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3,655 results for “Structural data”
Data from: NOVOWrap: an automated solution for plastid genome assembly and structure standardization
<p>Plastid genomes play an important role in genomics and evolutionary biology. Next-generation sequencing has revolutionized plastid genomic data acquisition to the point that genome assembly has become a bottlenecks for widespread utilization of plastid genome data. To solve this problem, we developed an open-source, cross-platform tool known as, NOVOWrap, which includes both command-line and graphical interfaces for automatically assembling plastid genomes on personal computers. With minimal inputs, settings, and user intervention, NOVOWrap can automatically assemble plastid genomes, validate results and standardize the structure using affordable computer resources. The performance of this software has been successfully benchmarked against the plastid genomes of 11 species belonging to lycopods, gymnosperms, and angiosperms. This program is expected to liberate researchers from laborious and cumbersome computer manipulations and create reliable and standardized genomic data.</p>
Data and code from "A dimmer shade of pale: revealing the faint signature of local assembly processes on the structure of strongly filtered plant communities"
<p>Trait-based ecology suggests that abiotic filtering is the main mechanism structuring the regional species pool in different subsets of habitat-specific species. At more local spatial scales, other ecological processes may add on giving rise to complex patterns of functional diversity (FD). Understanding how assembly processes operating on the habitat-specific species pools produce the locally observed plant assemblages is an ongoing challenge. Here, we evaluated the importance of different processes to community assembly in an alpine fellfield, assessing its effects on local plant trait FD. Using classical randomization tests and linear mixed models, we compared the observed FD with expectations from three null models that hierarchically incorporate additional assembly constraints: stochastic null models (random assembly), independence null models (each species responding individual and independently to abiotic environment), and co-occurrence null models (species responding to environmental variation and to the presence of other species). We sampled species composition in 115 quadrats across 24 locations in the central Pyrenees (Spain) that differed in soil conditions, solar radiation and elevation. Overall, the classical randomization tests were unable to find differences between the observed and expected functional patterns, suggesting that the strong abiotic filters that sort out the flora of extreme regional environments blur any signal of other local processes. However, our approach based on linear mixed models revealed the signature of different ecological processes. In the case of seed mass and leaf thickness, observed FD significantly deviated from the expectations of the stochastic model, suggesting that fine-scale abiotic filtering and facilitation can be behind these patterns. Our study highlights how the hierarchical incorporation of ecological additional constraints may shed light on the dim signal left by local assembly processes in alpine environments.</p>
Data from: Urbanization and plant invasion alter the structure of litter microarthropod communities
<p>Anthropogenic activity underpins the creation of urban ecosystems, often with introduced or invasive species playing a large role in structuring ecological communities. While the effects of urbanization on charismatic taxa such as birds, bees or butterflies have received much attention, the impacts on small and inconspicuous organisms remain poorly understood.</p> <p>Here, we assess how the community structure of leaf litter-inhabiting microarthropods in city parks varies along an urbanization gradient in Toronto, Canada. At each park, we established paired forest understory plots which were either dominated by native vegetation or dog-strangling vine (<em>Vincetoxicum rossicum</em>), an invasive species that is spreading throughout northeastern North America and abundant in urban areas. We compared microarthropod richness, abundance, and diversity in ecological traits between invaded and non-invaded plots as well as compositional dissimilarities among plots across the urbanization gradient.</p> <p>We recorded 123 genera and found: i) there was a negative effect of urbanization on microarthropod richness and abundance but only in invaded plots; ii) richness and abundance increased continuously with urbanization in non-invaded plots, but peaked at intermediate urbanization levels in invaded plots; and iii) there was significant turnover with increasing urbanization, with distinct communities represented in highly urbanized areas compared to less urbanized areas, regardless of whether invaded. We also found litter microarthropod richness and abundance increased with soil ammonium and decreased with nitrate. These trends were especially strong for fungivorous microarthropods, however there was no relationship between soil nutrients and urbanization or invasion.