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3,655 results for “Structural data”
Data from: Metapopulation structure of a seed-predator weevil and its host plants in arms race coevolution
Although the importance of gene flow in the geographic structuring of host–parasite interactions has been well discussed, little is known about how dispersal drives the spatial dynamics of other types of coevolutionary interactions in nature. We evaluated the roles of gene flow in the geographically structured processes of a predator–prey arms race involving a seed-predatory weevil with a long mouthpart and its host camellia plant with a thick fruit coat. Molecular genetic analyses showed that both weevil and camellia populations were structured at a spatial scale of several kilometers. Importantly, the spatial pattern of the migration of weevils, but not that of camellias, imposed significant effects on the geographic configuration of the levels of coevolutionary escalation. This result suggests that even if migration is limited in one species (camellia), local coevolution with the other species that migrates between neighboring localities (weevil) can reduce the inter-population difference in the local adaptive optima of the former species. Thus, gene flow of a species potentially homogenizes local biological environments provided by the species and thereby promotes the evolutionary convergence of its coevolving counterparts. Consequently, by focusing on coevolutionary interactions in natural communities, "indirect" effects of gene flow on the adaptive divergence of organisms could be identified.
Data from: Sound amplification by means of a horn-like roosting structure in Spix's disc-winged bat
While sound is a signal modality widely used by many animals, it is very susceptible to attenuation, hampering effective long-distance communication. A strategy to minimize sound attenuation that has been historically used by humans is to use acoustic horns; to date, no other animal is known to use a similar structure to increase sound intensity. Here, we describe how the use of a roosting structure that resembles an acoustic horn (the tapered tubes that form when new leaves of plants such as Heliconia or Calathea species start to unfurl) increases sound amplification of the incoming and outgoing social calls used by Spix's disc-winged bat (Thyroptera tricolor) to locate roosts and group members. Our results indicate that incoming calls are significantly amplified as a result of sound waves being increasingly compressed as they move into the narrow end of the leaf. Outgoing calls were faintly amplified, probably as a result of increased sound directionality. Both types of call, however, experienced significant sound distortion, which might explain the patterns of signal recognition previously observed in behavioural experiments. Our study provides the first evidence of the potential role that a roost can play in facilitating acoustic communication in bats.
Data from: Species traits as drivers of food web structure
The use of functional traits to describe community structure is a promising approach to reveal generalities across organisms and ecosystems. Plant ecologists have demonstrated the importance of traits in explaining community structure, competitive interactions as well as ecosystem functioning. The application of trait-based methods to more complex communities such as food webs is however more challenging owing to the diversity of animal characteristics and of interactions. The objective of this study was to determine how functional structure is related to food web structure. We consider that food web structure is the result of 1) the match between consumer and resource traits, which determine the occurence of a trophic interaction between them, and 2) the distribution of functional traits in the community. We implemented a statistical approach to assess whether or not 35 466 pairwise interactions between soil organisms are constrained by trait-matching and then used a Procrustes analysis to investigate correlations between functional indices and network properties across 48 sites. We found that the occurrence of trophic interactions is well predicted by matching the traits of the resource with those of the consumer. Taxonomy and body mass of both species were the most important traits for the determination of an interaction. As a consequence, functional evenness and the variance of certain traits in the community were correlated to trophic complementarity between species, while trait identity, more than diversity, was related to network topology. The analysis was however limited by trait data availability, and a coarse resolution of certain taxonomic groups in our dataset. These limitations explain the importance of taxonomy, as well as the complexity of the statistical model needed. Our results outline the important implications of trait composition on ecological networks, opening promising avenues of research into the relationship between functional diversity and ecosystem functioning in multi-trophic systems.
