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11,506 results for “Dynamics”
Optical properties and carrier dynamics in Co-doped ZnO nanorods
<p>The dataset includes the parts collected at EPFL, uploaded for open access in accordance to SNSF policy.</p>
Co-localization and cluster analysis data for paper "Dynamic regulation of CTCF stability and sub-nuclear localization in response to stress"
<p>This datasets contains all data for the co-localization and cluster analysis included in the following paper<br> "Dynamic regulation of CTCF stability and sub-nuclear localization in response to stress"</p>
Dataset for "Modelling impacts of spatially variable erosion drivers on suspended sediment dynamics"
<p>Dataset for publication:</p> <p>Battista, P. Molnar, and P. Burlando. Modelling impacts of spatially variable erosion drivers on suspended sediment dynamics. Earth Surface Dynamics, 8(3):619{635, jul 2020a. ISSN 2196-632X. doi: 10.5194/esurf-8-619-2020.</p>
Evaluation of metronomic chemotherapy response using diffusion and dynamic contrast-enhanced MRI
Purpose: To investigate the feasibility of using diffusion MRI (dMRI) and dynamic contrast-enhanced (DCE) MRI to evaluate the treatment response of metronomic chemotherapy (MCT) in the 4T1 mammary tumor model of locally advanced breast cancer. Methods: Twelve Balb/c mice with metastatic breast cancer were divided into treated and untreated (control) groups. The treated group (n=6) received five treatments of anti-metabolite agent 5-Fluorouracil (5FU) in the span of two weeks. dMRI and DCE-MRI were acquired for both treated and control groups before and after MCT. Immunohistochemically staining and measurements were performed after the post-MRI measurements for comparison. Results: The control mice had significantly ( p <0.005) larger tumors than the MCT treated mice. The DCE-MRI analysis showed a decrease in contrast enhancement for the control group, whereas the MCT mice had a more stable enhancement between the pre-chemo and post-chemo time points. This confirms the antiangiogenic effects of 5FU treatment. Comparing amplitude of enhancement revealed a significantly (p<0.05) higher enhancement in the MCT tumors than in the controls. Moreover, the MCT uptake rate was significantly (p<0.001) slower than the controls. dMRI analysis showed the MCT ADC values were significantly larger than the control group at the post-scan time point. Conclusion: dMRI and DCE-MRI can be used as potential biomarkers for assessing the treatment response of MCT. The MRI and pathology observations suggested that in addition to the cytotoxic effect of cell kills, the MCT with a cytotoxic drug, 5FU, induced changes in the tumor vasculature similar to the anti-angiogenic effect.
Individual simulation results of "New insight into the frequency-dependent megathrust rupture from dynamic simulations"
<p>The model settings and results of individual simulations in the work "New insight into the frequency-dependent megathrust rupture from dynamic simulations" by Yin and Denolle.</p>
Data accompanying "Switching dynamics of dark-pulse Kerr comb states in optical microresonators"
<p>This dataset contains figure plotting scripts and corresponding raw measurement data for the paper "Switching dynamics of dark-pulse Kerr comb states in optical microresonators"</p>
Fast Deterministic Algorithms for Highly-Dynamic Networks (video)
Full video presentation of the paper: Fast Deterministic Algorithms for Highly-Dynamic Networks.<br><br>Appears in Session 4 of the 24th International Conference on Principles of Distributed Systems OPODIS 2020<br><a href="https://opodis2020.unistra.fr">https://opodis2020.unistra.fr</a>
Broadcasting with mobile agents in dynamic networks (video)
Full video presentation of the paper: Broadcasting with mobile agents in dynamic networks.<br><br>Appears in Session 1 of the 24th International Conference on Principles of Distributed Systems OPODIS 2020<br><a href="https://opodis2020.unistra.fr">https://opodis2020.unistra.fr</a>
Data from: Non-rhythmic head-direction cells in the parahippocampal region are not constrained by attractor network dynamics
Computational models postulate that HD cells are part of an attractor network integrating angular head turns. This network requires inputs from visual landmarks to anchor the HD signal to the external world. We investigated whether information about HD and visual landmarks is integrated in the medial entorhinal cortex and parasubiculum, resulting in neurons expressing a conjunctive code for HD and visual landmarks. We found that parahippocampal HD cells could be divided into two classes based on their theta-rhythmic activity: non-rhythmic and theta-rhythmic HD cells. Manipulations of the visual landmarks caused tuning curve alterations in most HD cells, with the largest visually driven changes observed in non-rhythmic HD cells. Importantly, the tuning modifications of non-rhythmic HD cells were often non-coherent across cells, refuting the notion that attractor-like dynamics control non-rhythmic HD cells. These findings reveal a new population of non-rhythmic HD cells whose malleable organization is controlled by visual landmarks.
