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3,655 results for “Structural data”
Data from: Measuring researchers' potential scholarly impact with structural variations: four types of researchers in information science (1979–2018)
We propose a method to measure the potential scholarly impact of researchers based on network structural variations they introduced to the underlying author co-citation network of their field. We applied the method to the information science field based on 91,978 papers published between 1979 and 2018 from the Web of Science. We divided the entire period into eight consecutive intervals and measured structural variation change rates (DM) of individual authors in corresponding author co-citation networks. Four types of researchers are identified in terms of temporal dynamics of their potential scholarly impact—1) Increasing, 2) Decreasing, 3) Sustained, and 4) Transient. The study contributes to the understanding of how researchers' scholarly impact might evolve in a broad context of the corresponding research community. Specifically, this study illustrated a crucial role played by structural variation metrics in measuring and explaining the potential scholarly impact of a researcher. This method based on the structural variation analysis offers a theoretical framework and a practical platform to analyze the potential scholarly impact of researchers and their specific contributions.
Data from: Structural and catalytic properties of copper silicate nanomaterials
<p><span>Nanosized copper silicates with three different structural morphology (amorphous, nanotubes and MEL) were prepared using different synthesis methods. The physico-chemical properties of copper silicates were characterized by XRD, FT-IR, SEM, HRTEM, N<sub>2</sub>-physisorption, XPS and H<sub>2</sub>-TPR techniques. The results indicated that the preparation conditions affect reduction behavior and textural properties of nanosized copper silicates. Hydrothermal synthesis method yielded chrysocolla-like CuSiO<sub>3</sub> nanotubes, which possessed high surface area and pore volume with easy reducibility. The catalytic performances of synthesized copper silicate nanostructures were evaluated for dehydrogenation of methanol.<b> </b>It was found that dehydrogenation activity is depended on the structural properties of copper silicates. Highest activity was observed for copper silicates with nanotube morphology. Catalytic dehydrogenation activity of copper silicates was also related to presence of more number of Cu-O-Si species, easy reducibility and Lewis acid centers. The CuSiO<sub>3</sub> nanotubes sample also exhibited good stability under investigated reaction conditions that deactivation was not detected for 48 h.</span></p>
Data from: Using structured eradication feasibility assessment to prioritise the management of new and emerging invasive alien species in Europe
<p>Prioritising the management of invasive alien species (IAS) is of global importance and within Europe integral to the EU IAS regulation. To prioritise management effectively the risks posed by IAS need to be assessed, but so too does the feasibility of their management. While risk of IAS to the EU has been assessed, the feasibility of management has not. We assessed the feasibility of eradicating 60 new (not yet established) and 35 emerging (established with limited distribution) species that pose a threat to the EU, as identified by horizon scanning. The assessment was carried out by 34 experts in invasion management from across Europe, applying the Non-Native Risk Management scheme to defined invasion scenarios and eradication strategies for each species, assessing the feasibility of eradication using seven key risk management criteria. Management priorities were identified by combining scores for risk (derived from horizon scanning) and feasibility of eradication. The results show eradication feasibility score and risk score were not correlated, indicating that risk management evaluates different information than risk assessment. Seventeen new species were identified as particularly high priorities for eradication should they establish in the future, while fourteen emerging species were identified as priorities for eradication now. A number of species considered highest priority for eradication were terrestrial vertebrates, a group that has been the focus of a number of eradication attempts in the EU. However, eradication priorities also included a diverse range of other taxa (plants, invertebrates and fish) suggesting there is scope to broaden the taxonomic range of attempted eradication in the EU. We demonstrate that broad scale structured assessments of management feasibility can help prioritise IAS for management. Such frameworks are needed to support evidence based decision making.</p>
Data from: Sampling schemes and drift can bias admixture proportions inferred by STRUCTURE
