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1,548 results for “Trajectories”
Lung MRI Raw Data Acquired with 3D UTE Radial Trajectory
<p>This repository contains the raw data for the second lung MRI result in <a href="https://arxiv.org/abs/1909.13482">Extreme MRI: Large-Scale Volumetric Dynamic Imaging from Continuous Non-Gated Acquisitions</a>. The data is stored as numpy arrays, containing k-space data (ksp.npy), coordinates (coord.npy), and density compensation factors (dcf.npy). Code to process and reconstruct the data is available here: <a href="https://github.com/mikgroup/extreme_mri">https://github.com/mikgroup/extreme_mri</a></p> <p>For more information about how the data is acquired, please see the linked paper.</p>
Trajectories of RNA adsorption on a flat surface
<p>SPQR trajectories of a RNA fragment (40 nts). More to come...</p>
Migration trajectories of the diamondback moth Plutella xylostella in China inferred from population genomic variation
<p><span class="fontstyle01"><span><b>BACKGROUND</b></span></span><span class="fontstyle01"><span><b>:</b></span></span></p> <p><span class="fontstyle01"><span>The diamondback moth (DBM),</span></span><span class="fontstyle01"><span><i> Plutella xylostella</i></span></span><span class="fontstyle01"><span> (Lepidoptera: Plutellidae),</span></span><span class="fontstyle01"><span><i> </i></span></span><span class="fontstyle01"><span>is a notorious pest of cruciferous plants. In temperate areas, annual populations of DBM originate from adult migrants. However, the source populations and migration trajectories of immigrants remain unclear. Here, we investigated migration trajectories of DBM in China with genome-wide single nucleotide polymorphisms (SNPs) genotyped using double-digest RAD (ddRAD) sequencing. We first analyzed patterns of spatial and temporal genetic structure among southern source and northern recipient populations, then inferred migration trajectories into northern regions using discriminant analysis of principal components (DAPC), assignment tests and spatial kinship patterns.</span></span></p> <p><span class="fontstyle01"><span><b>RESULTS:</b></span></span></p> <p><span class="fontstyle01"><span>Temporal</span></span><span class="fontstyle01"><span><b> </b></span></span><span class="fontstyle01"><span>genetic differentiation among populations was low, indicating sources of </span></span><span class="fontstyle01"><span>recipient </span></span><span class="fontstyle01"><span>populations and migration trajectories are stable.</span></span><span class="fontstyle01"><span> Spatial genetic structure indicated three genetic clusters in the southern source populations. Assignment tests linked northern populations to the Sichuan cluster, and central-eastern populations to the South and Yunnan clusters, indicating that Sichuan populations are sources of northern immigrants and South and Yunnan populations are sources of central-eastern populations. First-order (full-sib) and second-order (half-sib) kin pairs were always found within populations, but about 35-40% of third-order (cousin) pairs were found in different populations. Closely related individuals in different populations were in about 35-40% of cases found at distances of 900 to 1500 km, while some were separated by over 2000 km.</span></span></p> <p><span class="fontstyle01"><span><b>CONCLUSION:</b></span></span></p> <p><span class="fontstyle01"><span>This study unravels seasonal migration patterns in the DBM. We demonstrate how careful sampling and population genomic analyses can be combined to help understand cryptic migration patterns in insects.</span></span></p>
Ecology directs host-parasite coevolutionary trajectories across Daphnia-microparasite populations
<p>Host-parasite interactions often fuel coevolutionary change. However, parasitism is one of a myriad of possible ecological interactions in nature. Biotic (<i>e.g., </i>predation) and abiotic (<i>e.g., </i>temperature) variation can amplify or dilute parasitism as a selective force on hosts and parasites, driving population variation in (co)evolutionary trajectories. We dissected the relationships between wider ecology and coevolutionary trajectory using 16 ecologically complex <i>Daphnia magna-Pasteuria ramosa</i> ponds seeded with an identical starting host (<i>Daphnia</i>) and parasite (<i>Pasteuria</i>) population. We show, using a time-shift experiment and outdoor population data, how multivariate biotic and abiotic ecological differences between ponds caused coevolutionary divergence. Wider ecology drove variation in host evolution of resistance, but not parasite infectivity; parasites subsequently coevolved in response to the changing complement of host genotypes, such that parasites adapted to historically resistant host genotypes. Parasitism was a stronger interaction for the parasite than for its host, likely because the host is the principal environment and selective force, whereas for hosts, parasite-mediated selection is one of many sources of selection. Our findings reveal the mechanisms through which wider ecology creates coevolutionary hotspots and coldspots in biologically realistic arenas of host-parasite interaction, and sheds light on how the ecological theatre can affect the (co)evolutionary play.</p>
