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11,506 results for “Dynamics”
Structure, Function and Dynamics in Acyl Carrier Proteins.
<p><strong>Original Article: </strong>https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0219435</p> <p><strong>Primary GitHub Repository:</strong> https://github.com/rohitfarmer/acp-dynamics</p> <p><strong>Folders</strong></p> <ul> <li><strong>Figures:</strong> Coordinates (.pdb) for structures used in figure panels. The number in the file name denotes the frame number in the simulation. Each frame was captured at 10 ps therefore frame number 100 would mean 100 X 10 = 1000 ps = 1 ns. <a href="https://pymolwiki.org/index.php/Linux_Install">Pymol</a> session files (.pse), and <a href="https://inkscape.org/">Inkscape</a> files (.svg) that were used to generate the figures are also provided.</li> <li><strong>Scripts:</strong> Perl scripts used in the project.</li> <li><strong>Simulations:</strong> Simulations are in compressed .pdb.zip format with the labelling corresponding to Table 1 in the main paper. To comply with the size allowance of GitHub, GROMACS trajectories that were initially recorded at 10 ps time intervals are reduced to 100 ps time intervals for 200 ns simulations and to 500 ps time intervals for 1 microsecond simulations. Trajectories are converted to PDB format with no water molecules and ions and compressed to individual zip files. Uncompressed simulation files can be visualized in <a href="https://www.ks.uiuc.edu/Research/vmd/">VMD</a>. <ul> <li><strong>amber99sb-ildn.ff:</strong> Amber 99 SB ILDN force field with added parameters from GAFF.</li> </ul> </li> </ul>
Simulation results for "Modeling the joint effects of vegetation characteristics and soil properties on ecosystem dynamics in a Panama tropical forest"
<p>This dataset is the ELM-FATES simulation outputs for the paper entitled "Modeling the joint effects of vegetation characteristics and soil properties on ecosystem dynamics in a Panama tropical forest". </p>
Spatial structure and dispersal dynamics in a house sparrow metapopulation
<p>1. The effects of spatial structure on metapopulation dynamics depend upon the interaction between local population dynamics and dispersal, and how this relationship is affected by the geographical isolation and spatial heterogeneity in habitat characteristics.</p> <p>2. Our aim is to examine how emigration and immigration of house sparrows, <i>Passer domesticus</i>, in a Norwegian archipelagic metapopulation are affected by key factors predicted by classic metapopulation models to affect dispersal: spatial and temporal variation in population size, inter-island distance, local demography and habitat characteristics.</p> <p>3. This metapopulation can be divided into two major habitat types: (1) islands closer to the mainland where sparrows breed in colonies on farms, and (2) islands without farms, situated farther away from the mainland where sparrows are exposed to harsher environmental conditions.</p> <p>4. Dispersal was spatially structured within the metapopulation; there was proportionally and numerically less emigration and immigration involving farm islands, as compared to non-farm islands. Furthermore, emigration and immigration occurred mostly between nearby islands. Moreover, emigration in response to spatial differences in mean population size differed between the habitat types, but populations with large mean received more immigrants in both habitat types. The number of emigrants and immigrants was negatively related to long-term recruit production, which was not the case in non-farm islands. The proportion and number of emigrants was positively related to temporal increases in recruit production on farm islands, however, not on non-farm islands.</p> <p>5. Our results demonstrate that spatial heterogeneity in environmental conditions influences how spatial variation in long-term mean population size, and temporal and spatial variation in recruit production, affects dispersal dynamics. The spatial structure of this metapopulation is therefore best described by a spatially explicit model in which the exchange of individuals within each habitat type is strongly affected by the degree of geographical isolation, population size and recruit production. However, these relationships differed between the two habitat types, with the non-farm islands showing similarities to a mainland-island model type of structure, whereas dispersal on the farm islands showed features more associated with source-sink or balanced dispersal models. Such differential dispersal dynamics between habitat types is expected to have important consequences for the ecological and evolutionary dynamics within this metapopulation.</p>
FIGURES 1–4 in Morphology and Postdepositional Dynamics of Eggs of the Predator Podisus distinctus (Stål) (Heteroptera: Pentatomidae: Asopinae)
FIGURES 1–4. Eggs of Podisus distinctus (Stål) (Heteroptera: Pentatomidae). Fig. 1. Egg four hours after laying exhibiting a base narrower than the apex (arrow) and a convex circular operculum (arrowhead). The chorion possesses spine-like projections on the egg lateral aspect arranged in irregular polygonal forms (P) and erect aero-micropylar processes (AM). Fig. 2. Oocyte showing the hexagonal pattern (arrowhead) and folded aero-micropylar processes (arrow). Fig. 3. Egg isolated from the common oviduct, exhibiting residues of follicular tissue (FT), curved aero-micropylar processes (arrow), and spine-like projections curved along the operculum surface (arrowhead). Fig. 4. Egg less than one hour after laying, with nearly erect spine-like projections and aero-micropylar processes.
