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9,882 results for “Scale”
msd-errors - Data for scaling figures2
Data for a figure that shows the scaling of uncertainty as a function of simulation length and number of atoms and step size, for both true and anitcorrelated random walks. This compares the kinisi approach (on just 32 unique walks) with the numerical values from (1024 unique walks). <br><br>Created using <a href="https://github.com/rodluger/showyourwork">showyourwork</a> from <a href="git@github.com:arm61/msd-errors/tree/900ea562a3de64ba9ec05ddfdf2d4c41f611c37c">this GitHub repo</a>.
FIGURE Phylogenetic relationships of the Coelastrella genus inferred from the 18S-ITS1-5.8S-ITS2 region. The Neighbor-Joining (NJ), Maximum Likelihood (ML) bootstrap values and Bayesian posterior probabilities (PP) are presented at the nodes (NJ/ML/PP). Only values above 75 are shown. Strains provided in this study are indicated in bold font. Authentic strains marked with asterisks. The scale bar represents the number of substitutions per site. The GenBank accession numbers of Coelastrella can be found in the Table 3. in Morphological and phylogenetic relations of members of the genus Coelastrella (Scenedesmaceae, Chlorophyta) from the Ural and Khentii Mountains (Russia, Mongolia)
FIGURE Phylogenetic relationships of the Coelastrella genus inferred from the 18S-ITS1-5.8S-ITS2 region. The Neighbor-Joining (NJ), Maximum Likelihood (ML) bootstrap values and Bayesian posterior probabilities (PP) are presented at the nodes (NJ/ML/PP). Only values above 75 are shown. Strains provided in this study are indicated in bold font. Authentic strains marked with asterisks. The scale bar represents the number of substitutions per site. The GenBank accession numbers of Coelastrella can be found in the Table 3.
FIGURE. Morphology of the studied Coelastrella strains. (4) IRK–A 2. (5) IRK–A 173. (А–D) vegetative cells and autosporangia. (E–G) cell wall ribs. (H) morphology of the old cells. Scale bar: 10μm. in Morphological and phylogenetic relations of members of the genus Coelastrella (Scenedesmaceae, Chlorophyta) from the Ural and Khentii Mountains (Russia, Mongolia)
FIGURE. Morphology of the studied Coelastrella strains. (4) IRK–A 2. (5) IRK–A 173. (А–D) vegetative cells and autosporangia. (E–G) cell wall ribs. (H) morphology of the old cells. Scale bar: 10μm.
FIGURE. SEM images of the studied Coelastrella strains: (A) SYKOA Ch-045-09. (B) SYKOA Ch-047-11. (C) SYKOA Ch-072-17. (D) IRK-A 173. (E) IRK-A 2. Scale bar: 10μm. in Morphological and phylogenetic relations of members of the genus Coelastrella (Scenedesmaceae, Chlorophyta) from the Ural and Khentii Mountains (Russia, Mongolia)
FIGURE. SEM images of the studied Coelastrella strains: (A) SYKOA Ch-045-09. (B) SYKOA Ch-047-11. (C) SYKOA Ch-072-17. (D) IRK-A 173. (E) IRK-A 2. Scale bar: 10μm.
Neutral and adaptive loci reveal fine-scale population structure in Eleginops maclovinus from North Patagonia
<p>Patagonia is an understudied area, especially when it comes to population genomic studies with relevance to fishery management. However, the dynamic and heterogeneous landscape in this area can harbor important but cryptic genetic population structure. Once such information is revealed, it can be integrated into the management of infrequently investigated species. <i>Eleginops maclovinus</i> is a protandrous hermaphrodite species with economic importance for local communities that is currently managed as a single genetic unit. In this study, we sampled five locations distributed across a salinity cline from Northern Patagonia to investigate the genetic population structure of <i>E</i>. <i>maclovinus</i>. We use Restriction-site Associated DNA (RAD) sequencing and outlier tests to obtain 11,712 neutral, 338 adaptive loci, and 78 loci associated to environmental variables. We identified a spatial pattern of structuration with gene flow and spatial selection by environmental association. Neutral and adaptive loci showed two and three genetic groups, respectively. The effective population sizes estimated ranged from 572 to 14,454 and were influenced more by locality than salinity cline. We found loci putatively associated with salinity suggesting that salinity may act as a selective driver in <i>E</i>. <i>maclovinus</i> populations. These results suggest a complex interaction between genetic drift, geneflow, and natural selection in this area. Our findings suggest that at least two to three genetic units exist in this area, and the information should be integrated into the management of this species. We discuss the significance of these results for fishery management and suggest future directions to improve our understanding of how <i>E</i>. <i>maclovinus</i> is adapted to the dynamic waters of Northern Patagonia.</p>
Large-scale homogenization of soil bacterial communities in response to agricultural practices in paddy fields, China
