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147 results for “dynamic processes”
Raw and processed data for publication "Quantitative microscopy reveals dynamics and fate of clustered IRE1alpha"
<p>This dataset contains all raw and processed data for our PNAS paper titled "Quantitative microscopy reveals dynamics and fate of clustered IRE1alpha". Using the associated analysis code (10.5281/zenodo.3544482), all figures in the paper can be reproduced from the data in this upload.</p> <p>Abstract of the paper is included below:</p> <p>"The endoplasmic reticulum (ER) membrane-resident stress sensor IRE1 governs the most evolutionarily conserved branch of the unfolded protein response. Upon sensing an accumulation of unfolded proteins in the ER lumen, IRE1 activates its cytoplasmic kinase and ribonuclease (RNase) domains to transduce the signal. IRE1 activity correlates with its assembly into large clusters, yet the biophysical characteristics of IRE1 clusters remain poorly characterized. We combined super-resolution microscopy, single-particle tracking, fluorescence recovery and photoconversion to examine IRE1 clustering quantitatively in living human and mouse cells. Our results revealed that (1) by contrast to qualitative impressions gleaned from microscopic images, IRE1 clusters comprise only a small fraction (~5%) of the total IRE1 in the cell. (2) IRE1 clusters have complex topologies that display features of higher-order organization. (3) IRE1 clusters contain a diffusionally constrained core, indicating that they are not phase-separated liquid condensates. (4) IRE1 molecules in clusters remain diffusionally accessible to the free pool of IRE1 molecules in the general ER network. (5) When IRE1 clusters disappear at later timepoints of ER stress as IRE1 signaling attenuates, their constituent molecules are released back into the ER network and not degraded. (6) IRE1 cluster assembly and disassembly are mechanistically distinct. (7) IRE1 clusters’ mobility is nearly independent of cluster size. Taken together, these insights define the clusters as dynamic assemblies with unique properties. The analysis tools developed for this study will be widely applicable to investigations of clustering behaviors in other signaling proteins."</p>
Molecular dynamics simulation: The process of phosphate transfer from fructose-1,6-bisphosphate to phosphoglycerate mutase 1
<p><span>Molecular dynamics (MD) simulations were performed to investigate the dynamic process of the binding and phosphorylation of PGAM1 by FBP. </span></p>
Data from: Disentangling invasion processes in a dynamic shipping - boating network
The relative importance of multiple vectors to the initial establishment, spread, and population dynamics of invasive species remains poorly understood. This study used molecular methods to clarify the roles of commercial shipping and recreational boating in the invasion by the cosmopolitan tunicate, Botryllus schlosseri. We evaluated i) single vs. multiple introduction scenarios, ii) the relative importance of shipping and boating to primary introductions, iii) the interaction between these vectors for spread (i.e., the presence of a shipping-boating network), and iv) the role of boating in determining population similarity. Tunicates were sampled from 26 populations along the Nova Scotia, Canada, coast that were exposed to either shipping (i.e., ports), or boating (i.e., marinas) activities. A total of 874 individuals (~30 per population) from 5 ports and 21 marinas was collected and analyzed using both mitochondrial cytochrome c oxidase subunit I gene (COI) and 10 nuclear microsatellite markers. The geographical location of multiple hotspot populations indicates that multiple invasions have occurred in Nova Scotia. A loss of genetic diversity from port to marina populations suggests a stronger influence of ships than recreational boats on primary coastal introductions. Population similarity analysis reveals a clear dependence of marina populations on those that had been previously established in ports and connectivity due to a boating network better explains patterns in population similarities than does natural spread. We conclude that frequent primary introductions arise by ships and that secondary spread occurs gradually thereafter around individual ports, facilitated by recreational boating.
