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460 results for “underlying mechanism”
Brain mechanisms underlying episodic future thinking of sustainable behaviors
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Data for: Ring Current Electron Precipitation During the 17 March 2013 Geomagnetic Storm: Underlying Mechanisms and Their Effect on the Atmosphere
<p>All data are included as MATLAB figure files, png files and MATLAB MAT files.</p><p>File precipitated_flux.mat contains a 4-D array of values of precipitated electron flux in [1/(s cm^2 keV)] for 289 time points from 16 March 2013 to 19 March 2013, with a 15 min time step; 100 values of energy in a range from 10 keV to 1 MeV, with a 10 keV step; on a spatial grid of 28 by 49 (P, R).</p><p>netCDF data can be opened with a variety of software tools, including Matlab, Origin or Python.</p>
Dataset for Charge collection efficiency, underlying recombination mechanisms, and the role of electrode distance of vented ionization chambers under ultra-high dose-per-pulse conditions
<p>Dataset for paper: Kranzer et al., <a href="https://www.sciencedirect.com/journal/physica-medica">Physica Medica</a> <a href="https://www.sciencedirect.com/journal/physica-medica/vol/104/suppl/C">Volume 104</a>, December 2022, Pages 10-17</p> <p><a href="https://doi.org/10.1016/j.ejmp.2022.10.021">https://doi.org/10.1016/j.ejmp.2022.10.021</a></p>
Molecular mechanisms underlying plasticity in a thermally varying environment
<p><span>Adaptation to environmental variability is a prerequisite for species' persistence in their natural environments. With climate change predicted to increase the frequency and severity of temperature fluctuations, ectothermic organisms may increasingly depend on acclimation capacity to accommodate thermal variability. To elucidate the molecular basis of fluctuating temperature induced phenotypic plasticity, we investigated heat tolerance and the mechanisms induced by acclimation to thermal variability as compared to those seen at constant temperature. We ran genome-wide transcriptomic analysis on <em>Drosophila melanogaster</em> subjected to acclimation at constant (19 </span><span>±</span><span> 0</span><span>°</span><span>C) and fluctuating (19 </span><span>±</span><span> 8</span><span>°</span><span>C) temperatures and contrasted the induction of molecular mechanisms in adult males, adult females, and larvae. We found life stage and sex specific dynamics of the acclimation responses to fluctuating temperatures. Adult flies exposed to temperature fluctuations showed a constitutive improvement in heat tolerance while heat tolerance of larvae tracked thermal fluctuations. A constitutive down-regulation of gene expression was observed for several genes in the case of larvae exposed to fluctuations. Our results for adult females showed that, for several genes, fluctuating temperature acclimation resulted in canalization of gene expression. Both transcriptional and post-transcriptional machinery were greatly affected by fluctuations in the case of adult males. Gene ontology analysis showed enrichment of heat stress response involving several major heat shock proteins in both larvae and adults exposed to fluctuating temperatures, even though fluctuations were in a benign range of temperatures. Finally, molecular mechanisms related to environmental sensing seem to be an important component of insect response to thermal variability. </span></p>
Single-cell profiling reveals immune-based mechanisms underlying tumor radiosensitization by a novel Mn porphyrin clinical candidate, MnTnBuOE-2-PyP5+ (BMX-001)
<p>Manganese porphyrins reportedly exhibit synergic effects when combined with irradiation. However, an in-depth understanding of intratumoral heterogeneity and immune pathways, as affected by Mn porphyrins, remains limited. Here, we explored the mechanisms underlying immunomodulation of a clinical candidate, MnTnBuOE-2-PyP<sup>5+</sup> (BMX-001, MnBuOE), using single-cell analysis in murine carcinoma<em> </em>model. Mice bearing 4T1 tumors were divided into 4 groups: control, MnBuOE, radiotherapy (RT), combined MnBuOE, and radiotherapy (MnBuOE/RT). In epithelial cells, epithelial-mesenchymal transition, TNF-α signaling via NF-кB, angiogenesis, and hypoxia-related genes were significantly downregulated in the MnBuOE/RT compared to the RT. All subtypes of cancer-associated fibroblasts (CAFs) were reduced in MnBuOE and MnBuOE/RT. Inhibitory receptor-ligand interactions, in which epithelial cells and CAFs interacted with CD8+ T cells, were significantly lower in the MnBuOE/RT than in the RT. Trajectory analysis showed that DC maturation-associated markers were increased in MnBuOE/RT. M1 macrophages were significantly increased in the MnBuOE/RT compared to the RT, whereas myeloid-derived suppressor cells were decreased. CellChat analysis showed that the number of cell-cell communications was the lowest in the MnBuOE/RT. Our study is the first to provide evidence for the combined radiotherapy with a novel Mn porphyrin clinical candidate, BMX-001 from the perspective of each cell type within the tumor microenvironment.</p>