<p><span>The interbreeding of individuals coming from genetically differentiated but incompletely isolated populations can lead to the formation of admixed populations, having important implications in ecology and evolution. In this simulation study, we evaluate how individual admixture proportions estimated by the software <span>structure</span> are quantitatively affected by different factors. Using various scenarios of admixture between two diverging populations, we found that unbalanced sampling from parental populations may seriously bias the inferred admixture proportions; moreover, proportionally large samples from the admixed population can also decrease the accuracy and precision of the inferences. As expected, weak differentiation between parental populations and drift after the admixture event strongly increase the biases caused by uneven sampling. We also show that admixture proportions are generally more biased when parental populations unequally contributed to the admixed population. Finally, with few exceptions, using a large number of markers reduces those biases, but using alternative priors for individual ancestry or the uncorrelated allele model only marginally affect the inference of admixture in most situations. We conclude that unbalanced sampling may cause important biases in the admixture proportions estimated by <span>structure</span>, especially when a small number of markers are used, and those biases can be worsened by the effect of drift and unequal genetic contribution of parental populations. Empirical studies should thus be careful with their sampling design and consider historical characteristics when using this software to estimate the ancestry of individuals from admixed populations.</span></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>
Ground Gamma-ray Spectrometry Data of the Araguainha Impact Structure
<p>This is a gamma-ray dataset that was collected during three field campaings in the Araguainha impact structure in Brazil. Araguainha is the largest impact strucutre of the country (~40 km wide). The available file provides the raw dataset in counts per unit of time, the concentration values of K, U and Th, and some derived products for geological interpretation.</p>
Data from: Repertoire-wide gene structure analyses: a case study comparing automatically predicted and manually annotated gene models
The location and modular structure of eukaryotic protein-coding genes in genomic sequences can be automatically predicted by gene annotation algorithms. These predictions are often used for comparative studies on gene structure, gene repertoires, and genome evolution. However, automatic annotation algorithms do not yet correctly identify all genes within a genome, and manual annotation is often necessary to obtain accurate gene models and gene sets. As manual annotation is time-consuming, only a fraction of the gene models in a genome is typically manually annotated, and this fraction often differs between species. To assess the impact of manual annotation efforts on genome-wide analyses of gene structural properties, we compared the structural properties of protein-coding genes in seven diverse insect species sequenced by the i5k initiative. Our results show that the subset of genes chosen for manual annotation by a research community (3.5-7% of gene models) may have structural properties (e.g., lengths and exon counts) that are not necessarily representative for a species' gene set as a whole. Nonetheless, the structural properties of automatically generated gene models are only altered marginally (if at all) through manual annotation. Major correlative trends, for example a negative correlation between genome size and exonic proportion, can be inferred from either the automatically predicted or manually annotated gene models alike. Vice versa, some previously reported trends did not appear in either the automatic or manually annotated gene sets, pointing towards insect-specific gene structural peculiarities. In our analysis of gene structural properties, automatically predicted gene models proved to be sufficiently reliable to recover the same gene-repertoire-wide correlative trends that we found when focusing on manually annotated gene models only. We acknowledge that analyses on the individual gene level clearly benefit from manual curation. However, as genome sequencing and annotation projects often differ in the extent of their manual annotation and curation efforts, our results indicate that comparative studies analyzing gene structural properties in these genomes can nonetheless be justifiable and informative.
Data and R code for What you see is where you go: visibility influences movement decisions of a forest bird navigating a 3D structured matrix
<p>Animal spatial behaviour is often presumed to reflect responses to visual cues. However, inference of behaviour in relation to the environment is challenged by the lack of objective methods to identify the information that effectively is available to an animal from a given location. In general, animals are assumed to have unconstrained information on the environment within a detection circle of a certain radius (the perceptual range; PR). However, visual cues are only available up to the first physical obstruction within an animal's PR, making information availability a function of an animal's location within the physical environment (the effective visual perceptual range; EVPR). By using LiDAR data and viewshed analysis, we model forest birds' EVPRs at each step along a movement path. We found that the EVPR was on average 0.063% that of an unconstrained PR and, by applying a step-selection analysis, that individuals are 1.57 times more likely to move to a tree within their EVPR than to an equivalent tree outside it. This demonstrates that behavioural choices can be substantially impacted by the characteristics of an individual's EVPR and highlights that inferences made from movement data may be improved by accounting for the EVPR.</p>
Data for "A Stepwise Clustered Hydrological Model for Addressing the Autocorrelation Structure of Streamflow in Irrigated Watersheds"