Data from: Investigating the production of sexual resting structures in a plant pathogen reveals unexpected self-fertility and genotype-by-environment effects
The sexual stage of pathogens governs recombination patterns and often also provides means of surviving the off-season. Despite its importance for evolutionary potential and between-season epidemiology, sexual systems have not been carefully investigated for many important pathogens, and what generates variation in successful sexual reproduction of pathogens remains unexplored. We surveyed the sexually produced resting structures (chasmothecia) across 86 natural populations of fungal pathogen Podosphaera plantaginis (Ascomycota) naturally infecting Plantago lanceolata in the Åland archipelago, southwest of Finland. For this pathosystem, these resting structures are a key life-history stage, as more than half of the local pathogen populations go extinct every winter. We uncovered substantial variation in the level of chasmothecia produced among populations, ranging from complete absence to presence on all infected leaves. We found that chasmothecia developed within clonal isolates (single strain cultures). Additionally, these clonal isolates all contained both MAT1-1-1 and MAT1-2-1 genes that characterize mating-types in Ascomycetes. Hence, contrary to expectations, we conclude that this species is capable of haploid selfing. In controlled inoculations we discovered that pathogen genotypes varied in their tendency to produce chasmothecia. Production of chasmothecia was also affected by ambient temperature (E), and by the interaction between temperature and pathogen genotype (G × E). These G, E and G × E effects found both at a European scale, as well as within Åland, may partly explain the high variability observed among populations in chasmothecia levels. Consequently, they may be key drivers of the evolutionary potential and epidemiology of this highly dynamic pathosystem.
Data from: Geographically structured genetic variation in the Medicago lupulina – Ensifer mutualism
Gene flow between genetically differentiated populations can maintain variation in species interactions, especially when population structure is congruent between interacting species. However, large-scale empirical comparisons of the population structure of interacting species are rare, particularly in positive interspecific interactions (mutualisms). One agriculturally and ecologically important mutualism is the partnership between legume plants and rhizobia. Through characterizing and comparing the population genomic structure of the legume Medicago lupulina and two rhizobial species (Ensifer medicae and E. meliloti), we explored the spatial scale of population differentiation between interacting partners in their introduced range in North America. We found high proportions of E. meliloti in southeastern populations and high proportions of E. medicae in northwestern populations. Medicago lupulina and the Ensifer genus showed similar patterns of spatial genetic structure (isolation by distance). However, we detected no evidence of isolation by distance or population structure within either species of bacteria. Genome-wide nucleotide diversity within each of the two Ensifer species was low, suggesting limited introduction of strains, founder events, or severe bottlenecks. Our results suggest that there is potential for geographically structured coevolution between M. lupulina and the Ensifer genus, but not between M. lupulina and either Ensifer species.
Data from: Three-dimensional preservation of cellular and subcellular structures reveal 1.6 billion-year-old probable crown-group red algae
The ~1.6 Ga Tirohan Dolomite of the Lower Vindhyan in central India contains phosphatized stromatolitic microbialites. We report from there uniquely well-preserved fossils interpreted as crown-group rhodophytes (red algae). The filamentous form Rafatazmia chitrakootensis n.gen, n.sp. has uniserial rows of large cells and grows through diffusely distributed septation. Each cell has a centrally suspended, conspicuous rhomboidal disk interpreted as a pyrenoid. The septa between the cells have central structures that may represent pit connections and pit plugs. Another filamentous form, Denaricion mendax n.gen., n.sp., has coin-like cells reminiscent of those in large sulfur-oxidizing bacteria, but much more recalcitrant than the liquid-vacuole-filled cells of the latter. Its wider affinities are uncertain. Ramathallus lobatus n.gen., n.sp. is a lobate sessile alga with pseudoparenchymatous thallus and apparent tetraspore formation, suggesting florideophycean affinity. Rafatazmia and Ramathallus are interpreted as crown-group multicellular rhodophytes, antedating the oldest previously accepted red alga in the fossil record by about 400 million years.
Data from: Within-group relatedness is correlated with colony-level social structure and reproductive sharing in a social fish.
