Species reintroductions offer an ideal opportunity to investigate the drivers and spatial scale of colonisation dynamics at the range edge. To this effect, we performed and monitored experimental translocations of water voles to quantify how colonisation and local persistence were influenced by habitat quality and occupancy. We used a novel statistical method to simultaneously consider effects across a range of spatial scales. Densely occupied neighbourhoods were highly persistent and frequently colonised. Persistence was more likely in high quality habitat, whereas influence of habitat quality on colonisation was less clear. Colonisation of suitable habitat in distant, sparsely occupied areas was much less frequent than expected from the well documented high dispersal ability of the species. Persistence of these distant populations was also low, which we attribute to the absence of a rescue effect in sparsely populated neighbourhoods. Our results illustrate a mismatch between the spatial scales of colonisation dynamics in the core and edge of a species range, suggesting that recolonisation dynamics in established populations may be a poor predictor of colonisation dynamics at the range edge. Such a mismatch leads to predictions of long lags between the emergence and colonisation of new habitat, with detrimental consequences for a species realised distribution, conservation status and contribution to ecosystem function. Conservation translocations that also reinforce existing populations at the range edge might stimulate the rescue effect and mitigate lags in expansion.
Data from: Realized niche and microhabitat selection of the eastern green lizard (Lacerta viridis) at the core and periphery of its distribution range
The available range of habitats and suitable abiotic conditions like temperature and radiation tend to be narrower towards the periphery of the distribution range of species. Peripheral populations of generalist species could then be more specialized and have a smaller and differentiated realized niche (habitat niche in our study) compared to populations at the core. Likewise, patterns of microhabitat selection can differ between periphery and core. In our study we compared niche size and microhabitat selection among core (Bulgaria) and northern peripheral (Germany, Czech Republic) populations of Lacerta viridis and estimated niche differentiation among regions. We collected data on vegetation structure and abiotic parameters at the microhabitat scale in each region. In order to compare niche size among regions and estimate niche differentiation we built multidimensional niche hypervolumes. We applied generalized linear mixed models and model averaging, accounting for spatial autocorrelation when necessary, to analyze microhabitat differences among regions and microhabitat selection in each region. Peripheral populations were more specialized, having a smaller niche than core ones, and their niche differed from that in the core (Sørensen overlap in all comparisons < 0.3). Microhabitats at the periphery had lower radiation and soil compaction and less structured vegetation. Microhabitat selection at the core depended solely on abiotic parameters, while at the periphery it was defined by only vegetation structure (Czech Republic) or a combination of both, vegetation structure and abiotic factors (Germany). Thus, peripheral populations seem to compensate for overall harsher climatic conditions by responding to different parameters of the microhabitat compared to core populations. We suggest specific conservation measures for L. virids in each studied region and point out the general implications of a higher specialization degree of peripheral populations in relation to climate change and habitat fragmentation.
Data from: Utilizing next-generation sequencing to resolve the backbone of the Core Goodeniaceae and inform future taxonomic and floral form studies
Though considerable progress has been made in inferring phylogenetic relationships of many plant lineages, deep unresolved nodes remain a common problem that can impact downstream efforts, including taxonomic decision-making and character reconstruction. The Core Goodeniaceae is a group affected by this issue: data from the plastid regions trnL-trnF and matK have been insufficient to generate adequate support at key nodes along the backbone of the phylogeny. We performed genome skimming for 24 taxa representing major clades within Core Goodeniaceae. The plastome coding regions (CDS) and nuclear ribosomal repeats (NRR) were assembled and complemented with additional accessions sequenced for nuclear G3PDH and plastid trnL-trnF and matk. The CDS, NRR, and G3PDH alignments were analyzed independently and topology tests were used to detect the alignments' ability to reject alternative topologies. The CDS, NRR, and G3PDH alignments independently supported a Brunonia (Scaevola s.l. (Coopernookia (Goodenia s.l.))) backbone topology, but within Goodenia s.l., the strongly-supported plastome topology (Goodenia A (Goodenia B (Velleia + Goodenia C))) contrasts with the poorly supported nuclear topology ((Goodenia A + Goodenia B) (Velleia + Goodenia C)). A fully resolved and maximally supported topology for Core Goodeniaceae was recovered from the plastome CDS, and there is excellent support for most of the major clades and relationships among them in all alignments. The composition of these seven major clades renders many of the current taxonomic divisions non-monophyletic, prompting us to suggest that Goodenia may be split into several segregate genera.