<p>This data set contains hydrological input (goundwater depth, streamflow and irrigation) for the study of "<strong>A Stepwise Clustered Hydrological Model for Addressing the Autocorrelation Structure of Streamflow in Irrigated Watersheds</strong>"</p> <p>For more information please contact the author.</p>
Data and code for: Dietzel et al. Long-term shifts in the colony size structure of coral populations along the Great Barrier Reef
<p>The age or size structure of a population has a marked influence on its demography and reproductive capacity. While declines in coral cover are well documented, concomitant shifts in the size frequency distribution of coral colonies are rarely measured at large spatial scales. Here we document major shifts in the colony size structure of coral populations along the 2,300km length of the Great Barrier Reef over the past two decades. Coral colony abundances on reef crests and slopes have declined sharply across all colony size classes and in all coral taxa compared to historical baselines. Declines were particularly pronounced in the Northern and Central regions of the Great Barrier Reef, following mass coral bleaching in 2016 and 2017. The relative abundances of large colonies remained relatively stable, but this apparent stability masks steep declines in absolute abundance. The potential for recovery of older fecund corals is uncertain given the increasing frequency and intensity of disturbance events. The systematic decline in smaller colonies across regions, habitats and taxa, suggests that a decline in recruitment has further eroded the recovery potential and resilience of coral populations.</p>
Data from: Phylogenetic structure and formation mechanism of shrub communities in arid and semi-arid areas of the Mongolian Plateau
<p>The mechanisms of species coexistence within a community have always been the focus in ecological research. Community phylogenetic structure reflects the relationship of historical processes, regional environments and interactions between species, and studying it is imperative to understand the formation and maintenance mechanisms of community composition and biodiversity.</p> <p>We studied the phylogenetic structure of the shrub communities in arid and semiarid areas of the Mongolian Plateau. First, the phylogenetic signals of four plant traits (height, canopy, leaf length and leaf width) of shrubs and subshrubs were measured to determine the phylogenetic conservation of these traits. Then the net relatedness index (NRI) of shrub communities was calculated to characterize their phylogenetic structure. Finally, the relationship between the NRI and current climate and paleoclimate (since the Last Glacial Maximum, LGM) factors was analyzed to understand the formation and maintenance mechanisms of these plant communities. We found that desert shrub communities showed a trend towards phylogenetic overdispersion, that is, limiting similarity was predominant in arid and semi-arid areas of the Mongolian Plateau despite the phylogenetic structure and formation mechanisms differing across habitats. The typical desert and sandy shrub communities showed a significant phylogenetic overdispersion, while the steppified desert shrub communities showed a weak phylogenetic clustering. It was found that mean winter temperature (i.e. in the driest quarter) was the major factor limiting steppified desert shrub phylogeny distribution. Both cold and drought (despite having opposite consequences) differentiated the typical desert to steppified desert shrub communities. The increase in temperature since the LGM is conducive to the invasion of shrub plants into steppe grassland, and this process may be intensified by global warming.</p>
Data from: The influence of disorder on the exciton spectra in two-dimensional structures
<p>We study the joint effect of disorder and Coulomb interaction screening on the exciton spectra in two-dimensional (2D) structures. These can be van der Waals structures or heterostructures of organic (polymeric) semiconductors as well as inorganic substances like transition metal dichalcogenides. We consider 2D screened hydrogenic problem with Rytova - Keldysh interaction by means if so-called fractional Scrodinger equation. Our main finding is that above synergy between screening and disorder either destroys the exciton (strong screening) or promote the creation of a bound state, leading to its collapse in the extreme case. Our second finding is energy levels crossing, i.e. the degeneracy (with respect to index µ) of the exciton eigenenergies at certain discrete value of screening radius. Latter effects may also be related to the quantum manifestations of chaotic exciton behavior in above 2D semiconductor structures. Hence, they should be considered in device applications, where the interplay between dielectric screening and disorder is important.</p>
Supplementary Data of Microbial structures in the surface sediments of Shenhu Area, South China Sea
<p>Supplementary Data</p>
Data from: Metacommunity structure of stream insects across three hierarchical spatial scales