hnRNPA1* and hSUMO-hnRNPA1* all-atom MD trajectories and protein-water rescaling MD trajectories
<pre>All-atom trajectories of hnRNPA1* and hSUMO-hnRNPA1* with varying NaCl concentrations back-mapped from CG simulations. CG trajectories of hnRNPA1* and hSUMO-hnRNPA1* with varying PW-rescaling parameter lambda (theta in file names). Supporting data for "Interplay of folded domains and the disordered low-complexity domain in mediating hnRNPA1 phase separation".</pre> <pre> </pre>
Data from: Dense infraspecific sampling reveals rapid and independent trajectories of plastome degradation in a heterotrophic orchid complex
Heterotrophic plants provide excellent opportunities to study the effects of altered selective regimes on genome evolution. Plastid genome (plastome) studies in heterotrophic plants are often based on one or a few highly divergent species or sequences as representatives of an entire lineage, thus missing important evolutionary-transitory events. Here we present the first infraspecific analysis of plastome evolution in any heterotrophic plant. By combining genome skimming and targeted sequence capture, we address hypotheses on the degree and rate of plastome degradation in a complex of leafless orchids (Corallorhiza striata) across its geographic range. Plastomes provide strong support for relationships and evidence of reciprocal monophyly between C. involuta and the endangered C. bentleyi. Plastome degradation is extensive, occurring rapidly over a few million years, with evidence of differing rates of substitution among the two principal clades of the complex. Genome skimming and targeted sequence capture differ widely in coverage depth overall, with depth in targeted sequence capture datasets varying immensely across the plastome as a function of GC content. These findings will help fill a knowledge gap in models of heterotrophic plastid genome evolution, and have implications for future studies in heterotrophs.
Data from: Plant selection initiates alternative successional trajectories in the soil microbial community after disturbance
Because interactions between plants and microbial organisms can influence species diversity and rates of nutrient cycling, how plants shape microbial communities is fundamental to understanding the structure of ecosystems. Despite this, the spatial and temporal scales over which plants influence microbial communities is poorly understood, particularly whether past abiotic or biotic legacies strongly constrain microbial community development. We examined biogeochemical cycling and microbial community structure in a coastal landscape where historical patterns of vegetation transition after a large fire in 1995 are well known, allowing us to account for past abiotic and biotic conditions. We found that alternative states in microbial community structure and ecosystem processes emerged under different plant species, regardless of past conditions. Greenhouse studies further demonstrated that these differences arise from direct plant selection of microbes, with selection stronger in roots compared with soils, especially for bacteria. Correlation of microbial community structure with seedling growth rates was also stronger for fungi compared to bacteria. Despite these effects, minimal overlap between seedling and field microbial communities indicates that the effects of initial plant selection are not stable, rather plant selection initiated alternative successional trajectories after the fire. Using data from a guild where we have abundant natural history information - ectomycorrhizal fungi - we show that greenhouse communities are dominated by ruderal taxa that are also common in the field after the fire, and that these ruderal fungi strongly alter spatial patterns in plant-soil feedback, enabling invasion and transformation of soils previously occupied by heterospecific plants, thus potentially acting as keystone mutualists.