</p> <p>Urbanization and biological invasion drive biodiversity change, and there is a need to disentangle these effects on ecological communities and related ecosystem processes. We show microarthropod communities change with urbanization, with the effects of invasion most prominent in non-urban areas. Here, there is high richness and abundance but low ecological trait diversity, possibly because certain feeding traits are excluded and others overrepresented.</p> <p>Understanding of urban ecological systems must include knowledge of the microarthropods that interact widely across food webs, form distinct communities in highly urban areas, and drive many of the important ecological functions upon which people in cities depend.</p>
Data from: Changes in age-structure over four decades were a key determinant of population growth rate in a long-lived mammal
<p>1. A changing environment directly influences birth and mortality rates, and thus population growth rates. However, population growth rates in the short-term are also influenced by population age-structure. Despite its importance, the contribution of age-structure to population growth rates has rarely been explored empirically in wildlife populations with long-term demographic data.</p> <p>2. Here, we assessed how changes in age-structure influenced short-term population dynamics in a semi-captive population of Asian elephants (Elephas maximus).</p> <p>3. We addressed this question using a demographic dataset of female Asian elephants from timber camps in Myanmar spanning 45 years (1970-2014). First, we explored temporal variation in age-structure. Then, using annual matrix population models, we used a retrospective approach to assess the contributions of age-structure and vital rates to short-term population growth rates with respect to the average environment.</p> <p>4. Age-structure was highly variable over the study period, with large proportions of juveniles in the years 1970 and 1985, and made a substantial contribution to annual population growth rate deviations. High adult birth rates between 1970-1980 would have resulted in large positive population growth rates, but these were prevented by a low proportion of reproductive-aged females.</p> <p>5. We highlight that an understanding of both age-specific vital rates and age-structure is needed to assess short-term population dynamics. Furthermore, this example from a human-managed system suggests that the importance of age-structure may be accentuated in populations experiencing human disturbance where age-structure is unstable, such as those in captivity or for endangered species. Ultimately, changes to the environment drive population dynamics by influencing birth and mortality rates, but understanding demographic structure is crucial for assessing population growth.</p>
Data for the paper "An Inversion Algorithm for Deriving Shallow Structure using Co-located Wind, Pressure, and Seismic Data"
<p>Wind, pressure, and seismic data used in the paper "An Inversion Algorithm for Deriving Shallow Structure using Co-located Wind, Pressure, and Seismic Data"</p>
Data from: Contrasting population structure and demographic history of cereal aphids in different environmental and agricultural landscapes
<p>Single Nucleotide Polymorphisms files and phylogonetic trees of S. miscanthi samples collected in China and S. avenae from the UK used to study the population genetics analyses of these species. These are:</p> <p>China_samples_vcf.zip: dataset of SNPs from S. miscanthi sampled in 10 populations of China obtained using FreeBayes (in vcf format).</p> <p>China_samples_vcf_filtered.zip: SNPs from S. miscanthi after filtering the file China_samples_vcf.zip using vcftools (max-missing 0.75, minDP 3, mac 3, minQ 30, remove-indels, thin 2000, max-missing 0.9, thin 5000). This file was used in all population genetic analyses of the Chinese populations in the paper, transforming to the appropriate formats.</p> <p>China_samples_SNPs.fas: fasta file of phased SNPs used to estimate the phylogeny of S. miscanthi haplotypes using RAxML.</p> <p>China_RAxML_phylogeny_newick.tre: RAxML phylogenetic tree in newick format obtained with China_samples_SNPs.fas.</p> <p>England_samples_vcf.zip: dataset of SNPs from S. avenae sampled in 12 populations of England obtained using FreeBayes (in vcf format).