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83 results for “regional interaction”
PhasAGE Training School 1 - Structure and protein interactions of repeated and low complexity regions - LECTURE
<p>The Training School 1 <strong>“Computational Methods to Study Protein Phase Separation”</strong> is the first edition of a series of PhasAGE training activities.</p> <p>The goal of this course is to provide participants with the basic knowledge to understand the phenomenon of <strong>Phase Separation</strong>, its role in biological processes and diseases. In addition, the course will provide <strong>an overview of the available computational resources</strong> to navigate this knowledge. Participants will have <strong>hands-on training</strong> in tools and resources available for life sciences, to collect information from the literature on biomolecular phase transitions, identify features triggering phase transitions, mutations associated with diseases, known or predicted PTMs and molecular interaction sites.</p>
Regional and local factors interact to shape colonization and extinction dynamics of invasive Hydrilla verticillata in a patchy landscape
<p>Understanding the response of species to global change requires disentangling the drivers of their distributions across landscapes. Colonization and extinction processes, shaped by the interplay of landscape-level and local patch-level factors, are key determinants of these distributions. However, disentangling the influence of these factors, when larger-scale processes manifest at local scales, remains a challenge. We addressed this challenge by investigating the colonization and extinction dynamics of the aquatic plant, <em>Hydrilla verticillata</em>, in a complex riverine rock pool system. This system, with hundreds of rock pools experiencing varying flooding frequencies, provided a natural laboratory to examine how a single landscape-level disturbance can differentially impact colonization and extinction depending on local patch characteristics to shape species distributions. Using five years of data across over 500 sites and more than 5,000 surveys, we employed dynamic occupancy models to model colonization, extinction, and changes in <em>Hydrilla</em> patch occupancy while accounting for imperfect detection. Our results revealed that larger, infrequently flooded pools closer to the river were more likely to be colonized. In contrast, local extinction of Hydrilla was more likely in smaller pools closer to the river that flooded frequently. These findings underscore the importance of considering context-dependence in species distribution models. The same landscape-level disturbance (flooding) had opposing effects on colonization and extinction, with the direction and magnitude of these effects varying with local patch characteristics. Our study highlights the need for integrating local and landscape-level factors, and considering how larger-scale processes play out at the patch level, to understand the complex dynamics that shape species distributions.</p>
Dataset for article: Co-evolutionary landscape at the interface and non-interface regions of protein-protein interaction complexes
<p>Proteins involved in interactions throughout the course of evolution tend to co-evolve and compensatory changes may occur in interacting proteins to maintain or refine such interactions. However, certain residue pair alterations may prove to be detrimental for functional interactions. Hence, determining co-evolutionary pairings that could be structurally or functionally relevant for maintaining the conservation of an inter-protein interaction is important. Inter-protein co-evolution analysis in several complexes utilizing multiple existing methodologies suggested that co-evolutionary pairings can occur in spatially proximal and distant regions in inter-protein interactions. Subsequently, the Co-Var (<b>Co</b>rrelated <b>Var</b>iation) method based on mutual information and Bhattacharyya coefficient was developed, validated, and found to perform relatively better than CAPS and EV-complex. Interestingly, while applying the Co-Var measure and EV-complex program on a set of protein-protein interaction complexes, co-evolutionary pairings were obtained in interface and non-interface regions in protein complexes. The Co-Var approach involves determining high degree co-evolutionary pairings that include multiple co-evolutionary connections between particular co-evolved residue positions in one protein with multiple residue positions in the binding partner. Detailed analyses of high degree co-evolutionary pairings in protein-protein complexes involved in cancer metastasis suggested that most of the residue positions forming such co-evolutionary connections mainly occurred within functional domains of constituent proteins and substitution mutations were also common among these positions. The physiological relevance of these predictions suggests that Co-Var can predict residues that could be crucial for preserving functional protein-protein interactions. Finally, <b>Co-Var </b>web server (<a href="http://www.hpppi.iicb.res.in/ishi/covar/index.html">http://www.hpppi.iicb.res.in/ishi/covar/index.html</a>) that implements this methodology identifies co-evolutionary pairings in intra and inter-protein interactions.</p>