In group-living species, the degree of relatedness among group members often governs the extent of reproductive sharing, cooperation and conflict within a group. Kinship among group members can be shaped by the presence and location of neighbouring groups, as these provide dispersal or mating opportunities that can dilute kinship among current group members. Here, we assessed how within-group relatedness varies with the density and position of neighbouring social groups in Neolamprologus pulcher, a colonial and group-living cichlid fish. We used restriction site-associated DNA sequencing (RADseq) methods to generate thousands of polymorphic SNPs. Relative to microsatellite data, RADseq data provided much tighter confidence intervals around our relatedness estimates. These data allowed us to document novel patterns of relatedness in relation to colony-level social structure. First, the density of neighbouring groups was negatively correlated with relatedness between subordinates and dominant females within a group, but no such patterns were observed between subordinates and dominant males. Second, subordinates at the colony edge were less related to dominant males in their group than subordinates in the colony centre, suggesting a shorter breeding tenure for dominant males at the colony edge. Finally, subordinates who were closely related to their same-sex dominant were more likely to reproduce, supporting some restraint models of reproductive skew. Collectively, these results demonstrate that within-group relatedness is influenced by the broader social context, and variation between groups in the degree of relatedness between dominants and subordinates can be explained by both patterns of reproductive sharing and the nature of the social landscape.
Data from: Genetic population structure of the round whitefish (Prosopium cylindraceum) in North America: multiple markers reveal glacial refugia and regional subdivision.
Round whitefish (Prosopium cylindraceum) have a broad, disjunct range across northern North America and Eurasia, and little is known about their genetic population structure. We performed genetic analyses of round whitefish from 17 sites across its range using nine microsatellites, two mitochondrial DNA (mtDNA) loci, and 4918 to 8835 single-nucleotide polymorphism (SNP) loci. Our analyses identified deep phylogenetic division between eastern and western portions of the range, likely indicative of origins from at least two separate Pleistocene glacial refugia. Regionally, microsatellites and SNPs identified congruent patterns in subdivision, and population structure was consistent with expectations based on hydrologic connectivity. Within the Laurentian Great Lakes, Lake Huron and Lake Ontario were identified as key areas of interest. Lake Huron appears to be a contemporary source population for several other Great Lakes, and Lake Ontario contains a genetically discrete group of round whitefish. In all cases, multiple genetic markers yielded similar patterns, but SNPs offered substantially enhanced resolution. We conclude that round whitefish have population subdivision on several scales important for understanding their evolutionary history and conservation planning.
fMRI free-viewing data, resting-state and structural in macaques associated with publication 'Social prediction modulates activity of macaque superior temporal cortex'
<p>Using a free-viewing and functional magnetic resonance imaging, we show that activity in a region of the macaque middle superior temporal (midSTS) cortex was specifically modulated by the predictability of social interactions. This region could be distinguished from other temporal regions involved in face processing. Using resting-state fMRI in anesthetized macaques, we showed that the connectivity between the face-responsive areas and the social prediction area was more integrated in macaques than in humans. We reproduce the social prediction results in a replication study and provide a control to rule out oculomotor implication through the FEF in the social prediction activity of the midSTS, using Transcranial Ultrasound Stimulation. Using standard geometric shape movement stimuli, we also show that macaques do not attribute mental state to shapes.</p>
Data from: Structural reorganization of the chromatin remodeling enzyme Chd1 upon engagement with nucleosomes
The yeast Chd1 protein acts to position nucleosomes across genomes. Here, we model the structure of the Chd1 protein in solution and when bound to nucleosomes. In the apo state, the DNA-binding domain contacts the edge of the nucleosome while in the presence of the non-hydrolyzable ATP analog, ADP-beryllium fluoride, we observe additional interactions between the ATPase domain and the adjacent DNA gyre 1.5 helical turns from the dyad axis of symmetry. Binding in this conformation involves unravelling the outer turn of nucleosomal DNA and requires substantial reorientation of the DNA-binding domain with respect to the ATPase domains. The orientation of the DNA-binding domain is mediated by sequences in the N-terminus and mutations to this part of the protein have positive and negative effects on Chd1 activity. These observations indicate that the unfavorable alignment of C-terminal DNA-binding region in solution contributes to an auto-inhibited state.