Data from: Adaptive maternal investment in the wild? Links between maternal growth trajectory and offspring size, growth, and survival in contrasting environments
Life history theory predicts that investment per offspring should correlate negatively with the quality of environment offspring are anticipated to encounter; parents may use their own experience as juveniles to predict this environment and may modulate offspring traits such as growth capacity as well as initial size. We manipulated nutrient levels in the juvenile habitat of wild Atlantic salmon Salmo salar to investigate the hypothesis that the egg size maximizing juvenile growth and survival depends on environmental quality. We also tested whether offspring traits were related to parental growth trajectory. Mothers that grew fast when young produced more, smaller offspring than mothers that had grown slowly to reach the same size. Despite their size disadvantage, offspring of faster-growing mothers grew faster than those of slow-growing mothers in all environments, counter to the expectation that they would be competitively disadvantaged. However, they had lower relative survival in environments where the density of older predatory/competitor fish was relatively high. These links between maternal (but not paternal) growth trajectory and offspring survival rate were independent of egg size, underscoring that mothers may be adjusting egg traits other than size to suit the anticipated environment faced by their offspring.
Data from: Environmental conditions alter successional trajectories on an ephemeral resource: a field experiment with beetles in dead wood
<p>Successional processes can be observed for many organisms and resources, but most studies of succession have focused on plants. A general framework has been proposed, advocating that successional patterns in species turnover are predominantly driven by competition, dispersal or abiotic limitation, and that the patterning of species accumulation over time gives clues to which process is most influential in a given system. We applied this framework to succession in communities of wood-living beetles, utilizing ephemeral resources in the form of 60 experimentally created dead aspen high stumps. High stumps were created at sun-exposed sites (high ambient temperature; favorable abiotic conditions) and shaded sites (low ambient temperature; abiotically limiting conditions). The sites were intermixed, ensuring similar dispersal opportunities. Beetle species richness and abundance were monitored with flight interception traps over four consecutive years. Consistent with predictions from the tested framework, several beetle functional groups accumulated species more slowly at the unfavorable shaded sites than at the favorable exposed sites. Species richness at the exposed sites increased rapidly to a plateau, consistent with a limiting effect of competition on community development. Similar results were obtained for beetle abundance and community structure. Part of the variance in beetle community structure was jointly explained by habitat and fungal community composition, suggesting that differences in the composition and developmental rate of fungal communities in the two habitats contributed to the observed patterns. Targeted experimental studies are now required to decisively establish what processes underlie the contrasting successional trajectories in the two environments.</p>
Data from: Predictable adaptive trajectories of sexual coloration in the wild: evidence from replicate experimental guppy populations
The question of whether populations evolve predictably and consistently under similar selective regimes is fundamental to understanding how adaptation proceeds in the wild. We address this question with a replicated evolution experiment focused upon male sexual coloration in guppies (Poecilia reticulata). Fish were transplanted from a single high predation population in the Guanapo River to four replicate, guppy‐free low predation headwater streams. Two streams had their canopies thinned to adjust the setting under which male coloration is displayed and perceived. We assessed evolutionary divergence using second‐generation lab‐bred offspring of fish sampled four to six years following translocation. A prior experiment of the same design, performed in an adjacent drainage, resulted in the evolution of more extensive orange, black and iridescent markings. We however found evidence for expansion only in structural coloration (iridescent blue/green), no change in orange, and a reduction in black. This response amplifies earlier findings for Guanapo fish, revealing that trajectories of color elaboration differ among drainages. We also found that color phenotypes evolved more greatly at the thinned‐canopy sites. Our findings support the predictability of sexual trait evolution in the wild, and underscore the importance of signaling conditions and ornamental starting points in shaping adaptive trajectories.
Data from: Behavioral syndromes shape evolutionary trajectories via conserved genetic architecture
Behaviors are often correlated within broader syndromes, creating the potential for evolution in one behavior to drive evolutionary changes in other behaviors. Despite demonstrations that behavioral syndromes are common, this potential for evolutionary effects has not been demonstrated. Here we show that populations of field crickets (Gryllus integer) exhibit a genetically conserved behavioral syndrome structure, despite differences in average behaviors. We found that the distribution of genetic variation and genetic covariance among behavioral traits was consistent with genes and cellular mechanisms underpinning behavioral syndromes rather than correlated selection. Moreover, divergence among populations' average behaviors was constrained by the genetically conserved behavioral syndrome. Our results demonstrate that a conserved genetic architecture linking behaviors has shaped the evolutionary trajectories of populations in disparate environments—illustrating an important way for behavioral syndromes to result in shared evolutionary fates.