Data from: Short term dynamics of diversity patterns: evidence of continual reassembly within lacustrine small eukaryotes
The short-term variation in the community structure of freshwater small eukaryotes (0.2-5 μm) was investigated in a mesotrophic lake every 2-3 days over one summer by coupling three molecular methods: 454 amplicon pyrosequencing, qPCR and TSA-FISH. The pyrosequencing approach unveiled a much more extensive small-eukaryotic diversity (991 OTUs) than has been described previously. The vast majority of the diversity described was represented by rare OTUs (≤ 0.01% of reads) belonging primarily to Cryptomycota, Dikarya and photosynthetic organisms, which were never detected as abundant in any of the samples. The small eukaryote community was characterized by a continual and important reassembly. These rearrangements involved the 20 "core taxa" (≥ 1% of reads), and, were essentially due to a handful of OTUs that were detected in intermediate abundance (0.01-1% of reads) and sporadically in dominant taxa. Putative bacterivorous (Ciliophora and Cercozoa) as well as parasitic and saprotrophic taxa (Perkinsozoa and Cryptomycota) were involved in these changes of diversity. A putative infection of microalgae by a lacustrine perkinsozoan was also reported for the first time in this study. Open questions regarding both the patterns that govern the rapid small eukaryote reassemblies and the possible biogeography of these organisms arise from this study.
Data from: Frequency of virus-resistant hosts determines experimental community dynamics
Parasites, such as bacterial viruses (phages), can have large effects on host populations both at the ecological and evolutionary levels. In the case of cyanobacteria, phages can reduce primary production and infected hosts release intracellular nutrients influencing planktonic food web structure, community dynamics and biogeochemical cycles. Cyanophages may be of great importance in aquatic food webs during large cyanobacterial blooms unless the host population becomes resistant to phage infection. The consequences on plankton community dynamics of the evolution of phage resistance in bloom forming cyanobacterial populations is still poorly studied. Here we examined the effect of different frequencies of a phage-resistant genotype within a filamentous nitrogen-fixing Nodularia spumigena population on an experimental plankton community. Three Nodularia populations with different initial frequencies (0%, 5% and 50%) of phage-resistant genotypes were inoculated in separate treatments with the phage 2AV2, the green alga Chlorella vulgaris and the rotifer Brachionus plicatilis which formed the experimental plankton community subjected to either nitrogen-limited or nitrogen-rich conditions. We found that the frequency of the phage-resistant Nodularia genotype determined experimental community dynamics. Cyanobacterial populations with a high frequency (50%) of the phage-resistant genotype dominated the cultures despite the presence of phages, retaining most of the intracellular nitrogen in the plankton community. In contrast, populations with low frequencies (0% and 5%) of the phage-resistant genotype were lysed and reduced to extinction by the phage, transferring the intracellular nitrogen held by Nodularia to Chlorella and rotifers, and allowing Chlorella to dominate the communities and rotifers to survive. This study shows that even though phages represent minuscule biomass, they can have key effects on community composition and eco-evolutionary feedbacks in plankton communities.