Regional and local factors interact to shape colonization and extinction dynamics of invasive Hydrilla verticillata in a patchy landscape
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Dataset for article: Co-evolutionary landscape at the interface and non-interface regions of protein-protein interaction complexes
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Data from: Local neighbourhood and regional climatic contexts interact to explain tree performance
Tree neighbourhood modelling has significantly contributed to our understanding of the mechanisms structuring communities. Investigations into the impact of neighbouring crowding on tree performance have generally been conducted at local scales, missing important regional-scale context such as the suitability of the climate for each species. Favourable climates may enhance tree performance, but this may come at the cost of increased neighbourhood crowding and competition negatively impacting survival and growth. Through the synthesis of continental-scale forest inventory and trait datasets from the northeast USA and Puerto Rico we present an analytical approach that elucidates the important interactions between local competitive and regional climatic contexts. Our results show strong asymmetries in competitive interactions and significant niche differences that are dependent on habitat suitability. The strong interaction between local neighbourhood and regional climate highlights the need for models that consider the interaction between these two processes that have been previously ignored.
The TELPERION Survey for Extended Emission Regions around AGN: a strongly-interacting and merging galaxy sample
<p>FITS files of narrowband and broadband images used in the search of the TELPERION merging-galaxy sample for AGN-ionized extended [O III] clouds, and confirming longslit spectrum as described in the manuscript. A full list of observation sites and dates, and guide to file names, are in the file 000Readme.txt</p> <p>Analysis is in the paper of the same title submitted to the Monthly Notices of the Royal Astronomical Society.</p> <p> </p>
Flushing the Lake Littoral Region: The Interaction of Differential Cooling and Mild Winds. Dataset
<p>Dataset for "Flushing the Lake Littoral Region: The Interaction of Differential Cooling and Mild Winds"<br> by Cintia L. Ramón, Hugo N. Ulloa, Tomy Doda, and Damien Bouffard. 2022<br> Water Resources Research<br> https://doi.org/10.1029/2021WR030943<br> *******************************<br> Folder: Content:<br> InputFiles_MITgcm Input files to run simulations (Table 1) with the MITgcm model.<br> InputFiles_MITgcm_2Dbathy Input files to reproduce Exp. 1 in Ulloa et al. (2022) with the MITgcm model.<br> FigureData Data displayed in Figures 2 to 6 in the main text and Figures S1-S6 in the Supporting information </p>
PhasAGE Training School 1 - Structure and protein interactions of repeated and low complexity regions - PRACTICAL
<p>The Training School 1 <strong>“Computational Methods to Study Protein Phase Separation”</strong> is the first edition of a series of PhasAGE training activities.</p> <p>The goal of this course is to provide participants with the basic knowledge to understand the phenomenon of <strong>Phase Separation</strong>, its role in biological processes and diseases. In addition, the course will provide <strong>an overview of the available computational resources</strong> to navigate this knowledge. Participants will have <strong>hands-on training</strong> in tools and resources available for life sciences, to collect information from the literature on biomolecular phase transitions, identify features triggering phase transitions, mutations associated with diseases, known or predicted PTMs and molecular interaction sites.</p>
Data and code: Global and regional ecological boundaries explain abrupt spatial discontinuities in avian frugivory interactions
<p>Species interactions can propagate disturbances across space via direct and indirect effects, potentially connecting species at a global scale. However, ecological and biogeographic boundaries may mitigate this spread by demarcating the limits of ecological networks. We tested whether large-scale ecological boundaries (ecoregions and biomes) and human disturbance gradients increase dissimilarity among plant-frugivore networks, while accounting for background spatial and elevational gradients and differences in network sampling. We assessed network dissimilarity patterns over a broad spatial scale, using 196 quantitative avian frugivory networks (encompassing 1,496 plant and 1,004 bird species) distributed across 67 ecoregions, 11 biomes, and 6 continents. We show that dissimilarities in species and interaction composition, but not network structure, are greater across ecoregion and biome boundaries and along different levels of human disturbance. Our findings indicate that biogeographic boundaries delineate the world's biodiversity of interactions and likely contribute to mitigating the propagation of disturbances at large spatial scales.</p>