Data from: Luck in food-finding affects individual performance and population trajectories
Energy harvesting by animals is important because it provides the power needed for all metabolic processes. Beyond this, efficient food-finding enhances individual fitness [1] and population viability [2], although rates of energy accumulation are affected by the environment and food distribution. Typically, differences between individuals in the rate of food acquisition are attributed to varying competencies [3] even though food encounter rates are known to be probabilistic [4]. We used animal-attached technology to quantify food intake in four disparate free-living vertebrates (condors, cheetahs, penguins and sheep) and found that inter-individual variability depended critically on the probability of food encounter. We modelled this to reveal that animals taking rarer food, such as apex predators and scavengers, are particularly susceptible to breeding failure because this variability results in larger proportions of the population failing to accrue the necessary resources for their young before they starve, and because even small changes in food abundance can affect this variability disproportionately. A test of our model on wild animals indicated why Magellanic penguins have a stable population while the congeneric African penguin population has declined for decades. We suggest that such models predicting probabilistic ruin can help predict the fortunes of species operating under globally changing conditions.
Plants 3D trajectory reconstructed from stereovision cameras
<p>Dataset of 3D trajectories (circumnutations) travelled by different points selected on the plant. 3D reconstruction obtained using a system based on stereovision with 2 cameras having both RGB and IR (infra-red) sensors to capture motion in dark conditions. Reconstruction performed by two different users.</p> <p>Plant Species: <em>Pisum Sativum</em></p> <p> </p>
Data from: Chemical defense over decadal scales: ontogenetic allocation trajectories and consequences for fitness in a foundation tree species
1. Expression of herbivore defense traits can change dramatically during the course of plant development. Little is known, however, about the degree of genetic or sexual variation in these ontogenetic defense trajectories or whether the trajectories themselves are adaptive, especially in long‐lived species. 2. We used a 13‐year dataset of chemical defense traits, growth, and survivorship from a common garden of trembling aspen (Populus tremuloides) genotypes to document long‐term defense trajectories and their relationship to tree fitness during juvenile and early mature stages. 3. Overall, concentrations of the two principal classes of aspen defense compounds (salicinoid phenolic glycosides [SPGs] and condensed tannins [CTs]) decreased to differing degrees in foliage of juvenile trees and then remained relatively constant in maturity. Initial values, juvenile rates of change, and average mature values all exhibited significant genetic variation for both SPGs and CTs. 4. Relationships between defense trajectory parameters and metrics of tree fitness (growth and survivorship) depended on compound type and tree sex. Females with higher‐allocation SPG trajectories (high initial juvenile concentrations, slow juvenile declines, high mature concentrations) grew more slowly relative to females with lower‐allocation trajectories. In males, higher‐allocation SPG trajectories had a lesser effect on growth but were associated with reduced mortality. Juvenile CT trajectories were not correlated with tree fitness, but average CT concentration in maturity was positively related to growth in females. 5. These results suggest that ontogenetic defense trajectories are adaptive and subject to natural selection. Genotypic variation and ontogeny shape tree defensive chemistry, both independently and interactively. These patterns of defense expression have the potential to structure trophic interactions and the genetic composition of forests in both space and time.