Data from: Genomics detects population structure within and between ocean basins in a circumpolar seabird: the white-chinned petrel
<p>The Southern Ocean represents a continuous stretch of circumpolar marine habitat, but the potential physical and ecological drivers of evolutionary genetic differentiation across this vast ecosystem remain unclear. We tested for genetic structure across the full circumpolar range of the white-chinned petrel (<i>Procellaria aequinoctialis</i>) to unravel the potential drivers of population differentiation and test alternative population differentiation hypotheses. Following range-wide comprehensive sampling, we applied genomic (genotyping-by-sequencing or GBS; 60,709 loci) and standard mitochondrial-marker approaches (cytochrome b and 1st domain of control region) to quantify genetic diversity within and among island populations, test for isolation by distance, and quantify the number of genetic clusters using neutral and outlier (non-neutral) loci. Our results supported the multi-region hypothesis, with a range of analyses showing clear three-region genetic population structure, split by ocean basin, within two evolutionary units. The most significant differentiation between these regions confirmed previous work distinguishing New Zealand and nominate subspecies. Although there was little evidence of structure within the island groups of the Indian or Atlantic oceans, a small set of highly-discriminatory outlier loci could assign petrels to ocean basin and potentially to island group, though the latter needs further verification. Genomic data hold the key to revealing substantial regional genetic structure within wide-ranging circumpolar species previously assumed to be panmictic.</p>
Scaling and structural properties of juvenile bull kelp (Nereocystis luetkeana) Data
<p>Bull kelp (<i>Nereocystis luetkeana</i>), the only canopy-forming kelp in the Salish Sea, provides primary production in the nearshore subtidal environment and serves as important habitat for economically and ecologically important species. An annual species, each year juvenile bull kelp sporophytes must grow from the hydrodynamically more benign benthos to the water column, where they experience substantial drag at the surface. Because of the differences in morphology and ecology across life stages, and the fact that previous work has focused mainly on adult bull kelp, we tested whether morphology and structural properties change with stipe length, investigating scaling of both juvenile (stipe length <40 cm) and mature (stipe length > 40cm) kelp, and testing how juvenile stipes fail. Juvenile bull kelp grow proportionally (isometric growth) when young, but lengthen more quickly than would be predicted by bulb size (negative allometry) at maturity. Based on our data, the predicted breakpoint between isometric and allometric growth occurred at about 33 cm, likely ~ one to two weeks of growth. Cross sectional area of the stipe, Force to failure, Work to failure, and stiffness (Young's Modulus) all grow more slowly than would be predicted based on length, while Maximum Stress and Toughness increase more quickly than predicted. There is no change in extensibility over the size range we tested, suggesting that this material property does not change with stipe length. The differences in biomechanics between juvenile and adult kelp are likely a response to the varied hydrodynamic environments experienced during the annual lifecycle, which highlights the importance of studying organisms across life stages.</p>
A Deep Learning Approach to the Forward Prediction and Inverse Design of Plasmonic Metasurface Structural Color - Raw Data
<p>Reflection spectra of PDMS - Al nanorod metamaterials were collected using LUMERICAL FDTD simulations. PDMS material properties were defined using a refractive index of 1.41 and Al material properties were defined using frequency selective permittivities from the handbook of Palik. A total of 4620 structures were simulated, sweeping the following dimension parameters:</p> <ul> <li>Aluminium thickness (t)</li> <li>Pillar height (h)</li> <li>Pillar diameter (d)</li> </ul> <p>Reflectance spectra were converted into CIE 1931 chromaticity values (x,y). This dataset is comprehensive and allows for the development of deep learning models for the forward and inverse design of the given metamaterial structure as detailed in the associated manuscript. The associated manuscript and supporting documentation provide extensive details of data collection and processing methods.</p> <p> </p>
MD data for "Selective G protein signaling driven by Substance P-Neurokinin Receptor structural dynamics"
<p>Molecular dynamics (MD) data for "Selective G protein signaling driven by Substance P-Neurokinin Receptor structural dynamics" (Harris <em>et al.</em>, Nature Chemical Biology (2021), DOI: 10.1038/s41589-021-00890-8, URL: https://www.nature.com/articles/s41589-021-00890-8). See the included readme.txt for more details. Please cite the paper if you use these data.</p>
Data from: Harvest is associated with the disruption of social and fine-scale genetic structure among matrilines of a solitary large carnivore