<div>This dataset contains data from 257 sites in four typical rice-growing regions across a 4,000-km transect in China, including geographic location data and environment factors data.</div> <div> <br> The study was conducted across a 4,000-km transect of China's rice-growing areas, from Heilong Jiang province to Yunnan province (100°55′ E to 134°08′° E, 22°46′ N to 48°02′ N, Table S1). Four typical rice-growing regions were selected along this transect: Sanjiang Plain (modern mechanical farming), Taihu Plain (mechanical plus minor manual farming), Lianghu Plain (manual plus minor mechanical farming), and Hani Terrace (traditional manual farming).</div> <div> <br> Field sampling was conducted during July and August in 2014 and 2015. Soil samples were collected from 178 flooded paddy fields and 79 surrounding non-paddy areas across four typical rice-growing regions of China. At each site, one homogenized sample was obtained, which was then separated into two parts. One part, which was obtained for DNA extraction, was placed into a sterile plastic tube then immediately placed in liquid nitrogen for short-term transportation. After shipping to the laboratory, these tubes were stored at −80 °C. The second part of the soil sample was placed into a plastic bag and stored at 4.0 °C for determining the soil physicochemical properties.</div> <div> <br> Main results of the experiments are that: (1) Distance–decay patterns of bacterial communities in paddy fields revealed reduced β-diversity compared to surrounding natural habitats. (2) Modern rice farming practices (plowing with machines) caused stronger homogenization of soil bacterial communities than traditional farming (plowing by hand). Among the four paddy regions, plowing by hand retained the highest soil bacterial β-diversity. (3) Moreover, a significant inverse correlation was observed between bacterial β-diversity and the agricultural mechanization level. (4) Among multiple environmental factors, dramatic spatial homogenization of soil physicochemical properties, particularly soil nutrient contents, and reduced dispersal limitation caused by modern farming activities both strongly predict a reduction of bacterial β-diversity in modern paddy fields.</div>
FIGURE 5. Leucoagaricus gongylophorus F.T.F. 192. A. Basidiospores. B. Basidia. Scale bars are 10 in Taxonomic and nomenclatural novelties in Leucoagaricus (Agaricaceae) from Brazil
FIGURE 5. Leucoagaricus gongylophorus F.T.F. 192. A. Basidiospores. B. Basidia. Scale bars are 10 µm. Illustration by C. Heisecke.
FIGURE 3. Begonia nigritarum. A. habit. B. inflorescence. C. staminate flower. D. pistillate flower. E. developing capsule. F. leaf, abaxial view. G. rhizome. Scale bars for A in Begonia ×dinglensis, a natural hybrid of Philippine Begonia section Baryandra, as evidenced by morphological, phylogenetic and cytological data
FIGURE 3. Begonia nigritarum. A. habit. B. inflorescence. C. staminate flower. D. pistillate flower. E. developing capsule. F. leaf, abaxial view. G. rhizome. Scale bars for A is 10 cm, B and G are 1 cm, C–E are 0.5 cm, F is 3 cm. [All photos from Ching-I Peng 23858 (HAST).]
FIGURE 2. Begonia camiguinensis. A. habit. B. inflorescence. C. staminate flower. D. pistillate flower. E. developing capsule. F. leaf, abaxial view. G. rhizome. Scale bars for A in Begonia ×dinglensis, a natural hybrid of Philippine Begonia section Baryandra, as evidenced by morphological, phylogenetic and cytological data
FIGURE 2. Begonia camiguinensis. A. habit. B. inflorescence. C. staminate flower. D. pistillate flower. E. developing capsule. F. leaf, abaxial view. G. rhizome. Scale bars for A is 10 cm, B and G are 1 cm, C–E are 0.5 cm, F is 3 cm. [All photos from Ching-I Peng 23853 (HAST).]
Ecological network complexity scales with area
<p><span><span><span><span><span><span><span><span><span><span><span>Larger geographical areas contain more species–an observation raised to a law in ecology. Less explored is whether biodiversity changes are accompanied by a modification of interaction networks. We use data from 32 spatial interaction networks from different ecosystems to analyse how network structure changes with area. We find that basic community structure descriptors (number of species, links, and links per species) increase with area following a power-law. Yet, the distribution of links per species varies little with area, indicating that the fundamental organization of interactions within networks is conserved. Our null model analyses suggest that the spatial scaling of network structure is determined by factors beyond species richness and the number of links. We demonstrate that biodiversity–area relationships can be extended from species counts to higher levels of network complexity. Therefore, the consequences of anthropogenic habitat destruction may extend from species loss to wider simplification of natural communities.</span></span></span></span></span></span></span></span></span></span></span></p>
FIGURE. Conlarium sichuanense (HKAS 113024, holotype) a–c Colonies on dead branches. d–k Conidiogenous cells and conidia. l Germinated conidium. m, n Colony on PDA from surface and reverse. Scale bars: d-k = 10 μm, l = 20 μm. in Conlarium sichuanense sp. nov., on Ficus virens from Sichuan Province, China
FIGURE. Conlarium sichuanense (HKAS 113024, holotype) a–c Colonies on dead branches. d–k Conidiogenous cells and conidia. l Germinated conidium. m, n Colony on PDA from surface and reverse. Scale bars: d-k = 10 μm, l = 20 μm.