MD simulation trajectory and related files for POPC bilayer in low hydration (Berger model delivered by Tieleman, Gromacs 4.5)
<p>Equilibrated POPC lipid bilayer simulation in low hydration (7 water per lipid molecule) ran with Gromacs 4.5, Berger force field delivered by Peter Tieleman (http://wcm.ucalgary.ca/tieleman/downloads) with fixed double bond dihedrals, 60ns, T=298K, 128 POPC molecules, 896 water molecules. This data is used in the nmrlipids.blospot.fi project. More details from nmrlipids.blospot.fi and https://github.com/NMRLipids/nmrlipids.blogspot.fi. If data is used, please cite the nmrlipids.blogspot.fi project and the original publications related to the force field.</p>
MD simulation trajectory and related files for POPC bilayer in low hydration (GAFFlipid, Gromacs 4.5)
<p>Equilibrated POPC lipid bilayer simulation ran with Gromacs 4.5, GAFFlipid force field (http://dx.doi.org/10.1039/C2SM26007G) in low hydration, 40ns, T=303K, 126 POPC molecules, 896 water molecules. This data is ran for the nmrlipids.blospot.fi project. More details from nmrlipids.blospot.fi and https://github.com/NMRLipids/nmrlipids.blogspot.fi. If data is used, please cite nmrlipids.blogspot.fi project and the original publication of the parameters: Dickson et al. Soft Matter, 2012,8, 9617-9627 http://dx.doi.org/10.1039/C2SM26007G.</p>
MD simulation trajectory and related files for POPC bilayer (Lipid14, Gromacs 4.5)
<p>Equilibrated POPC lipid bilayer simulation ran with Gromacs 4.5, Lipid14 force field (http://dx.doi.org/10.1021/ct4010307), 50ns, T=303K, 72 POPC molecules, 2234 water molecules. This data is ran for the nmrlipids.blospot.fi project. More details from nmrlipids.blospot.fi and https://github.com/NMRLipids/nmrlipids.blogspot.fi. If data is used, please cite nmrlipids.blogspot.fi project.</p>
MD simulation trajectory and related files for DPPC bilayer (CHARMM36, Gromacs 4.5)
<p>Equilibrated DPPC lipid bilayer simulation ran with Gromacs 4.5, CHARMM36 force field (dx.doi.org/10.1021/jp101759q), 25ns, T=323K, 72 POPC molecules, 2189 water molecules. This data is ran for the nmrlipids.blospot.fi project. More details from nmrlipids.blospot.fi and https://github.com/NMRLipids/nmrlipids.blogspot.fi. If data is used, please cite nmrlipids.blogspot.fi project and the original publication of the parameters (dx.doi.org/10.1021/jp101759q).</p>
MD simulation trajectory and related files for POPC bilayer, Högberg et al parameters (J.Comp.Chem., 29, 2359 (2008))
<p>MD simulation trajectory and related files for POPC bilayer,<br /> A.L.Rabinovich, A.P.Lyubartsev, Journal of Physics: Conference series, 510, 012022 (2014)</p> <p>20 ns( excluded) + 80 ns trajectory<br /> T=303K, 128 lipids + 3840 H2O</p> <p>Force field: from Högberg et al, J.Comp.Chem., 29, 2359 (2008)</p> <p>Software: MDynaMix v 5.2</p> <p>Relevant files:</p> <p>md.input : main MD input file</p> <p>160181_pc.mmol : lipid topology/force field file<br /> H2O.mmol : SPC water</p> <p>ord_160181.in : Input for the analysis utility to extract order parameters</p> <p>Trajectory:</p> <p>160181_pc_mem.102 - 160181_pc_mem.501 - trajectory files, 200 frames / 200 ps in each</p>
MD simulation trajectory and related files for DMPC bilayer, Högberg et al, J.Comp.Chem., 29, 2359 (2008)
<p>MD simulation trajectory and related files for DMPC bilayer, from paper: C.J.Högberg, A.M,Nikitin, A.P.Lyubartsev, J.Comp.Chem., 29, 2359 (2008)</p> <p>25ns( excluded) + 55 ns trajectory<br /> T=303K, 98 lipids + 2700 H2O<br /> software: MDynaMix v 5.0</p> <p>Relevant files:</p> <p>md.input : main MD input file</p> <p>dmpc_2008.mmol : lipid topology/force field file<br /> H2O.mmol : SPC water</p> <p>order.in : Input for the analysis utility to extract order parameters</p> <p>Trajectory files:</p> <p>dmpc_NewMod.250 - dmpc_NewMod.849</p> <p>Most of files contain 100 frames taken with 1 ps interval</p>
ScienceDex guides
Understand access before you commit
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.