Dataset related to article "Glia-to-neuron transfer of miRNAs via extracellular vesicles: a new mechanism underlying inflammation-induced synaptic alterations"
<p>This record contains raw data related to article "Glia-to-neuron transfer of miRNAs via extracellular vesicles: a new mechanism underlying inflammation-induced synaptic alterations"</p> <p>Recent evidence indicates synaptic dysfunction as an early mechanism affected in neuroinflammatory diseases, such as multiple sclerosis, which are characterized by chronic microglia activation. However, the mode(s) of action of reactive microglia in causing synaptic defects are not fully understood. In this study, we show that inflammatory microglia produce extracellular vesicles (EVs) which are enriched in a set of miRNAs that regulate the expression of key synaptic proteins. Among them, miR-146a-5p, a microglia-specific miRNA not present in hippocampal neurons, controls the expression of presynaptic synaptotagmin1 (Syt1) and postsynaptic neuroligin1 (Nlg1), an adhesion protein which play a crucial role in dendritic spine formation and synaptic stability. Using a Renilla-based sensor, we provide formal proof that inflammatory EVs transfer their miR-146a-5p cargo to neuron. By western blot and immunofluorescence analysis we show that vesicular miR-146a-5p suppresses Syt1 and Nlg1 expression in receiving neurons. Microglia-to-neuron miR-146a-5p transfer and Syt1 and Nlg1 downregulation do not occur when EV-neuron contact is inhibited by cloaking vesicular phosphatidylserine residues and when neurons are exposed to EVs either depleted of miR-146a-5p, produced by pro-regenerative microglia, or storing inactive miR-146a-5p, produced by cells transfected with an anti-miR-146a-5p. Morphological analysis reveals that prolonged exposure to inflammatory EVs leads to significant decrease in dendritic spine density in hippocampal neurons in vivo and in primary culture, which is rescued in vitro by transfection of a miR-insensitive Nlg1 form. Dendritic spine loss is accompanied by a decrease in the density and strength of excitatory synapses, as indicated by reduced mEPSC frequency and amplitude. These findings link inflammatory microglia and enhanced EV production to loss of excitatory synapses, uncovering a previously unrecognized role for microglia-enriched miRNAs, released in association to EVs, in silencing of key synaptic genes.</p>
Data from: Whole genomes reveal evolutionary relationships and mechanisms underlying gene-tree discordance in Neodiprion sawflies
<p>Rapidly evolving taxa are excellent models for understanding the mechanisms that give rise to biodiversity. However, developing an accurate historical framework for comparative analysis of such lineages remains a challenge due to ubiquitous incomplete lineage sorting and introgression. Here, we use a whole-genome alignment, multiple locus-sampling strategies, and locus-based and SNP-based species-tree methods to infer a species tree for eastern North American <em>Neodiprion</em> species, a clade of pine-feeding sawflies (Order: Hymenopteran; Family: Diprionidae). We recovered a well-supported species tree that—except for three uncertain relationships—is robust to different strategies for analyzing whole-genome data. Despite this consistency, underlying gene-tree discordance is high. To understand this discordance, we use multiple regression to model topological discordance as a function of several genomic features. We find that gene-tree discordance tends to be higher in regions of the genome that may be more prone to gene-tree estimation error, as indicated by a lower density of parsimony-informative sites, a higher density of genes, a higher average pairwise genetic distance, and gene trees with lower average bootstrap support. Also, contrary to the expectation that discordance via incomplete lineage sorting is reduced in low-recombination regions of