</p> <p>England_samples_vcf_filtered.zip: SNPs from S. avenae after filtering the file England_samples_vcf.zip using vcftools (max-missing 0.5, mac 3, minQ 30, minDP 3, max-missing 0.5, exclude individuals with 50% missing data, max-missing 0.75, remove-indels, thin 2000). This file was used in all population genetic analyses of the English populations in the paper, transforming the vcf to the corresponding formats.</p> <p>England_samples_SNPs.fas: fasta file of phased SNPs.</p> <p>England_samples_SNPs_polymorphic.fas: fasta file of phased SNPs used in the phylogenetic reconstruction of S. avenae haplotypes using RAxML. This file is the same as England_samples_SNPs.fas after removing sites which were not polymorphic (e.g. a site that contains N and T in different samples is not considered polymorphic for RAxML and has to be removed)</p> <p>England_RAxML_phylogeny_newick.tre: RAxML phylogenetic tree in newick format obtained with England_samples_SNPs_polymorphic.fas.</p>
Research data for "Understanding the geometric diversity of inorganic and hybrid frameworks through structural coarse-graining"
<p>This dataset supports the paper: "Understanding the geometric diversity of inorganic and hybrid frameworks through structural coarse-graining", available at the following DOI: 10.1039/d0sc03287e.</p> <p>The cleaned-up, coarse-grained, and re-scaled structures are provided here in both XYZ and CIF format. The data presented in the journal publication is also included; namely, MDS coordinates, T densities, and A-site heterogeneities for each structure in the dataset. T densities -- defined as: metals per unit volume (nm-3) -- are calculated using the re-scaled structures.</p>
IPBES Data Management Tutorials - Session 3.2: Structure of a data management report and versioning
<p>The <em>IPBES data management tutorials</em> are short videos to help experts implement the IPBES data management Policy. They cover topics ranging from data management policy, reports, active research data, tools, and examples.</p> <p>The <em>IPBES data management reports </em>chapter provides an overview and discussion of specific elements of IPBES data management reports.</p> <p>This session, <em>Structure of a data management report and versioning</em>, details the structure of a data management report and guidelines for versioning. </p>
Data and code for: Time of night and moonlight structure vertical space use by insectivorous bats in a Neotropical rainforest: an acoustic monitoring study
<p>Abstract</p> <p>Previous research has shown diverse vertical space use by various taxa, highlighting the importance of forest canopy. Yet, we often fail to explore how this three-dimensional space use changes over time. Here we use canopy tower systems in French Guiana to monitor neotropical bat activity above and below the forest canopy throughout nine nights in the wet season. We show that different bats use both canopy and understory space differently, and that this can change throughout the night. We find that bats are overall more active in the canopy, but multiple species/acoustic complexes are more active in the understory. We also find that species that do not seem to prefer understory or canopy, when data are aggregated by night, do show temporally changing preferences in hourly activity. This work highlights the need to consider temporal axes in studies of space use, both throughout daily cycles and across seasons.</p>
Data from: Structure, gene order, and nucleotide composition of mitochondrial genomes in parasitic lice from Amblycera
<p>Parasitic lice have unique mitochondrial (mt) genomes characterized by rearranged gene orders, variable genome structures, and less AT content compared to most other insects. However, relatively little is known about the mt genomes of Amblycera, the suborder sister to all other parasitic lice. Comparing among nine different genera (including representative of all seven families), we show that Amblycera have variable and highly rearranged mt genomes. Some genera have fragmented genomes that vary considerably in length, whereas others have a single mt chromosome. Notably, these genomes are more AT-biased than most other lice. We also recover genus-level phylogenetic relationships among Amblycera that are consistent with those reported from large nuclear datasets, indicating that mt sequences are reliable for reconstructing evolutionary relationships in Amblycera. However, gene order data cannot reliably recover these same relationships. Overall, our results suggest that the mt genomes of lice, already know to be distinctive, are even more variable than previously thought.</p>
Microsatellite genotypes and associated data for: The contribution of clonality to population genetic structure in the sea anemone Diadumene lineata