FIGURES 5–8 in Morphology and Postdepositional Dynamics of Eggs of the Predator Podisus distinctus (Stål) (Heteroptera: Pentatomidae: Asopinae)
FIGURES 5–8. Eggs of Podisus distinctus (Stål) (Heteroptera: Pentatomidae). Fig. 5. Mature egg, four hours after laying with completely erect spine-like projections above the operculum and aero-micropylar processes. Fig. 6. Mature egg, two-day-old after laying with radially positioned spine-like projections emanating from the base of the posterior pole. Fig. 7. Mature egg, two-day-old after laying showing bound spine-like projections on the egg lateral aspect (arrowhead) and smooth aeromicropylar processes (arrow). Fig. 8. Mature egg, two-day-old after laying with eclosion line (EL) internal to the aeromicropylar processes. The region has no signs of spine-like projections and is surrounded by a row of short spine-like projections (arrow), followed by the operculum long spine-like projections (arrowhead).
dataset Master Thesis Optimising parity game solvers using dynamic SCC maintenance
<p>Complete dataset of my Master Thesis Optimising parity game solvers using dynamic SCC maintenance</p>
Foraging in a dynamic environment: response of four sympatric sub-Antarctic albatross species to interannual environmental variability
Seasonal and annual climate variations are linked to fluctuations in the abundance and distribution of resources, posing a significant challenge to animals that need to adjust their foraging behaviour accordingly. Particularly during adverse conditions, and while energetically constrained when breeding, animals ideally need to be flexible in their foraging behaviour. Such behavioural plasticity may separate 'winners' from 'losers' in light of rapid environmental changes due to climate change. Here, the foraging behaviour of four sub-Antarctic albatross species was investigated from 2015/16 to 2017/18, a period characterized by pronounced environmental variability. Over three breeding seasons on Marion Island, Prince Edward Archipelago, incubating wandering (WA, Diomedea exulans; n=45), grey-headed (GHA, Thalassarche chrysostoma; n=26), sooty (SA, Phoebetria fusca; n=23) and light-mantled (LMSA, P. palpebrata; n=22) albatrosses were tracked with GPS loggers. The response of birds to environmental variability was investigated by quantifying inter-annual changes in their foraging behaviour along two axes: spatial distribution, using kernel density analysis, and foraging habitat preference, using generalized additive mixed models and Bayesian mixed models. All four species were shown to respond behaviourally to environmental variability, but with substantial differences in their foraging strategies. WA was most general in its habitat use defined by sea surface height, eddy kinetic energy, wind speed, ocean floor slope and sea level anomaly, with individuals foraging in a range of habitats. In contrast, the three smaller albatrosses exploited two main foraging habitats, with habitat use varying between years. Generalist habitat use by WA and inter-annually variable use of habitats by GHA, SA and LMSA would likely offer these species some resilience to predicted changes in climate such as warming seas and strengthening of westerly winds. However, future investigations need to consider other life history stages coupled with demographic studies, to better understand the link between behavioural plasticity and population responses.