the genome, we find a <em>negative</em> correlation between recombination rate and topological discordance. We offer potential explanations for this pattern and hypothesize that it may be unique to lineages that have diverged with gene flow. Our analysis also reveals an unexpected discordance hotspot on Chromosome 1, which contains several genes potentially involved in mitochondrial-nuclear interactions and produces a gene-tree that resembles a highly discordant mitochondrial tree. Based on these observations, we hypothesize that our genome-wide scan for topological discordance has identified a nuclear locus involved in a mito-nuclear incompatibility. Together, these results demonstrate how phylogenomic analysis coupled with high-quality, annotated genomes can generate novel hypotheses about the mechanisms that drive divergence and produce variable genealogical histories across genomes.</p>
Circuit mechanisms underlying embryonic retinal waves
<p>Spontaneous activity is a hallmark of developing neural systems. In the retina, spontaneous activity comes in the form of retinal waves, comprised of three stages persisting from embryonic day 16 (E16) to eye opening at postnatal day 14 (P14). Though postnatal retinal waves have been well characterized, little is known about the spatiotemporal properties or the mechanisms mediating embryonic retinal waves, designated Stage 1 waves. Using a custom-built macroscope to record spontaneous calcium transients from whole embryonic retinas, we show that Stage 1 waves are initiated at several locations across the retina and propagate across a broad range of areas. A gap junction antagonist, meclofenamic acid, reduced the frequency and size of Stage 1 waves, nearly abolishing them. The general nAChR antagonist, hexamethonium similarly nearly abolished Stage 1 waves. Application of the α4β2 nAChR antagonist dihydro-ß-erythroidine only slightly reduced the frequency of waves but significantly reduced the number of cells that participated in waves. Thus, Stage 1 waves are mediated by a complex circuitry involving subtypes of nAChRs and gap junctions. Stage 1 waves in mice lacking the β2 subunit of the nAChRs (β2-nAChR-KO) were reduced, but in contrast to WT mice, they persisted in the hexamethonium and were completely blocked by meclofenamic acid. To assay the impact of Stage 1 waves on retinal development, we compared the spatial distribution of a subtype of retinal ganglion cells, intrinsically photosensitive retinal ganglion cells (ipRGCs), which undergo a significant amount of cell death, in WT and β2-nAChR-KO mice. We found that the developmental decrease of ipRGC density is preserved between WT and β2-nAChR-KO mice, indicating that processes regulating ipRGC distribution are not influenced by spontaneous activity.</p>
Computational mechanisms underlying latent value updating of unchosen actions
<p><span>Current studies suggest that individuals estimate the value of their choices based on observed feedback. Here, we ask whether individuals also update the value of their unchosen actions, even when the associated feedback remains unknown. </span><span>One hundred and seventy-eight</span><span> individuals completed a multi-armed bandit task, making choices to gain rewards. We found robust evidence suggesting latent value updating of unchosen actions based on the chosen action's outcome. Computational modeling results suggested that this effect is mainly explained by a value updating mechanism whereby individuals integrate the outcome history for choosing an option with that of rejecting the alternative. Properties of the deliberation (i.e., duration/difficulty) did not moderate the latent value updating of unchosen actions, suggesting that memory traces generated during deliberation might take a smaller role in this specific phenomenon than previously thought. We discuss the mechanisms facilitating credit assignment to unchosen actions and their implications for human decision-making.</span></p>
Molecular mechanisms underlying plasticity in a thermally varying environment
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Single-cell profiling reveals immune-based mechanisms underlying tumor radiosensitization by a novel Mn porphyrin clinical candidate, MnTnBuOE-2-PyP5+ (BMX-001)
Open the record for dataset details and reuse information.
Data from: Whole genomes reveal evolutionary relationships and mechanisms underlying gene-tree discordance in Neodiprion sawflies
Open the record for dataset details and reuse information.