Data from: EEG theta dynamics within frontal and parietal cortices for error processing during reaching movements in a prism adaptation study altering visuo-motor predictive planning
Modulation of frontal midline theta (fmθ) is observed during error commission, but little is known about the role of theta oscillations in correcting motor behaviours. We investigate EEG activity of healthy partipants executing a reaching task under variable degrees of prism-induced visuo-motor distortion and visual occlusion of the initial arm trajectory. This task introduces directional errors of different magnitudes. The discrepancy between predicted and actual movement directions (i.e. the error), at the time when visual feedback (hand appearance) became available, elicits a signal that triggers on-line movement correction. Analysis were performed on 25 EEG channels. For each participant, the median value of the angular error of all reaching trials was used to partition the EEG epochs into high- and low-error conditions. We computed event-related spectral perturbations (ERSP) time-locked either to visual feedback or to the onset of movement correction. ERSP time-locked to the onset of visual feedback showed that fmθ increased in the high- but not in the low-error condition with an approximate time lag of 200 ms. Moreover, when single epochs were sorted by the degree of motor error, fmθ started to increase when a certain level of error was exceeded and, then, scaled with error magnitude. When ERSP were time-locked to the onset of movement correction, the fmθ increase anticipated this event with an approximate time lead of 50 ms. During successive trials, an error reduction was observed which was associated with indices of adaptations (i.e., aftereffects) suggesting the need to explore if theta oscillations may facilitate learning. To our knowledge this is the first study where the EEG signal recorded during reaching movements was time-locked to the onset of the error visual feedback. This allowed us to conclude that theta oscillations putatively generated by anterior cingulate cortex activation are implicated in error processing in semi-naturalistic motor behaviours.
Data from: Variation in three community features across habitat types and scales within a 15-ha subtropical evergreen-deciduous broadleaved mixed forest dynamics plot in China
The evergreen and deciduous broadleaved mixed forests (EDBMFs) belong to one of the ecosystems most sensitive to environmental change, however, little is known about the environmental determinants for their plant diversity and forest structure at different habitat types and spatial scales. Here, we used data from a 15-ha (300×500 m) forest dynamic plot (FDP) of an old-growth EDBMF to examine the patterns and determinants of the three community features (stem abundance, rarefied species richness and basal area) in three habitat types (ridge, hillside and foothill) and at three spatial scales (20×20 m, 50×50 m and 100×100 m). We found that the three community features significantly changed with habitat type, but only one of them (rarefied richness) changed with scale. Among spatial scales, the principle environmental factors that widely affected community features were pH, SOM and TP, while these effects only taken place at certain habitat. Variations in the three community features explained by soil conditions were generally greater than those explained by topographical conditions. With changes in habitat type, the proportion of variations explained by environmental conditions was 31-53%, 8-25%, and 18-26% for abundance, rarefied richness and basal area (BA), respectively. With increasing spatial scale, the variations explained by environmental conditions were 44-75% for abundance, 28-95% for rarefied richness, and 18-86% for BA. Our study demonstrated that environmental factors had great impacts on the plant diversity and forest structure in the EDBMFs, especially the soil factors such as pH. In addition, the importance of the environmental determinants on these community features was highly related to the spatial scale.
Data from: Avoiding tipping points in fisheries management through Gaussian process dynamic programming
Model uncertainty and limited data are fundamental challenges to robust management of human intervention in a natural system. These challenges are acutely highlighted by concerns that many ecological systems may contain tipping points, such as Allee population sizes. Before a collapse, we do not know where the tipping points lie, if they exist at all. Hence, we know neither a complete model of the system dynamics nor do we have access to data in some large region of state space where such a tipping point might exist. We illustrate how a Bayesian non-parametric approach using a Gaussian process (GP) prior provides a flexible representation of this inherent uncertainty. We embed GPs in a stochastic dynamic programming framework in order to make robust management predictions with both model uncertainty and limited data. We use simulations to evaluate this approach as compared with the standard approach of using model selection to choose from a set of candidate models. We find that model selection erroneously favours models without tipping points, leading to harvest policies that guarantee extinction. The Gaussian process dynamic programming (GPDP) performs nearly as well as the true model and significantly outperforms standard approaches. We illustrate this using examples of simulated single-species dynamics, where the standard model selection approach should be most effective and find that it still fails to account for uncertainty appropriately and leads to population crashes, while management based on the GPDP does not, as it does not underestimate the uncertainty outside of the observed data.