<p>A major challenge in community ecology is to understand the underlying factors driving metacommunity (i.e. a set of local communities connected through species dispersal) dynamics. However, little is known about the effects of varying spatial scale on the relative importance of environmental and spatial (i.e. dispersal related) factors in shaping metacommunities and on the relevance of different dispersal pathways. Using a hierarchy of insect metacommunities at three spatial scales (a small, within-stream scale, intermediate, among-stream scale, and large, among-sub-basin scale), we assessed whether the relative importance of environmental and spatial factors shaping metacommunity structure varies predictably across spatial scales, and tested how the importance of different dispersal routes vary across spatial scales. We also studied if different dispersal ability groups differ in the balance between environmental and spatial control. Variation partitioning showed that environmental factors relative to spatial factors were more important for community composition at the within-stream scale. In contrast, spatial factors (i.e. eigenvectors from Moran's eigenvector maps) relative to environmental factors were more important at the among-sub-basin scale. These results indicate that environmental filtering is likely to be more important at the smallest scale with highest connectivity, while dispersal limitation seems to be more important at the largest scale with lowest connectivity. Community variation at the among-stream and among-sub-basin scales were strongly explained by geographical and topographical distances, indicating that overland pathways might be the main dispersal route at the larger scales among more isolated sites. The relative effect of environmental and spatial factors on insect communities varied between low and high dispersal ability groups; this variation was inconsistent among three hierarchical scales. In sum, our study indicates that spatial scale, connectivity and dispersal ability jointly shape stream metacommunities.</p>
Data from: Structural consequence of the most frequently recurring cancer-associated substitution in DNA polymerase ε
The most frequently recurring cancer-associated DNA polymerase ε (Pol ε) mutation is a P286R substitution in the exonuclease domain. While originally proposed to increase genome instability by disrupting exonucleolytic proofreading, the P286R variant was later found to be significantly more pathogenic than Pol ε proofreading deficiency per se. The mechanisms underlying its stronger impact remained unclear. Here we report the crystal structure of the yeast orthologue, Pol ε−P301R, complexed with DNA and an incoming dNTP. Structural changes in the protein are confined to the exonuclease domain, with R301 pointing towards the exonuclease site. Molecular dynamics simulations suggest that R301 interferes with DNA binding to the exonuclease site, an outcome not observed with the exonuclease-inactive Pol ε−D290A,E292A variant lacking the catalytic residues. These results reveal a distinct mechanism of exonuclease inactivation by the P301R substitution and a likely basis for its dramatically higher mutagenic and tumorigenic effects.
Data from: Environmental and genetic control of brain and song structure in the zebra finch
Birdsong is a classic example of a learned trait with cultural inheritance, with selection acting on trait expression. To understand how song responds to selection, it is vital to determine the extent to which variation in song learning and neuroanatomy is attributable to genetic variation, environmental conditions, or their interactions. Using a partial cross fostering design with an experimental stressor, we quantified the heritability of song structure and key brain nuclei in the song control system of the zebra finch and the genotype-by-environment (G × E) interactions. Neuroanatomy and song structure both showed low levels of heritability and are unlikely to be under selection as indicators of genetic quality. HVC, in particular, was almost entirely under environmental control. G × E interaction was important for brain development and may provide a mechanism by which additive genetic variation is maintained, which in turn may promote sexual selection through female choice. Our study suggests that selection may act on the genes determining vocal learning, rather than directly on the underlying neuroanatomy, and emphasizes the fundamental importance of environmental conditions for vocal learning and neural development in songbirds.
Data from: The influence of cactus spine surface structure on puncture performance and anchoring ability is tuned for ecology
Spines are common morphological features found in almost all major biological groups offering an opportunity to explore large-scale evolutionary convergence across disparate clades. As an example, opuntioid cacti have spines with barbed ornamentation that is remarkably similar in form and scale to that found on porcupine quills, suggesting specific biomechanical convergence across the animal and plant kingdoms. While the mechanics of porcupine quills as defensive mechanisms has been previously tested, the mechanics of cacti spines (which have evolved to fill a number of functions including defense, climbing and dispersal) has not been characterized. Here we study the puncturing and anchoring ability of six species of cactus, including both barbed and non-barbed spines. We found that barbed spines require less work to puncture a variety of targets than non-barbed spines. Barbed spines also require more work than non-barbed spines to withdraw from biological materials, due to their barbs engaging with tissue fibers. These results closely match those found previously for barbed vs. non-barbed porcupine quills, implying biomechanical convergence. The variation in performance of barbed versus non-barbed spines, as well as between barbed spines from different species, is likely tied to the diversity of ecological functions of cactus spines.