Large-scale Three-dimensional Hydraulic Tomography Analyses of Long-term Municipal Wellfield Operations
<p>This file includes all the datasets utilized to accomplish the above study. Basically, it includes the information of grid for groundwater modeling, the distribution of wells, as well as water-level variations for model calibration and validation.</p>
data for modeling scale of representation of heterogeneity on simulated salinity and saltwater circulation in coastal aquifers
<p>This is the modeling data for modeling scale of representation of heterogeneity on simulated salinity and saltwater circulation in coastal aquifers. We setup a series of SEAWAT models to see the scale-dependent heterogeneity in simulations of saltwater circulation and cautions</p>
Data and output files for the paper, "Dynamical systems inference at scale reveals intrinsic instability in the dysbiotic microbiome"
<p>The above files contain the output of the model, which we call MDSINE2, developed in the paper titled, "<em>Dynamical systems inference at scale reveals intrinsic instability in the dysbiotic microbiome</em>" (See https://github.com/gerberlab/MDSINE2_Paper for implementation details). More specifically, forward_sims.tgz contains the output of forward simulations in .npy format; mixed_prior_fixed.tgz contains the pickle files corresponding to the output of the MCMC simulations for fixed topology; mixed_prior_unfixed.tgz contains the pickle files corresponding to the output of the MCMC simulations for unfixed topology; other_files contains information on eigenvalues and cycles, results for Phylogenetic Neighborhood Analysis, Keystoneness Analysis and the output in .npy format for comparator methods; ASV_OTU_aggregate_and_plylogeneteic trees contains the plots of trajectories (relative abundance) of OTUS and their constituent ASVs, and of phylogenetic trees. </p>
Harnessing large-scale herbarium image datasets through representation learning (application images)
<p>Herbarium specimen images used in the manuscript <a href="https://www.frontiersin.org/articles/10.3389/fpls.2021.806407/full"><em>Harnessing large-scale herbarium image datasets through representation learning</em></a> for application tasks 2 and 3. These tasks were formulated to test the applicability of representations learned by three different neural networks trained on <a href="https://www.kaggle.com/c/herbarium-2021-fgvc8">the Half-Earth Challenge dataset</a>.</p> <p>All images are for specimens held by Royal Botanic Gardens, Kew. The images from Kew's HerbCat service, using URLs collated by <a href="https://www.idigbio.org/portal/search">iDigBio</a>. We first search iDigBio for the specimens we wanted, then downloaded the associated occurrence and image metadata files. We then used the URLs in the image metadata files to download the specimen images. The code used to download these images can be found in the <a href="https://doi.org/10.5281/zenodo.5776894">GitHub repository for the paper</a>.</p> <p>We searched iDigBio using these parameters:</p> <pre><code>[x] Must have media Genus: Dendrobium Institution Code: K Basis of Record: PreservedSpecimen</code></pre> <p> </p> <p>©<em> All images copyright of the Board of Trustees of the Royal Botanic Gardens, Kew.</em></p>
Data: Environmentally associated chromosomal structural variation influences fine-scale population structure of Atlantic Salmon
<p>Chromosomal rearrangements (e.g., inversions, fusions, and translocations) have long been associated with environmental variation in wild populations. New genomic tools provide the opportunity to examine the role of these structural variants in shaping adaptive differences within and among wild populations of non-model organisms. In Atlantic Salmon (Salmo salar), variations in chromosomal rearrangements exist across the species natural range, yet the role and importance of these structural variants in maintaining adaptive differences among wild populations remains poorly understood. We genotyped Atlantic Salmon (n = 1429) from 26 populations within a highly genetically structured region of southern Newfoundland, Canada with a 220K SNP array. Multivariate analysis, across two independent years, consistently identified variation in a structural variant (translocation between chromosomes Ssa01 and Ssa23), previously associated with evidence of trans-Atlantic secondary contact, as the dominant factor influencing population structure in the region. Redundancy analysis suggested that variation in the Ssa01/Ssa23 chromosomal translocation is strongly correlated with temperature. Our analyses suggest environmentally mediated selection acting on standing genetic variation in genomic architecture introduced through secondary contact may underpin fine-scale local adaptation in Placentia Bay, Newfoundland, Canada, a large and deep embayment, highlighting the importance of chromosomal structural variation as a driver of contemporary adaptive divergence.</p>
Female reproductive mode shapes allometric scaling of male traits in livebearing fishes (family Poeciliidae)