Data for "Unveiling the effect of Ni on the formation and structure of Earth's inner core"
<p>The source data for the figures in the manuscript "Unveiling the effect of Ni on the formation and structure of Earth’s inner core".</p> <p>The .xlsx files can be read via Microsoft Excel.</p> <p> </p>
Data and Codes of A Deep Learning-Based Consistency Test for Earth System Models on Heterogeneous Many-Core Systems
<p>These are the supporting information to verify the results in the paper, including input data, model outputs, the postprocessing scripts and the source codes.</p>
Geochemical data for a peat core XY 1801 from Guizhou province, SW China
<p>Geochemical and chromaticity data obtained by XRF-CS, as well as chronology of a peat core XY1801 from Guizhou province.</p>
seltmann/taxonomy-darwin-core: A GitHub Approach to Publishing Darwin Core Formatted Occurrence Data for Taxonomic Studies
<p><strong>A GitHub Approach to Publishing Darwin Core Formatted Occurrence Data for Taxonomic Studies</strong></p> <p><strong>Description</strong><br> This repository contains a Darwin Core Archive template and instructions for revisionary taxonomists to use to publish their data as a Darwin Core Archive or Darwin Core Compliant CSV file. This repository contains the Darwin Core Archive for "A taxonomic revision of <em>Gryonoides</em> Dodd, 1920 (Hymenoptera: Scelionidae), with a review of the hosts of Teleasinae." The archive was produced by the authors from data contained in mx (Yoder et al. 2006–present).</p> <p><strong>Summary</strong><br> Darwin core archives have emerged as the accepted data-sharing standard for occurrence data about organisms. These occurrences could be observations or specimens in natural history collections. The standard is applied by natural history collections worldwide to share their data between various repositories, including Global Biodiversity Information Faculty (GBIF) and Integrated Digitized Bio collections (iDigBio). This repository can be repurposed as an example template for publishing material examined as a Darwin Core Archive, accessible for data aggregators, journals, and conforming to community standards. This method can be used for any occurrence dataset, such as material examined, species monitoring observation records, ecological observations, or natural history collection data.</p> <p><strong>How to Create a Darwin Core Archive Using this Repository</strong><br> 1- Fork repository on GitHub or download its contents.</p> <p>2- Use the occurrences.csv file as a template. Delete the *Gryonoides* data and add your own. Do not change the column number or order. It is ok to leave in extra columns that you do not use. The only columns that need to be filled out are <em>occurrenceID</em> and <em>BasisOfRecord</em>. Specific definitions of the field names can be found in the Darwin Core Documentation under the <a href="https://dwc.tdwg.org/terms/#occurrence">Occurrence Core</a>.</p> <p>3- Do not touch the meta.xml. This file describes the columns in the occurrences.csv file.</p> <p>4- Edit the eml.xml files to include information about your institution and project. </p> <p>5- Zip the folder to create the archive. If you are using GitHub you can use the zip function for the repository using Code -> Download ZIP.</p> <p>6- Validate the archive using the <a href="https://www.gbif.org/tools/data-validator">GBIF Data Validator tool</a>.</p> <p><strong>Citations</strong></p> <p>Yoder, M.J., Dole, K., Seltmann, K., and Deans, A. 2006-Present. Mx, a collaborative web based content management for biological systematists. http://mx.phenomix.org/index.php/Main_Page<br> </p>
Data and Codes of Characterizing Uncertainties of Earth System Modeling with Heterogeneous Many-core Architecture Computing
<p>These are the supporting information to verify the results in the paper, including input data, model outputs, the postprocessing scripts and the source codes.</p>
Alkane data in the SZY18 peat core