<p>Ecological and evolutionary processes differ depending on how genetic diversity is organized in space. For clonal organisms, the organization of both genetic and genotypic diversity can influence the fitness effects of competition, the mating system, and reproductive mode, which are key drivers of life cycle evolution. Understanding how individual reproductive behavior contributes to population genetic structure is essential for disentangling these forces, particularly in species with complex and plastic life cycles. The widespread sea anemone <i>Diadumene lineata</i> exhibits temperature-dependent fission which contributes to predictable variation in clonal rate along the Atlantic coast of the United States, part of its non-native range. Because warmer conditions lead to higher rates of clonality, we expected to find lower genotypic and genetic diversity in lower versus higher latitude populations. We developed primers for 11 microsatellite loci and genotyped 207 anemones collected from 8 sites ranging from Florida to Massachusetts. We found clonal influence at all sites, and as predicted, the largest clones were found at lower latitude sites. We also found genetic signatures of sex in the parts of the range where gametogenesis is most common. Evidence of sex outside the native range is novel for this species and provides insights into the dynamics of this successful invader. Our findings also illustrate challenges that partially clonal taxa pose for eco-evolutionary studies, such as difficulty sampling statistically robust numbers of genets and interpretating common population genetic metrics. For example, we found high among-locus variation in F<i><sub>is, </sub></i>which makes the meaning of mean multilocus F<i><sub>is</sub></i> unclear.</p>
Snapshots, frequency contact maps analysis, Poisson Boltzmann calculations, and data scripts for characterization of structural and energetic differences between conformations of the SARS-CoV-2 spike protein
<p><strong>Molecular dynamics simulation</strong> trajectories, which have been performed using the Amber ff14SB force field running with the Amber18 package at the NSF-funded (OAC-1826915, OAC-1828163) ELSA high performance computing cluster at The College of New Jersey. Simulation methodology and further details are described in [1] and [2]. For further details on the trajectories, please contact Joseph Baker (bakerj@tcnj.edu).</p> <p>The <strong>Poisson Boltzmann </strong>energy calculations have been achieved by using the input_files.tar.xz found here and solving the Poisson Boltzmann equation with pygbe. A more detailed example and tutorial can be found at [4]. For further details contact Horacio V Guzman.</p> <p><strong>The dataset contains </strong></p> <ul> <li><strong>A total of 30 snapshots of the three trajectories (10 snapshots each system = two per replica x 5 replicas/system):</strong></li> </ul> <ol> <li>SARS-CoV-2002 spike protein with three RBD in the down positions: "COV2-DDD/PDB/" .</li> <li>SARS-CoV-2002 spike protein with one RBD in the up and two RBD in the down positions: "COV2-UDD/PDB/".</li> <li>SARS-CoV-2002 spike protein with two RBD in the up and one RBD in the down positions: "COV2-DUU/PDB/".</li> </ol> <ul> <li><strong>Input files for Poisson-Boltzmann analysis</strong>:</li> </ul> <ol> <li>PoissonBoltzmann/input_files.tar.xz</li> </ol> <ul> <li><strong>Data for the frequency contact map and processing scripts</strong>:</li> </ul> <ol> <li>cov2-ddd.pdb, cov2-udd.pdb, cov2-duu.pdb reference PDB files.</li> <li>Contact maps [3] at "COV2-DDD/CONTACT_MAP/", "COV2-UDD/CONTACT_MAP/", "COV2-DUU/CONTACT_MAP/".</li> <li>frequency.lua: get frequency of contacts from a set of contacts map files.</li> <li>diff_frequency.lua: get differential frequency of contacts from a set of frequency files.</li> <li>Frequency of contacts listed in frequency.data files at "COV2-DDD/", "COV2-UDD/" and "COV2-DUU/" directories.</li> </ol> <p>Read the "INFO" files for further informations.</p> <p>This dataset and the code is part of a collaboration between:</p> <ul> <li>The Institute of Fundamental Technological Research, Polish Academy of Sciences, Warsaw, Poland (supported by the National Science Centre, Poland, under grant No. 2017/26/D/NZ1/0046)</li> <li>Department of Chemistry, The College of New Jersey, New Jersey, United States (supported by National Science Foundation under grant numbers OAC-1826915 and OAC-1828163).</li> <li>Jozef Stefan Institute, Ljubljana, Slovenia (supported by the Slovenian Research Agency (Funding No. P1-0055)).</li> <li>School of engineering in bioinformatics, University of Talca, Talca, Chile.</li> </ul> <p>[1] Rodrigo A. Moreira, Mateusz Chwastyk, Joseph L. Baker, Horacio V Guzman, & Adolfo B. Poma. (2020). All-atom simulations snapshots and contact maps analysis scripts for SARS-CoV-2002 and SARS-CoV-2 spike proteins with and without ACE2 enzyme (Version 0.1) [Data set]. Zenodo. http://doi.org/10.5281/zenodo.3817447</p> <p>[2] Chad W. Hopkins, Scott Le Grand, Ross C. Walker, and Adrian E. Roitberg. Long-Time-Step Molecular Dynamics through Hydrogen Mass Repartitioning. Journal of Chemical Theory and Computation 2015 11 (4), 1864-1874. http://doi.org/10.1021/ct5010406</p> <p>[3] Rodrigo A. Moreira, Mateusz Chwastyk, Joseph L. Baker, Horacio V Guzman, & Adolfo B. Poma. Quantitative determination of mechanical stability in the novel coronavirus spike protein. Nanoscale, 2020,12, 16409-16413. <a href="https://doi.org/10.1039/D0NR03969A">https://doi.org/10.1039/D0NR03969A</a></p> <p>[4] https://github.com/pyF4all</p>