<p>Reproductive mode is predicted to influence the form of sexual selection. The viviparity driven conflict hypothesis posits that a shift from lecithotrophic (yolk-nourished) to matrotrophic (mother-nourished or placental) viviparity drives a shift from pre-copulatory toward post-copulatory sexual selection. In lecithotrophic species, we predict that pre-copulatory sexual selection will manifest as males exhibiting a broad distribution of sizes, and small and large males exhibiting contrasting phenotypes (morphology and coloration); conversely, in matrotrophic species an emphasis on post-copulatory sexual selection will preclude these patterns. We test these predictions by gathering data on male size, morphology, and coloration for five sympatric Costa Rican poeciliid species that differ in reproductive mode (i.e. lecithotrophy vs matrotrophy). We find tentative support for these predictions of the viviparity driven conflict hypothesis, with some interesting caveats and subtleties. In particular, we find that the three lecithotrophic species tend to show a broader distribution of male sizes than matrotrophic species. Furthermore, large males of such species tend to exhibit proportionately large dorsal and caudal fins and short gonopodia relative to small males, while these patterns are expressed to a lesser extent in the two matrotrophic species. Finally, large males in some of the lecithotrophic species exhibit darker fins relative to small males, a pattern not evident in either matrotrophic species. One unexpected finding was that even in the matrotrophic species <i>Poeciliopsis retropinna</i> and <i>Poeciliopsis paucimaculata</i>, which lack courtship and dichromatic coloration, some morphological traits exhibit significant allometric relationships, suggesting that even in these species pre-copulatory sexual selection may be present and shaping size-specific male phenotypes in subtle ways.</p>
Predicting wildlife susceptibility to infectious diseases atglobal scales
<p>Dataset included as supplementary material of the paper entitled https://doi.org/10.5281/zenodo.4914750. It contains phylogenetic, geographical and environmental distance for birds and bats, counts of incidence of <em>Plasmodium relictum</em> on birds, counts of incidence of West Nile Virus on birds and counts of incidence of coronavirus in bats, and susceptibility calculated by the random forest algorithm. Also we include the r scripts to run the models, and the outputs of the models after 1000 runs. </p>
Supporting Information: Environmental benefits of large-scale second-generation bioethanol production in the EU: An integrated supply chain network optimization and Life Cycle Assessment approache
<p>This supporting information provides all input data of the model, the assumptions made and the literature and database references for the publication<em> Environmental benefits of large-scale second-generation bioethanol production in the EU: An integrated supply chain network optimization and Life Cycle Assessment approache</em>. The environmental data is based on life cycle assessments, with full information on the life cycle inventory and the results of the life cycle impact assessment based on the ReCiPe method. It also includes detailed results for all objective functions in all scenarios (optimization of 18 midpoints, 3 endpoints, and economic optimization in 5 tax scenarios and 2 feedstock scenarios), and detailed results of the sensitivity analysis and Pareto optimization.</p>
A method for identifying environmental stimuli and genes responsible for genotype-by-environment interactions from a large-scale multi-environment data set
<p>It has not been fully understood in real fields what environment stimuli cause the genotype-by-environment (G × E) interactions, when they occur, and what genes react to them. Large-scale multi-environment data sets are attractive data sources for these purposes because they potentially experienced various environmental conditions. In this study, we developed a data-driven approach termed <u>E</u>nvironmental <u>C</u>ovariate Search Affecting <u>G</u>enetic <u>C</u>orrelations (ECGC) to identify environmental stimuli and genes responsible for the G × E interactions from large-scale multi-environment data sets. ECGC was applied to a soybean (<i>Glycine max</i>) data set that consisted of 25,158 records collected at 52 environments. ECGC illustrated what meteorological factors shaped the G × E interactions in six traits including yield, flowering time, and protein content and when they were involved. For example, it illustrated the relevance of precipitation around sowing dates and hours of sunshine just before maturity to the interactions observed for yield. Moreover, genome-wide association mapping on the sensitivities to the identified stimuli discovered candidate and known genes responsible for the G × E interactions. Our results demonstrate the capability of data-driven approaches to bring novel insights on the G × E interactions observed in fields. This dataset provides the data used in this study and supplementary tables cited in the manuscript.</p>
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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.