Data from: Dispersal capacity predicts both population genetic structure and species richness in reef fishes
Dispersal is a fundamental species characteristic that should directly affect both rates of gene flow among spatially distributed populations and opportunities for speciation. Yet no single trait associated with dispersal has been demonstrated to affect both micro- and macroevolutionary patterns of diversity across a diverse biological assemblage. Here, we examine patterns of genetic differentiation and species richness in reef fishes, an assemblage of over 7,000 species comprising approximately one-third of the extant bony fishes and over one-tenth of living vertebrates. In reef fishes, dispersal occurs primarily during a planktonic larval stage. There are two major reproductive and parental investment syndromes among reef fishes, and the differences between them have implications for dispersal: (1) benthic guarding fishes lay negatively buoyant eggs, typically guarded by the male parent, and from these eggs hatch large, strongly swimming larvae; in contrast, (2) pelagic spawning fishes release small floating eggs directly into the water column, which drift unprotected before small weakly swimming larvae hatch. Using phylogenetic comparative methods, we show that benthic guarders have significantly greater population structure than pelagic spawners and additionally that taxonomic families of benthic guarders are more species rich than families of pelagic spawners. Our findings provide a compelling case for the continuity between micro- and macroevolutionary processes of biological diversification and underscore the importance of dispersal-related traits in influencing the mode and tempo of evolution.
Data from: Outlier SNP markers reveal fine-scale genetic structuring across European hake populations (Merluccius merluccius)
Shallow population structure is generally reported for most marine fish and explained as a consequence of high dispersal, connectivity and large population size. Targeted gene analyses and more recently genome-wide studies have challenged such view, suggesting that adaptive divergence might occur even when neutral markers provide genetic homogeneity across populations. Here, 381 SNPs located in transcribed regions were used to assess large- and fine-scale population structure in the European hake (Merluccius merluccius), a widely distributed demersal species of high priority for the European fishery. Analysis of 850 individuals from 19 locations across the entire distribution range showed evidence for several outlier loci, with significantly higher resolving power. While 299 putatively neutral SNPs confirmed the genetic break between basins (FCT = 0.016) and weak differentiation within basins, outlier loci revealed a dramatic divergence between Atlantic and Mediterranean populations (FCT range 0.275–0.705) and fine-scale significant population structure. Outlier loci separated North Sea and Northern Portugal populations from all other Atlantic samples and revealed a strong differentiation among Western, Central and Eastern Mediterranean geographical samples. Significant correlation of allele frequencies at outlier loci with seawater surface temperature and salinity supported the hypothesis that populations might be adapted to local conditions. Such evidence highlights the importance of integrating information from neutral and adaptive evolutionary patterns towards a better assessment of genetic diversity. Accordingly, the generated outlier SNP data could be used for tackling illegal practices in hake fishing and commercialization as well as to develop explicit spatial models for defining management units and stock boundaries.
Data from: A structured population model suggests that long life and post-reproductive lifespan promote the evolution of cooperation
Social organization correlates with longevity across animal taxa. This correlation has been explained by selection for longevity by social evolution. The reverse causality is also conceivable but has not been sufficiently considered. We constructed a simple, spatially structured population model of asexually reproducing individuals to study the effect of temporal life history structuring on the evolution of cooperation. Individuals employed fixed strategies of cooperation or defection towards all neighbours in a basic Prisoner׳s Dilemma paradigm. Individuals aged and transitioned through different life history stages asynchronously without migration. An individual׳s death triggered a reproductive event by one immediate neighbour. The specific neighbour was chosen probabilistically according to the cumulative payoff from all local interactions. Varying the duration of pre-reproductive, reproductive, and post-reproductive life history stages, long-term simulations allowed a systematic evaluation of the influence of the duration of these specific life history stages. Our results revealed complex interactions among the effects of the three basic life history stages and the benefit to defect. Overall, a long post-reproductive stage promoted the evolution of cooperation, while a prolonged pre-reproductive stage has a negative effect. In general, the total length of life also increased the probability of the evolution of cooperation. Thus, our specific model suggests that the timing of life history transitions and total duration of life history stages may affect the evolution of cooperative behaviour. We conclude that the causation of the empirically observed association of life expectancy and sociality may be more complex than previously realized.
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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.