Computational mechanisms underlying latent value updating of unchosen actions
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Circuit mechanisms underlying embryonic retinal waves
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Underlying data for "Global alignment and assessment of TRP channel transmembrane domain structures to explore functional mechanisms"
<p><strong>Output Files from Structural Alignment of TRP Channels</strong><br> The archive contains the key output files resulting from the structural alignment of members of the TRP channel family described in "Global alignment and assessment of TRP channel transmembrane domain structures to explore functional mechanisms", Huffer et al., (2020), eLife.</p> <p><strong>Contents of trp_struct_align_outputs.tar.gz</strong><br> <em>Aligned_structures</em><br> For each alignment where the transmembrane (TM) domain of the mobile structure was aligned to the TM domain of the stationary/reference structure (6co7):<br> 1) mobile_stationary_full_align.pdb: aligned based on Fr-TM-Align output matrix, contains all residues<br> 2) mobile_stationary_tmem_align.pdb: aligned based on Fr-TM-Align output matrix, contains only TM residues used for alignment<br> 3) mobile_stationary_hole.pdb: aligned based on Fr-TM-Align output matrix, contains HOLE profile of mobile structure</p> <p><em>Alignments</em><br> Multiple sequence alignments constructed using the TM domain of each structure as the stationary/reference structure, with all other structures aligned pairwise.<br> 1) stationary_full.ali: Full multiple sequence alignment containing all TM residues from all stationary and mobile structures.<br> 2) stationary_nogap.ali: Multiple sequence alignment containing all TM residues from the stationary structure. Any gaps in the stationary structure removed, which removes any residue in any mobile structure that does not align to the stationary/reference structure.</p> <p><em>Fr-TM-Align_outputs</em><br> - frtmalign_output.csv: contains all information from Fr-TM-Align output files for each pairwise alignment of TM domains, including PDB IDs of mobile and stationary structures, lengths of mobile and stationary structures, length of pairwise alignment sequence, RMSD of alignment, TM-score of alignment, and sequence identity of alignment.<br> - aligned_length.csv, RMSD.csv, sequence_identity.csv, and TM_score.csv: csv files containing the specified values for all pairwise alignments of TM domains, with the mobile structure in rows and stationary structure in columns</p> <p><strong>Reproducibility</strong><br> Code to reproduce this alignment and analysis is available on GitHub at: <a href="https://github.com/kehuffer/TRP_Structural_Alignment">https://github.com/kehuffer/TRP_Structural_Alignment</a></p>
The Neural Mechanism Underlying The Effect of Musical Training on Phonological Awareness of preschoolers : A Meta-Analysis
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Mentalising mechanisms underly strategic coordination in Guinea baboons (Papio papio)
<p>It remains controversial whether the ability to mentalise is confined to humans. To address this question, Guinea baboons living in a social colony freely came to play a 2-players coordination game with any other baboon, or alone (social vs solo conditions). In fact, in both conditions, they interacted with an identical Artificial Agent. Their choice behaviour depended on the social context and their relative dominance hierarchy. A mentalising computational model accounted for baboons' behaviour better than simpler models without mentalizing components in the social condition while the same baboons used a simpler strategy when they played alone. Together, these findings indicate that computations required for mentalising and used for coordination learning may have evolved in the common ancestor of the Old-World monkey and apes.</p>
All-atom simulations elucidate the molecular mechanism underlying RNA-membrane interactions
<p>Topology files and frames extracted from the minimum of the free energy profile F(d_z) (or F(d_min) for single-stranded RNAs), within 2.5kBT. These files can be used to reproduce the hydrogen bond analyses in the manuscript.</p> <p>Scripts which were used to extract hydrogen bond information are available on <a href="https://github.com/salvatoredimarco/rna-membrane">https://github.com/salvatoredimarco/rna-membrane</a></p> <p><strong>Systems:</strong></p> <p>4xN: nucleosides</p> <p>4xN2: dinucleotides</p> <p>4xN3: trinucleotides</p> <p>4xN_OPC: nucleosides simulated with OPC water model. Energy threshold is here 1.0*kBT, because of weaker binding.</p> <p>1xGA, 1xGU, 1xGC, 1xCU</p> <p>1xGGC, 1xGCG</p> <p>1xquadruplex: G-quadruplex</p> <p>1xstrand: 19-mer RNA strand</p> <p>1xhairpin: 16-mer folded hairpin</p> <p>1x16mer_elong: 16-mer unfolded, restrained</p> <p>2x16mer_loose1/2: 16-mer unfolded, unrestrained</p>
Partitioning beta diversity to untangle mechanisms underlying the assembly of bird communities in Mediterranean olive groves