Dynamic Regulation of N6 ,2′-O-dimethyladenosine (m6Am) in Obesity
<p>Proteomics raw data.</p> <p>Abstract:</p> <p>The prevalent m6Am mRNA cap modification was recently identified as a valid target for removal by the human obesity gene FTO along with the previously established m6A mRNA modification. However, the deposition and dynamics of m6Am in regulating obesity are unknown. Here, we investigated the liver m6A/m methylomes in mice fed on a high fat Western-diet and in ob/ob mice. We found that FTO levels were elevated in fat mice, and that genes which lost m6Am marking under obesity were overly downregulated, including the two fatty-acid-binding proteins Fabp2, and Fabp5. Furthermore, the cellular perturbation of FTO correspondingly affected protein levels of its targets. Notably, generally m6Am- but not m6A-methylated genes, were found to be highly enriched in metabolic processes. Finally, we depleted all m6A background via Mettl3 knockout, and unequivocally uncovered the association of m6Am methylation with increased mRNA stability, translation efficiency, and higher protein expression. Together, these results strongly implicate a dynamic role for m6Am in obesity-related translation regulation.</p>
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>
Figure 7 in A dynamic model for the evolution of sabrecat predatory bite mechanics
Figure 7. The relative force output at the upper canine [(I(Tf(cos Q))/Oca) where I, inlever moment arm; Tf, theoretical force output from the muscle fibre; Q, angle between the effective (rotational) torque about the temporomandibular joint and T; O, outlever moment arm to the centre of C1] at gape angles from occlusion to maximal inferred gape in: A, deep f ca masseter + zygomaticomandibularis fibre 1; B, deep masseter + zygomaticomandibularis fibre 2; C, deep masseter + zygomaticomandibularis fibre 3; D, deep masseter + zygomaticomandibularis fibre 4; E, deep masseter + zygomaticomandibularis fibre 5; F, superficial masseter. Negative values imply that an adductor has shifted to becoming an abductor at this gape angle.
Figure 3 in A dynamic model for the evolution of sabrecat predatory bite mechanics
Figure 3. The angle (Q) between the effective (rotational) torque about the temporomandibular joint (Te) and the theoretical force output from the muscle fibre (Tf) at gape angles from occlusion to maximal inferred gape in: A, deep masseter + zygomaticomandibularis fibre 1; B, deep masseter + zygomaticomandibularis fibre 2; C, deep masseter + zygomaticomandibularis fibre 3; D, deep masseter + zygomaticomandibularis fibre 4; E, deep masseter + zygomaticomandibularis fibre 5; F, superficial masseter.
Figure 2 in A dynamic model for the evolution of sabrecat predatory bite mechanics
Figure 2. The angle (Q) between the effective (rotational) torque about the temporomandibular joint (Te) and the theoretical force output from the muscle fibre (Tf) at gape angles from occlusion to maximal inferred gape in: A, temporalis fibre 1; B, temporalis fibre 3; C, temporalis fibre 5; D, temporalis fibre 7; E, temporalis fibre 8; F, temporalis fibre 10.
Figure 5 in A dynamic model for the evolution of sabrecat predatory bite mechanics
Figure 5. The relative ability of individual muscle fibres to generate rotational torque about the temporomandibular joint (TMJ) [effective (rotational) torque about the TMJ divided by the theoretical force output from the muscle fibre (Te/Tf)] at gape angles from occlusion to maximal inferred gape in: A, deep masseter + zygomaticomandibularis fibre 1; B, deep masseter + zygomaticomandibularis fibre 2; C, deep masseter + zygomaticomandibularis fibre 3; D, deep masseter + zygomaticomandibularis fibre 4; E, deep masseter + zygomaticomandibularis fibre 5; F, superficial masseter.