Hypothalamic interaction with reward-related regions during subjective evaluation of foods
<p>The reward system implemented in the midbrain, ventral striatum, orbitofrontal cortex, and ventromedial prefrontal cortex evaluates and compares various types of rewards given to the organisms. It has been suggested that autonomic factors influence reward-related processing via the hypothalamus, but how the hypothalamus modulates the reward system remains elusive. In this functional magnetic resonance imaging study, the hypothalamus was parcellated into individual hypothalamic nuclei performing different autonomic functions using boundary mapping parcellation analyses. The effective interaction during subjective evaluation of foods in a reward task was then investigated between the human hypothalamic nuclei and the reward-related regions. We found significant brain activity decrease in the paraventricular nucleus (PVH) and lateral nucleus in the hypothalamus in food evaluation compared with monetary evaluation. A psychophysiological interaction analysis revealed dual interactions between the PVH and (1) midbrain region and (2) ventromedial prefrontal cortex, with the former correlated with the stronger tendency of participants toward food-seeking. A dynamic causal modeling analysis further revealed unidirectional interactions from the PVH to the midbrain and ventromedial prefrontal cortex. These results suggest that the PVH in the human hypothalamus interacts with the reward-related regions in the cerebral cortex via multiple pathways (i.e., the midbrain pathway and ventromedial prefrontal pathway) to evaluate rewards for subsequent decision-making.</p>
Basic helix-loop-helix pioneer factors interact with the histone octamer to invade nucleosomes and generate nucleosome depleted regions.
<p>This dataset includes all time traces from single-molecule experiments as well as raw gel images used in the manuscript. All time traces from single-molecule experiments and can be viewed using vbFRET (https://vbfret.sourceforge.net/). </p>
Orchid-mycorrhizal fungi interactions reveal a duality in their network structure in two European regions differing in climate
<p><span>Network analysis is an effective tool to describe and quantify the ecological interactions between plants and root-associated fungi.</span><span> Mycoheterotrophic plants, such as orchids, critically rely on mycorrhizal fungi for nutrients to survive, therefore, investigating the structure of those intimate interactions brings new insights into the plant community assembly and coexistence. So far, there is little consensus on the structure of those interactions, described either as nested (generalist interactions), modular (highly specific interactions) or of both topologies. Biotic factors (e.g., mycorrhizal specificity) were shown to influence the network structure, while there is less evidence of abiotic factor effects. By</span><span> using next-generation sequencing of the orchid mycorrhizal fungal (OMF) community associated with 238 plant individuals belonging to 17 orchid species, we assessed the structure of four orchid-OMF networks in two European regions under contrasting climatic conditions (Mediterranean vs Continental).</span> <span>Each network contained four to 12 co-occurring orchid species, including up to eight species shared among the sites</span><span>. All four networks were both nested and modular, and fungal communities were different between co-occurring orchid species, despite multiple sharing of fungi across some orchids. Co-occurring orchid species growing in Mediterranean climates were associated with more dissimilar fungal communities, consistent with a greater modular structure compared to the Continental ones. The OMF diversity was comparable among orchid species since most orchids were associated with multiple rarer fungi and with only a few highly dominant ones in the roots. Our results provide useful highlights on potential factors involved in structuring plant-mycorrhizal fungi interactions in different climatic conditions.</span></p>
Orchid-mycorrhizal fungi interactions reveal a duality in their network structure in two European regions differing in climate
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Hypothalamic interaction with reward-related regions during subjective evaluation of foods
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Data and code: Global and regional ecological boundaries explain abrupt spatial discontinuities in avian frugivory interactions