Data from: Cortical recruitment determines learning dynamics and strategy
Salience is a broad and widely used concept in neuroscience whose neuronal correlates, however, remain elusive. In behavioral conditioning, salience is used to explain various effects, such as stimulus overshadowing, and refers to how fast and strongly a stimulus can be associated with a conditioned event. Here, we identify sounds of equal intensity and perceptual detectability, which due to their spectro-temporal content recruit different levels of population activity in mouse auditory cortex. When using these sounds as cues in a Go/NoGo discrimination task, the degree of cortical recruitment matches the salience parameter of a reinforcement learning model used to analyze learning speed. We test an essential prediction of this model by training mice to discriminate light-sculpted optogenetic activity patterns in auditory cortex, and verify that cortical recruitment causally determines association or overshadowing of the stimulus components. This demonstrates that cortical recruitment underlies major aspects of stimulus salience during reinforcement learning.
Data from: Beak color dynamically signals changes in fasting status and parasite loads in king penguins
Dynamic ornamental signals that vary over minutes, hours or weeks can yield continuous information on individual condition (e.g., energy reserves or immune status), and may therefore be under strong social and/or sexual selection. In vertebrates, the coloration of the integument is often viewed as a dynamic ornament, which in birds can be apparent in the beak. King penguins (Aptenodytes patagonicus) are monomorphic seabirds that possess conspicuous yellow–orange (YO) and ultraviolet (UV) beak spots that are used by both males and females in mate choice. We studied the dynamicity of beak spot sexual traits, and to what extent they reflected changes in individual condition in fasting king penguins and in penguins treated with an anti-parasitic drug. We also describe the maturation of this colorful ornament during the yearly catastrophic moult. On a time-scale of days to weeks, beak spot coloration changed in response to fasting and experimental changes in parasite load. Beak spot UV brightness decreased over a 10-day fast in breeding birds. For birds caught during courtship and held in captivity YO chroma decreased after a 24-day fast. Birds that were treated with an anti-parasitic solution showed an increase in UV coloration after parasite removal. Altogether, our results show that beak spot coloration is a dynamic ornament that reflects multiple dimensions of changes in individual condition in breeding-fasting penguins.
Ant community dynamics in the Big Thicket National Preserve of east Texas
<p>Rare and extreme climatic events can leave important but difficult-to-study legacies for ecological communities. Theory suggests that the relative abundance and even presence of species in communities may be driven as much by historical contingencies associated with rare events as by filtering from average environmental conditions. Much of what we know about the consequences of extreme events comes from opportunistic studies, where ecologists were in the right place at the right time. Climate change forecasts for the 21st century include an increase in frequency of extreme events, and ecologists are increasingly called upon to predict their consequences. We must therefore exploit opportunities to quantify the ecological effects of climatic extremes when and where we can. This study examined how a rare and extreme forcing event – the unprecedented flooding associated with Hurricane Harvey – modified the composition of ant communities in east Texas. We surveyed ant communities of the Big Thicket National Preserve (BTNP) through pitfall trapping at 18 sites throughout BTNP. We conducted twice-annual sampling in 2014 and 2015, before the hurricane, and monthly sampling for one year in the aftermath of Hurricane Harvey (August 2017), beginning in November 2017. BTNP ant communities include many native species as well as two conspicuous invaders: the fire and Solenopsis invicta and the tawny crazy ant Nylanderia fulva. Thus, beyond characterizing overall trends in ant community composition, we were particularly interested in the temporal dynamics of these species' distribution and abundance throughout the Big Thicket preserve, and their responses to Hurricane Harvey. </p>
Data from: Geographic ranges of genera and their constituent species: structure, evolutionary dynamics, and extinction resistance
We explore the relationships among the geographic ranges of genera, the ranges and positions of their constituent species, and the number of species they contain, considering variation among coeval genera and changes within genera over time. Measuring range size as the maximal distance, or extent, between occurrences within a taxon, we find that the range of the most widespread species is a good predictor of the range of the genus, and that the number of species is a better predictor still. This analysis is complicated by a forced correlation: the range of a genus must be at least as large as that of each of its constituent species. We therefore focus on a second measure of range, the mean squared distance, or dispersion, of occurrences from the geographic centroid, which, by analogy to the analysis of variance, allows the total dispersion of a genus to be compared to the mean within-species dispersion and the dispersion among species centroids. We find that among-species dispersion is the principal determinant of genus dispersion. Within-species dispersion also plays a major role. The role of species richness is relatively small. Our results are not artifacts of temporal variation in the geographic breadth of sampled data. The relationship between changes in genus dispersion and changes in within- and among-species dispersion shows a symmetry, being similar in cases when the genus range is expanding and when it is contracting. We also show that genera with greater dispersion have greater extinction resistance, but that within- and among-species dispersion are not demonstrable predictors of survival once the dispersion of the genus is accounted for. Thus it is the range of the genus, rather than how it is attained, that is most relevant to its fate. Species richness is also a clear predictor of survival, beyond its effects on geographic range.