<p>Harvest can disrupt wildlife populations by removing adults with naturally high survival. This can reshape sociospatial structure, genetic composition, fitness, and potentially affect evolution. Genetic tools can detect changes in local, fine-scale genetic structure (FGS) and assess the interplay between harvest-caused social and FGS in populations. We used data on 1,614 brown bears, <i>Ursus arctos</i>, genotyped with 16 microsatellites, to investigate whether harvest intensity (mean low: 0.13 from 1990-2005, mean high: 0.28 from 2006-2011) caused changes in FGS among matrilines (8 matrilines; 109 females ≥ 4 years of age), sex-specific survival and putative dispersal distances, female spatial genetic autocorrelation, matriline persistence, and male mating patterns. Increased harvest decreased FGS of matrilines. Female dispersal distances decreased and male reproductive success was redistributed more evenly. Adult males had lower survival during high harvest, suggesting that higher male turnover caused this redistribution and helped explain decreased structure among matrilines, despite shorter female dispersal distances. Adult female survival and survival probability of both mother and daughter were lower during high harvest, indicating that matriline persistence was also lower. Our findings indicate a crucial role of regulated harvest in shaping populations, decreasing differences among 'groups', even for solitary-living species, and potentially altering the evolutionary trajectory of wild populations.</p>
Data from: Temperature and vegetation complexity structure mixed-species flocks along a gradient of elevation in the tropical Andes
<p>Mixed-species flocks constitute community modules that can help test mechanisms driving changes to community composition across environmental gradients. Here, we examined elevational patterns of flock diversity (species richness, taxonomic diversity, species and guild composition) and asked if these patterns were reflections of the full bird community at a given elevation (open-membership hypothesis), or if they were instead structured by environmental variables. We surveyed both the overall avian community and mixed-species flocks across an undisturbed elevational gradient (~1350 – 3550 m) in the Bolivian Andes. We then tested for the role of temperature (a surrogate for abiotic stress), resource diversity (arthropods, fruits) and foraging niche diversity (vegetation vertical complexity) in structuring these patterns. Patterns for the overall and flocking communities were similar, supporting our open-membership hypothesis that Andean flocks represent dynamic, unstructured aggregations. Membership openness and the resulting flock composition, however, also varied with elevation in response to temperature and vegetation complexity. We found a mid-elevation peak in flock species richness, size, and Shannon's diversity at ~2300 m. The transition of flocking behavior towards a more open-membership system at this elevation may explain a similar peak in the proportion of insectivores joining flocks. At high elevations, increasing abiotic stress and decreasing fruit diversity led more generalist, gregarious tanagers (Thraupidae) to join flocks, resulting in larger yet more even flocks alongside a loss of vegetation structure. At lower elevations, flock species richness increased with greater vegetation complexity, but a greater diversity of foraging niches resulted in flocks that were more segregated into separate canopy and understory sub-types. This segregation likely results from increased costs of interspecific competition and activity matching (i.e., constraints on movement and foraging rate) for insectivores. Mid-elevation flocks (~2300 m) seemed, therefore, to benefit from both the open-membership composition of high-elevation flocks and the high vegetation complexity of mid- and low-elevation forests.</p>
Data from: Tropical forests structure and diversity: a comparison of methodological choices
<p>1. Large-scale data compilation is increasing steadily in tropical forest research, but the lack of standardized methods for data collection limits drawing inference from large datasets and cross-biome analyses. Different inclusion methods and minimum tree diameter threshold are among these varying factors. To tackle this issue, we evaluated how different approaches for tree sampling affects our understanding of diversity and functioning in different tropical vegetation types.</p> <p>2. We used a unique dataset of 44 inventory plots (43.54 ha) encompassing an aridity gradient: evergreen moist forests, semideciduous and deciduous tropical forests. Data were collected using the by-tree inclusion method, in which, all stems are measured if the equivalent diameter of the tree reaches the minimum threshold. We simulated the impact of adopting different inclusion methods (by-stem and by-tree) and different minimum diameter thresholds on the estimation of number of trees and stems, biomass and species richness. We used linear mixed models to investigate the effect of minimum diameter threshold and inclusion method on our different response variables. We also evaluated species chance to be sampled under different minimum inclusion criteria.