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Data from: Local neighbourhood and regional climatic contexts interact to explain tree performance
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Data from: Fine nurse variations explain discrepancies in the stress-interaction relationship in alpine regions
Despite a large consensus on increasing facilitation among plants with increasing stress in alpine regions, a number of different outcomes of interaction have been observed, which impedes the generalisation of the 'stress-gradient hypothesis' (SGH). With the aim to reconcile the different viewpoints on the stress-interaction relationship in alpine environments we hypothesized that fine nurse variations within a single life form (cushion) may explain this pattern variability To test this hypothesis, we compared the magnitude of the stress-interaction relationship in a single study area with that observed in existing studies involving cushions, worldwide. We characterized the nurse effects of cushions on the whole plant community at inter-specific, intra-specific and intra-individual levels along a stress gradient in the dry, alpine tropics of Bolivia (4400 m, 4700 m and 4900 m a.s.l). Using a relative index of interaction (RII) we included our data in a meta-analysis on the nurse effects of cushions along alpine gradients, worldwide. At inter-specific level, the loose cushion Pycnophyllum was a better nurse than the compact Azorella compacta. However, at intra-individual level facilitation was higher at the periphery than at the centre of cushions, exceeding in magnitude the variation observed at inter-specific level. This pattern was associated with higher minimum temperature and lower mortality at the periphery of cushions. The net effects of cushions on plant communities became more positive at higher elevation, corroborating the SGH. Within our single site in Bolivia, fine morphological nurse variations captured a similar variability in the stress-interaction relationship as that observed in a subset of studies on cushions on a worldwide scale. This suggests that fine variations in nurse traits, in general those not considered in protocols dealing with facilitation or in restoration/conservation management plans, explain in part the current discrepancies among SGH studies in alpine regions.
Simulation data for WRF-GC (v2.0): online two-way coupling of WRF (v3.9.1.1) and GEOS-Chem (v12.7.2) for modeling regional atmospheric chemistry–meteorology interactions
<p>This repository provides the test simulation data for "WRF-GC (v2.0): online two-way coupling of WRF (v3.9.1.1) and GEOS-Chem (v12.7.2) for modeling regional atmospheric chemistry–meteorology interactions" published in Geoscientific Model Development. The configurations for sensitivity experiments are described in this paper. Please contact the corresponding author Tzung-May Fu (fuzm@sustech.edu.cn) for more details.</p>
GEOLAB Project FROSPER: FROst heaving soils-Solar Panel foundations interaction in cold European Regions: an experimental study
<p>The objective of the proposed project is to investigate the<strong> resilience of solar panels foundations in cold climates</strong>. The efficiency of solar panels is overall better in cold climates, when the direct sunlight is available, due to the lower temperature-induced dispersion. For this reason, large solar fields tend to be installed in cold regions, such as northern Europe or Canada. A solar field with <i>e.g.</i>, 10 MW, requires a great number of solar panels (~6000) whose foundations are generally<strong> steel piles</strong> driven into the soil down to a depth of 2÷5 m below the ground surface. In the cold regions, the shallow layers of soil are periodically subjected to <strong>freezing thus to the frost-heaving phenomena</strong>. The latter can increase the <strong>risk of uplift failure mechanism of the pile foundation</strong> compromising the exercise of the entire solar panel row.</p><p>This project aims to investigate the interaction between saturated soils and solar panel foundations under frozen conditions in <strong>scaled centrifuge models</strong>. The steel piles will be at first driven into the saturated soil sample, then a set of the <strong>freezing-thawing cycles</strong> will be reproduced in the centrifuge. <strong>Possible practical interventions to reduce the soil frost-heaving effects</strong> will also be explored, as the use of protective insulating mantel at the ground surface all around the head of the pile.</p><p>This project will represent a breakthrough in the understanding of the solar panel foundations behaviour, allowing a deeper insight into possible uplift failure mechanisms. The motivation of the study lies in the reduction of the costs and in the resilience improvement of critical infrastructures for the generation of energy in the EU territories. </p>
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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.