Data from: Phylogenetically driven sequencing of extremely halophilic archaea reveals strategies for static and dynamic osmo-response
Organisms across the tree of life use a variety of mechanisms to respond to stress-inducing fluctuations in osmotic conditions. Cellular response mechanisms and phenotypes associated with osmoadaptation also play important roles in bacterial virulence, human health, agricultural production and many other biological systems. To improve understanding of osmoadaptive strategies, we have generated 59 high-quality draft genomes for the haloarchaea (a euryarchaeal clade whose members thrive in hypersaline environments and routinely experience drastic changes in environmental salinity) and analyzed these new genomes in combination with those from 21 previously sequenced haloarchaeal isolates. We propose a generalized model for haloarchaeal management of cytoplasmic osmolarity in response to osmotic shifts, where potassium accumulation and sodium expulsion during osmotic upshock are accomplished via secondary transport using the proton gradient as an energy source, and potassium loss during downshock is via a combination of secondary transport and non-specific ion loss through mechanosensitive channels. We also propose new mechanisms for magnesium and chloride accumulation. We describe the expansion and differentiation of haloarchaeal general transcription factor families, including two novel expansions of the TATA-binding protein family, and discuss their potential for enabling rapid adaptation to environmental fluxes. We challenge a recent high-profile proposal regarding the evolutionary origins of the haloarchaea by showing that inclusion of additional genomes significantly reduces support for a proposed large-scale horizontal gene transfer into the ancestral haloarchaeon from the bacterial domain. The combination of broad (17 genera) and deep (≥5 species in four genera) sampling of a phenotypically unified clade has enabled us to uncover both highly conserved and specialized features of osmoadaptation. Finally, we demonstrate the broad utility of such datasets, for metagenomics, improvements to automated gene annotation and investigations of evolutionary processes.
Data from: Modelling dynamics in protein crystal structures by ensemble refinement
Single-structure models derived from X-ray data do not adequately account for the inherent, functionally important dynamics of protein molecules. We generated ensembles of structures by time-averaged refinement, where local molecular vibrations were sampled by molecular-dynamics (MD) simulation whilst global disorder was partitioned into an underlying overall translation–libration–screw (TLS) model. Modeling of 20 protein datasets at 1.1–3.1 Å resolution reduced cross-validated R_free values by 0.3–4.9%, indicating that ensemble models fit the X-ray data better than single structures. The ensembles revealed that, while most proteins display a well-ordered core, some proteins exhibit a 'molten core' likely supporting functionally important dynamics in ligand binding, enzyme activity and protomer assembly. Order–disorder changes in HIV protease indicate a mechanism of entropy compensation for ordering the catalytic residues upon ligand binding by disordering specific core residues. Thus, ensemble refinement extracts dynamical details from the X-ray data that allow a more comprehensive understanding of structure–dynamics–function relationships.
ScienceDex guides
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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.