Data for 'Ultrafast strain engineering and coherent structural dynamics from resonantly driven optical phonons in LaAlO3'
<p>This folder contains all the raw data required to generate the figures in the work 'Ultrafast strain engineering and coherent structural dynamics from resonantly driven optical phonons in LaAlO3'. </p> <p> </p> <p><strong>Contents</strong></p> <p><em>Figure 2:</em></p> <p>(a) Time resolved balanced reflection data for the short and long time periods: LongTimeData.txt and ShortTimeData.txt. The corresponding Fourier spectra shown in the inset: InsetFourier_LongTimeData.txt and InsetFourier_ShortTimeData.txt</p> <p>(b) Time resolved polarization rotation data for the short and long time periods: LongTimeData.txt and ShortTimeData.txt. The corresponding Fourier spectra shown in the inset: InsetFourier_LongTimeData.txt and InsetFourier_ShortTimeData.txt</p> <p><em>Figure 3:</em></p> <p>(a) Time-resolved polarization rotation data after excitation at two different pump photon energies: trace_85meV_excitation.txt and trace_124meV_excitation.txt. Amplitude as function of central pump photon energy: Inset_Wavelength_dependence.txt and the absorption of LaAlO3: Inset_absorption.txt</p> <p>(b) The raw data for different polarizations: traces_angle_dependence.txt</p> <p>(c) The experimentally obtained (AmplitudeExperiment.txt) and DFT calculated values (AmplitudeDFT.txt).</p> <p><em>Figure 4</em></p> <p>(a) Fourier spectra (and double Gaussian fit) corresponding to time-resolved measurments after excitation at different central photon energies: FourierSpectraData.txt (and FourierSpectraFits). Inset: Extracted peak amplitude (Inset_StrainvsWavelength.txt) and Gaussian fit of the TA strain (Inset_GaussianFit.txt). </p> <p>(b)The TA/LA ratio as function of pump photon energy (SoundWaveRatio.txt) and the Lorentzian fit (RatioFit.txt). And the absorption of LaAlO3 (Absorption_coefficient.txt).</p> <p> </p> <p> </p> <p> </p> <p> </p>
Dataset accompanying paper submission for "Toward data-driven generation and evaluation of model structure for integrated representations of human behavior in water resources systems"
<p>This data set accompanies code archived at DOI: <a href="https://doi.org/10.5281/zenodo.3833186">10.5281/zenodo.3833186</a>, which was used in the experiments for the paper submission "Toward data-driven generation and evaluation of model structure for integrated representations of human behavior in water resources systems"</p>
Supplementary Data for "Influence of First And Second Coordination Environment on Structural Fe(II) Sites in MIL-101 for C-H Bond Activation in Methane"
<p>Cartesian coordinates for all the optimized geometries reported in "Influence of First And Second Coordination Environment on Structural Fe(II) Sites in MIL-101 for C-H Bond Activation in Methane" (acscatal.0c03906)</p>
Data from: Characterizing morphological (co)variation using structural equation models: body size, allometric relationships and evolvability in a house sparrow metapopulation
Body size plays a key role in the ecology and evolution of all organisms. Therefore, quantifying the sources of morphological (co)variation, dependent and independent of body size, is of key importance when trying to understand and predict responses to selection. We combine structural equation modeling with quantitative genetics analyses to study morphological (co)variation in a meta-population of house sparrows (Passer domesticus). As expected, we found evidence of a latent variable 'body size', causing genetic and environmental covariation between morphological traits. Estimates of conditional evolvability show that allometric relationships constrain the independent evolution of house sparrow morphology. We also found spatial differences in general body size and its allometric relationships. On islands where birds are more dispersive and mobile, individuals were smaller and had proportionally longer wings for their body size. While in islands where sparrows are more sedentary and nest in dense colonies, individuals were larger and had proportionally longer tarsi for their body size. We corroborated these results using simulations and show that our analyses produce unbiased allometric slope estimates. This study highlights that in the short term allometric relationships may constrain phenotypic evolution, but that in the long term selection pressures can also shape allometric relationships.