<p>Exploring the seasonal atmospheric processes involved with hydroclimate changes of the East Asian Summer Monsoon (EASM) during the Mystery Interval (MI, 17.5-14.5 ka BP) will enhance understanding of the EASM climate system. Here the δ<sup>2</sup>H values of leaf wax <em>n</em>-alkanes (δ<sup>2</sup>H<sub>alk</sub>) in a wetland core retrieved from southern China are relatively negative during the MI, contrasting to positive excursion recorded by stalagmite δ<sup>18</sup>O. Considering the overlap of the primary synthesis time of leaf waxes in deciduous woody plants and periods of precipitation δ<sup>2</sup>H alteration in the EASM (late spring to early summer), we interpret the relatively negative signal of δ<sup>2</sup>H<sub>alk</sub> in the wetland core as the early onset of summer rainfall during the MI. The early onset of summer rainfall was likely due to the early northeastward shifting of the Western Pacific subtropical high due to the low land-sea thermogradient between the Qinghai-Tibet Plateau and the West Pacific Ocean.</p>
Core outcome set for burn care research: Delphi survey data
<p><strong>Background:</strong> Collated evidence from systematic reviews supports clinicians in identifying optimal treatment for patients. Evidence is created from outcomes that, in burn care, include survival, function, cosmesis, pain, and psychological well-being. Currently, this is limited because of variation in outcomes reported across trials. Improved selection and reporting of outcomes in primary research in burn care could improve treatment globally by improving data synthesis and the quality of evidence. The availability of a Core Outcome Set (COS), a minimum set of the most important outcomes to be reported in all trials of a medical condition, would resolve this issue. The aim of this study is to develop a COS for international burn care research.</p> <p><strong>Methods and findings</strong>: Candidate outcomes were identified from systematic reviews and stakeholder interviews. Through two rounds of a Delphi survey, international multi-disciplinary clinicians, researchers, and UK patients and carers prioritised the outcomes. Anonymised feedback aimed to achieve consensus. Pre-defined criteria for retaining and dropping outcomes were agreed upon. A consensus meeting with voting was held to finalise the COS.</p> <p>Examination of all data sources identified 1,021 unique outcomes grouped into 88 candidate outcomes. Stakeholders included 668 health professionals from 77 countries and 126 UK patients/carers; 25% of clinical participants were from low- or low-middle-income countries. After Round 1, one outcome was discarded, and 13 new outcomes were added. After Round 2, 69 items were discarded, leaving 31 outcomes for the consensus meeting.<em> </em>Discussion and voting agreed on seven core outcomes: death, specified complications, ability to do daily tasks, time to wound healing, neuropathic pain and itch, psychological well-being, and time to return to school/work.</p> <p><strong>Conclusions</strong>: This is the first COS for international burn care research. Implementation is now needed to improve data synthesis, and support evidence-based clinical decision-making in global burn care. It is recommended that future trials include measures of these seven outcomes.</p>
Data for "Diverging fates of the Pacific Ocean oxygen minimum zone and its core in a warming world" (2022, AGU Advances)
<p>Preprocessed Plotting Data to reproduce Figures from "Diverging fates of the Pacific Ocean oxygen minimum zone and its core in a warming world" (2022, AGU Advances)</p>
Data for Enhanced soft magnetic properties with high frequency stability of pure iron powder cores via high-pressure compaction – an environment and cost saving solution as a prospective alternative to soft magnetic composites
<p>Data for the scientific paper Enhanced soft magnetic properties with high frequency stability of pure iron powder<br>cores via high-pressure compaction – an environment and cost saving solution as a<br>prospective alternative to soft magnetic composites</p>
Supporting data for "Femtosecond core-level spectroscopy reveals involvement of triplet states in the gas-phase photodissociation of Fe(CO)5"
Open the record for dataset details and reuse information.
Shadowgraph measurements of rotating convective planetary core-style flows (data, code, and figures)
<p>Data files and accompanying matlab analysis code for the paper: "Shadowgraph Measurements of Rotating Convective Planetary Core-Style Flows"</p>
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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.