<p><span><span><span><span><span><span><span><span><span><span><span><i>Aim</i>: We investigated taxonomic and functional beta diversity of bird communities inhabiting Mediterranean olive groves subject to either intensive or extensive management of the ground cover and located in landscapes with different degrees of complexity.</span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span><i>Location</i>: Andalusia, southern Spain.</span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span><i>Methods</i>: We partitioned taxonomic and functional beta diversity into its two additive components, turnover and nestedness. We also explored the contributions of single sites to overall beta diversity (LCBD) and separated the effects of species replacement (turnover) and richness difference (nestedness) in order to identify ecologically unique sites -keystone communities- within the metacommunity. In a further step, we employed abundance- and functional-based indicator species analyses to characterize bird assemblages. </span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span><i>Results</i>: Taxonomic beta diversity increased with landscape complexity. Although both taxonomic and functional differences among assemblages were driven mainly by species replacement (regardless of management or landscape type), the contribution of trait replacement to the total functional beta diversity was much lower, suggesting that species performing similar functions replace each other between sites. There were no differences in LCBD between management types or categories of landscape complexity, but the contributions of sites to beta diversity decreased as the percentage cover of olive groves increased. Species richness was also important in explaining variation in LCBD as species-poor sites tended to contribute the most to the local-to-regional beta diversity. However, some farms displayed high values of LCBD due to the existence of a high replacement component, indicating that some species recorded in these sites were scarce elsewhere. The indicator species analyses revealed that the woodchat shrike <i>Lanius senator</i> may constitute an excellent indicator of biodiversity in this agro-forestry-system. </span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span><i>Main conclusions</i>: Our results show that agricultural expansion promotes biotic homogenization and exemplify how the identification of both keystone species and communities can represent a powerful tool for the management of anthropized landscapes.</span></span></span></span></span></span></span></span></span></span></span></p>
Mechanisms underlying altitudinal and horizontal range contraction: The western black crested gibbon
<p>Aim: Species ranges in mountain areas may shift both horizontally and altitudinally, resulting from climate change and anthropogenic impact. Two hypotheses (the abundant center hypothesis and the contagion hypothesis) have been proposed to account for patterns of horizontal range contraction. However, undulating topograph causes a mosaic of unsuitable habitats, which may complicate the spatial pattern of range contraction. We develop a framework incorporating horizontal and altitudinal range contraction patterns of a species living in mountain areas, to better understand the underlying mechanisms of species range contraction.</p> <p>Location: China, North Laos, and North Vietnam</p> <p>Taxon: Western black crested gibbon, <i>Nomascus concolor</i></p> <p>Methods: We collected occurrence data of the gibbons from various sources and modelled their potential distribution range in the 1950s, 1980s, and 2010s, using ecological niche modelling. We compared distances from the center point of the potential range in 1950s to center points of the largest 100 patches in the 1950s and the 2010s to understand the patterns of horizontal range contraction. We also calculated potential distribution within different altitudinal range for six populations in each period to understand the patterns of altitudinal range contraction.</p> <p>Results: Potential horizontal distribution of the gibbons decreased by 69% from the 1950s to the 2010s. We found the 100 largest patches in 2010s were further apart from the center point of the potential range in 1950s compared to the 100 largest patches in 1950s, supporting the contagion hypothesis. No populations extended their range to higher altitude, suggesting climate change did not have a profound effect on gibbon range upward shift. All populations lost a substantial proportion of their ranges in lower altitude (500 – 1,500 m) but to different degrees, suggesting that populations experienced different anthropogenic pressures.</p> <p>Main conclusions: Anthropogenic threats probably including human population increase, agricultural expansion and hunting, were more likely than climate change to have caused range contraction in western black-crested gibbons. This study highlights the importance of studying horizontal and altitudinal range contraction simultaneously.</p>
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.