Data used in 'The joint role of coevolutionary selection and network structure in shaping trait complementarity in mutualisms' manuscript
<p>The files in this repository correspond to the raw and processed data described in the 'The joint role of coevolutionary selection and network structure in shaping trait complementarity in mutualisms' manuscript.</p> <p>Once expanded, the zip files contains two directories and one documentation file, named data_documentation. Please refer to this file for a thorough description of the organization and contents of raw and processed data files.</p>
Supplementary Data for Secondary structure and DNA binding domain prediction
<p><strong>This project contains the following extended data:</strong></p> <ul> <li><strong>Supplementary Table 1: </strong>Summary table of DNA binding domains (DBD), the counts of target regions within the genome and statistical analysis. (DNA_BINDING_DOMAINS_ID.tsv)</li> <li><strong>Sequence</strong>: ecCEBPα secondary structure prediction with RNAplfold at a pairing probability cut off of 0.1. N represents all sequences with pairing probability greater than 0.1. (predicted_secondary_structure_of_ecCEBPA.fa)</li> </ul>
Data from: Multi-modal ultra-high resolution structural 7-Tesla MRI data repository
Structural brain data is key for the understanding of brain function and networks, i.e., connectomics. Here we present data sets available from the 'atlasing of the basal ganglia (ATAG)' project, which provides ultra-high resolution 7Tesla (T) magnetic resonance imaging (MRI) scans from young, middle-aged, and elderly participants. The ATAG data set includes whole-brain and reduced field-of-view MP2RAGE and T2*-weighted scans of the subcortex and brainstem with ultra-high resolution at a sub-millimeter scale. The data can be used to develop new algorithms that help building high-resolution atlases both relevant for the basic and clinical neurosciences. Importantly, the present data repository may also be used to inform the exact positioning of electrodes used for deep-brain-stimulation in patients with Parkinson's disease and neuropsychiatric diseases.
Data from: Fine-scale genetic structure due to adaptive divergence among microhabitats
It has been suggested that adaptive evolution on ecological timescales shapes communities. However, adaptation among environments relies on isolation or large selection coefficients that exceed migration effects. This reliance is tempered if adaptation is polygenic—does not depend on one allele completely replacing another but instead requires small allele frequency changes at many loci. Thus, whether individuals can evolve adaptation to fine-scale habitat variation (for example, microhabitats) is not resolved. Here we analyze the genetic divergence of the teleost fish, Fundulus heteroclitus, among microhabitats that are <200 m apart in three separate saltmarshes using 4741 single-nucleotide polymorphisms (SNPs). Among these SNPs, 1.3–2.3% have large and highly significant differences among microhabitats (mean FST=0.15; false discovery rate less than or equal to1%). The divergence among microhabitats for these outlier SNPs is larger than that among populations, exceeds neutral expectation and indicates surprising population structure among microhabitats. Thus, we suggest that polygenic selection is surprisingly effective in altering allele frequencies among many different SNPs that share similar biological functions in response to environmental and ecological differences over very small geographic distances. We acknowledge the evolutionary difficulty of large genetic divergence among well-connected habitats. Therefore, these studies are only the first step to discern whether natural selection is responsible and capable of effecting genetic divergence on such a fine scale.
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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.