</p> <p>3. Inclusion method and minimum diameter threshold mainly affect the estimation of number of trees and stems and species richness, especially in deciduous and semideciduous forests, where resprouting is a prevalent strategy. In these forests, many trees that have several stems do not reach the minimum size individually when adopting the by-stem method, yet they do reach the minimum size threshold when all stems are considered together. For these environments under water stress, our analysis showed that using large minimum sizes, such as the 10 cm typically used in rainforests, implies large sampling losses, especially when used jointly with the by-stem inclusion method.</p> <p>4. The by-tree inclusion method represents an alternative approach that offers a more reliable sampling in different vegetation types, particularly in those habitats where resprouting is a widely encountered strategy along all age classes. We demonstrate the infeasibility of adopting broad and standard minimum thresholds for different tropical vegetation types, particularly considering their widely different ecological strategies.</p>
Data from: Genetic structuring among colonies of a pantropical seabird: Implication for subspecies validation and conservation
Appendix S1 <table> <tbody> <tr> <td>Table S1</td> <td>Details of field researchers and licences under which they took blood samples from white-tailed tropicbirds from populations in the years of study</td> </tr> <tr> <td>Table S2</td> <td>Morphometrics of 616 individual white-tailed tropicbirds from 11 populations. Population codes are as described in Table 1.</td> </tr> <tr> <td>Table S3</td> <td>Raw microsatellite genotypes for 382 individual White-tailed tropicbird from 13 populations. Population codes are as described in Table 1</td> </tr> <tr> <td>Table S4</td> <td>Details of mtDNA sequences </td> </tr> <tr> <td>Table S5</td> <td>Tests of bottleneck (P-values for one-tailed Wilcoxon's signed rank test for heterozygosity excess) based on 10 microsatellites in 13 populations of Phaethon lepturus</td> </tr> <tr> <td>Table S6</td> <td>Pairwise FST estimates based on nuclear microsatellite variation (above diagonal), and ΦST estimates based on mtDNA sequence (below diagonal) for 11 populations with sample sizes >5 ('Pop's) of Phaethon lepturus (see Table 1 for population codes)</td> </tr> </tbody> </table>
Comparing full-field data from structural components with complicated geometries
<p>A new decomposition algorithm based on QR factorisation is introduced for processing and comparing irregularly shaped stress and deformation datasets found in structural analysis. The algorithm improves the comparison of two-dimensional data fields from the surface of components where data is missing from the field of view due to obstructed measurement systems or component geometry that results in areas where no data is present. The technique enables the comparison of these irregularly shaped datasets without the need for interpolation or warping of the data. This ensures comparisons are only made between the available data in each dataset and thus similarity metrics are not biased by missing data. The decomposition and comparison technique has been applied during an impact experiment, a modal analysis, and a fatigue study, with the stress and displacement data obtained from finite element analysis, digital image correlation and thermoelastic stress analysis. The results demonstrate that the technique can be used to process data from a range of sources and suggests the technique has the potential for use in a wide variety of applications.</p>
Data from: Structural variation and its potential impact on genome instability: novel discoveries in the EGFR landscape by long-read sequencing
<p>Studies of structural variation (SV) have been challenging due to technological contraints. With the advent of third generation (long-read) sequencing technology, exploration of longer stretches of DNA not easily examined previously has been made possible. In the present study, we utilized third generation (long-read) sequencing techniques to examime SV in the <em>EGFR </em>landscape of four haplotypes derived from two human samples. We analyzed the <em>EGFR</em> gene and its landscape (+/- 500,000 base pairs) using this sequencing approach and were able to identify regions of non-coding DNA which had relatively high similarity to the most common activating <em>EGFR</em> mutation in non-small cell lung cancer. We discovered that reverse complements to the exon 19 deletion mutation which had at least 60% homology to the <em>EGFR</em> exon 19 canonical deletion and were within ± 421,000 bp of the deletion varied across the five haploid genomes examined (4 patient landscapes and hg38). Although the sample size is limited in this study, the estimated variation observed in genomic stability between the five <em>EGFR</em> haplotypes examined is novel and encourages further work to examine structural variation in larger cohorts.</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.