Figure 4 in A dynamic model for the evolution of sabrecat predatory bite mechanics
Figure 4. The relative ability of individual muscle fibres to generate rotational torque about the temporomandibular joint (TMJ) [effective (rotational) torque about the TMJ divided by the theoretical force output from the muscle fibre (Te/Tf)] at gape angles from occlusion to maximal inferred gape in: A, temporalis fibre 1; B, temporalis fibre 3; C, temporalis fibre 5; D, temporalis fibre 7; E, temporalis fibre 8; F, temporalis fibre 10.
Figure 6 in A dynamic model for the evolution of sabrecat predatory bite mechanics
Figure 6. The relative force output at the upper canine [(I(Tf(cos Q))/Oca) where I, inlever moment arm; Tf, theoretical force output from the muscle fibre; Q, angle between the effective (rotational) torque about the temporomandibular joint and T; O, outlever moment arm to the centre of C1] at gape angles from occlusion to maximal inferred gape in: A, f ca temporalis fibre 1; B, temporalis fibre 3; C, temporalis fibre 5; D, temporalis fibre 7; E, temporalis fibre 8; F, temporalis fibre 10. Negative values imply that an adductor has shifted to becoming an abductor at this gape angle.
Figure 1 in A dynamic model for the evolution of sabrecat predatory bite mechanics
Figure 1. The ability of the mandibular adductors to generate torque about the temporomandibular joint (TMJ) was estimated at ten regularly spaced intervals of the M. temporalis (T1–T10); at five regularly spaced intervals of the M. masseter profunda + M. zygomaticomandibularis (M1–M5); and the anterior-most insertion of the M. masseter superficialis. A, lion (Panthera leo; CN3503; ♂), with mandible at occlusion and at estimated maximal gape, illustrating torque about the TMJ at T1 (green vectors); B, Smilodon fatalis [LACMHC2001-173 (cranium) and LACMHC2001-4543 (mandible)] with mandible at occlusion and at estimated maximal gape, illustrating torque about the TMJ at M2 (blue vectors), and at SM (red vectors). Abbreviations: Im, inlever moment arm for masseter muscle fibre torque about the TMJ; I, inlever moment arm for temporalis muscle fibre torque about the TMJ; O, outlever moment arm to the carnassial (P4) t c paracone apex; O, outlever moment arm to the centre of C1; T, effective (rotational) torque about the TMJ; T, theoretical ca e f force output from the muscle fibre; Q, angle between Te and Tf. Scale bars = 10 cm.
Aboveground carbon stocks and dynamics in Andean forests
<p>This dataset (Andean_AGB.xlsx) has the data employed in the paper entitled <i>Old-growth Andean forests as globally important carbon sinks and future carbon refuges</i>. The data was compiled as the results of the work of several research teams spread out across the Andean region. The information available here has data about aboveground carbon stocks and dynamics and the main explanatory variables, such as climate and symbiotic root associations.</p>
FIGURE 4 in Sustainable weed management and predatory mite (Acari: Phytoseiidae) dynamics in Tunisian citrus orchards
FIGURE 4: Mean Phytoseiidae densities (a) per citrus leaf, (b) per weed quadrat and (c) per trap for the two weeding modalities in three citrus species orchards of the experimental 2.
FIGURE 3 in Sustainable weed management and predatory mite (Acari: Phytoseiidae) dynamics in Tunisian citrus orchards
FIGURE 3: Mean Phytoseiidae densities per date (a) per citrus leaf, (b) per weed quadrat and (c) per trap for the four weeding modalities in the experimental site 1.
Replication package for: Entrepreneurial Human Capital and Firm Dynamics
<p>This replication package contains publicly available data and code to replicate the figures and tables in:</p> <p>Queiró, Francisco. 2021. Entrepreneurial Human Capital and Firm Dynamics.</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.