Precise measurements of chromatin diffusion dynamics by modeling using Gaussian processes (Inter-Mito)
<p>Microscopy movies corresponding to interphase and mitotic cells in publication (add DOI when available).</p>
Precise measurements of chromatin diffusion dynamics by modeling using Gaussian processes (code)
<p>GP-FBM and GP-Tool codes and algorithms as in publication day. For updated version: https://github.com/guilmont/GP-Tool</p>
A basic community dynamics experiment: Disentangling deterministic and stochastic processes in structuring ecological communities
<p>Community dynamics are governed by two opposed processes: species sorting, which produces deterministic dynamics leading to an equilibrium state, and ecological drift, which produces stochastic dynamics. Despite a great deal of theoretical and empirical work aiming to demonstrate the predominance of one or the other of these processes, the importance of drift in structuring communities and maintaining species diversity remains contested. Here we present the results of a basic community dynamics experiment using floating aquatic plants, designed to measure the relative contributions of species sorting and ecological drift to community change over about a dozen generations. We found that species sorting became overwhelmingly dominant as the experiment progressed, and directed communities towards a stable equilibrium state maintained by negative frequency-dependent selection. The dynamics of any particular species depended on how far its initial frequency was from its equilibrium frequency, however, and consequently the balance of sorting and drift varied among species.</p>
Data from: In situ 15N-N2O site preference and O2 concentration dynamics disclose the complexity of N2O production processes in agricultural soil
<p class="MsoNormal"><span>Arable soil continues to be the dominant anthropogenic source of nitrous oxide (N<sub>2</sub>O) emissions owing to application of nitrogen (N) fertilizers </span><span>and manures across the world. Using</span><span> laboratory </span><span>and </span><em><span>in-situ</span></em><span> studies to elucidate the key factors controlling soil N<sub>2</sub>O emissions remains challenging due to the potential importance of multiple complex processes. We<em> </em>examined soil surface N<sub>2</sub>O fluxes in an arable soil, combined with<em> in-situ</em> high</span><span>-</span><span>frequency measurements of soil matrix oxygen (O<sub>2</sub>) and N<sub>2</sub>O concentrations, </span><em><span>in situ</span></em><span> <sup>15</sup>N labeling, and</span><span> N<sub>2</sub>O <sup>15</sup>N site preference (SP). The </span><em><span>in situ</span></em><span> O<sub>2</sub> concentration and further microcosm visualized spatiotemporal distribution of O<sub>2</sub> both suggested that O<sub>2</sub> dynamics were the proximal determining factor to matrix N<sub>2</sub>O concentration and fluxes due to quick O<sub>2</sub> depletion after N fertilization. Further SP analysis<em> </em>and<em> in situ</em> <sup>15</sup>N labeling experiment revealed </span><span>that the main source for N<sub>2</sub>O emissions was bacterial denitrification during the hot-wet summer with lower soil </span><span>O<sub>2</sub></span><span> concentration, while nitrification or fungal denitrification contributed about 50<span>.0</span>% to total emissions during the cold-dry winter with higher soil </span><span>O<sub>2</sub></span><span> concentration. </span><span>The robust positive correlation between O<sub>2</sub> concentration and SP values underpinned that the O<sub>2</sub> dynamics were the key factor to differentiate the composite processes of N<sub>2</sub>O production in <em>in situ</em> structured soil. Our findings deciphered the complexity of N<sub>2</sub>O production processes in real field conditions, and suggest that O<sub>2</sub> dynamics rather than stimulation of functional gene abundances play a key role in controlling soil N<sub>2</sub>O production processes in undisturbed structure soils. </span><span>Our results help to develop targeted N<sub>2</sub>O mitigation measures and to improve process models for constraining global N<sub>2</sub>O budget.</span></p>
The Feasibility of a Dynamic Exercise Intervention. Psychosocial Effects and Process Evaluation of the Experimental Design.
ClinicalTrials.gov study NCT04932408. IPD Sharing: NO. Countries: 1. Publications: 10.
Data from: Dynamic pore structure evolution of the ion adsorbed rare earth ore during the ion exchange process
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A basic community dynamics experiment: Disentangling deterministic and stochastic processes in structuring ecological communities
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Data from: Scaling of processes shaping the clonal dynamics and genetic mosaic of seagrasses through temporal genetic monitoring
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Data from: Regulation of reproductive processes with Dynamic Energy Budgets
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Data from: Disentangling invasion processes in a dynamic shipping - boating network
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Data from: In situ 15N-N2O site preference and O2 concentration dynamics disclose the complexity of N2O production processes in agricultural soil
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Data from: The effect of static versus dynamic stimuli on visual processing of sexual cues in androphilic women and gynephilic men
Models of sexual response posit that attentional processing of sexual cues is requisite for sexual responding. Despite hypothesized similarities in the underlying processes resulting in sexual response, gender differences in sexual arousal patterns are abundant. One such gender difference relates to the stimulus features (e.g., gender cues, sexual activity cues) that elicit a response in men and women. In the current study, we examined how stimulus modality (static visual images versus dynamic audiovisual films) and stimulus features (gender, sexual activity, and nonsexual contextual cues) influences attentional (i.e., gaze) and elaborative (i.e., self-reported attraction, self-reported arousal) processing of sexual stimuli. Men's initial and controlled attention was consistently gender-specific (i.e., greater attention towards female targets), and this was not influenced by stimulus modality or the presence of sexual activity cues. In contrast, gender-specificity of women's attention patterns differed as a function of attentional stage, stimulus modality, and the features within the stimulus. Degree of specificity was positively predictive of self-reported attraction in both genders; however, it was not significantly predictive of self-reported arousal. These findings are discussed in the context of gendered processing of visual sexual information, including a discussion of implications for research designs.
Assessing the interaction of oceanic and riverine processes on coastal phytoplankton dynamics in the East China Sea
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Assessing the interaction of oceanic and riverine processes on coastal phytoplankton dynamics in the East China Sea
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Processed Data, Code, & Supplementary Material for de la Torre Cerro et al. (2024) Modelling asynchrony in phenology using a dynamic representation of meteorological variables
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Precise measurements of chromatin diffusion dynamics by modeling using Gaussian processes (T1T2 Anchor)
<p>Microscopy movies corresponding to T1-T2 anchor cell lines of publication (add DOI when available).</p>
Precise measurements of chromatin diffusion dynamics by modeling using Gaussian processes (T2T3 Anchor)
<p>Microscopy movies corresponding to T2-T3 anchor cell lines of publication (add DOI when available).</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.