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7,228 results for “Modules”
Data from: Markov-modulated continuous-time Markov chains to identify site- and branch-specific evolutionary variation in BEAST
<p>Markov models of character substitution on phylogenies form the foundation of phylogenetic inference frameworks. Early models made the simplifying assumption that the substitution process is homogeneous over time and across sites in the molecular sequence alignment. While standard practice adopts extensions that accommodate heterogeneity of substitution rates across sites, heterogeneity in the process over time in a site-specific manner remains frequently overlooked. This is problematic, as evolutionary processes that act at the molecular level are highly variable, subjecting different sites to different selective constraints over time, impacting their substitution behaviour. We propose incorporating time variability through Markov-modulated models (MMMs), which extend covarion-like models and allow the substitution process (including relative character exchange rates as well as the overall substitution rate) at individual sites to vary across lineages. We implement a general MMM framework in BEAST, a popular Bayesian phylogenetic inference software package, allowing researchers to compose a wide range of MMMs through flexible XML specification. Using examples from bacterial, viral and plastid genome evolution, we show that MMMs impact phylogenetic tree estimation and can substantially improve model fit compared to standard substitution models. Through simulations, we show that marginal likelihood estimation accurately identifies the generative model and does not systematically prefer the more parameter-rich MMMs. To mitigate the increased computational demands associated with MMMs, our implementation exploits recent developments in BEAGLE, a high-performance computational library for phylogenetic inference.</p>
Supplementary data for article: Central insulin modulates dopamine signaling in the human striatum
<p><b>Objective:</b> Activity in the dopaminergic pathways of the brain is highly sensitive to body weight and metabolic states. Animal studies show that dopamine neurons are important targets for the metabolic hormone insulin with abolished effects in the insulin resistant state, leading to increases in body weight and food intake. In humans, the influence of central acting insulin on dopamine and effects of their interplay are still elusive.</p> <p><b>Research Design and Methods:</b> We investigated whether central administered insulin influences dopaminergic activity in striatal regions and whole-brain neural activity. Using a PET/MRI hybrid scanner, we simultaneously performed [<sup>11</sup>C]-raclopride-PET and resting state fMRI in 10 healthy normal weight men after application of intranasal insulin or placebo on two separate days in a randomized, placebo-controlled, blinded, crossover trial.</p> <p><b>Results:</b> In response to central insulin compared to placebo administration, we observed greater [<sup>11</sup>C]-raclopride binding potential (BP<sub>nd</sub>) in the bilateral ventral and dorsal striatum. This suggests an insulin-induced reduction in synaptic dopamine levels. Resting-state striatal activity was lower 15 and 30 min after nasal insulin compared to placebo. Functional connectivity of the mesocorticolimbic circuitry associated with differences in dopamine levels: individuals with a stronger insulin-induced effect on dopamine levels showed a stronger increase in functional connectivity 45 min after intranasal insulin.</p> <p><b>Conclusions</b>: This study indicates that central insulin modulates dopaminergic tone in the striatum, which may affect regional brain activity and connectivity. Our results deepen the understanding of the insulin-dopamine interaction and the complex network that underlies the regulation of whole-body metabolism.</p>
DATA for MS wave modulation
<p>DATA for the paper of Modulation of magnetosonic waves by background plasma density in a dipole magnetic field: 2-D PIC simulation</p>
Structural modulation of π-conjugated linkers in D-π-A dyes based on Triphenylamine dicyanovinylene framework to explore the NLO properties
<p>A donor-π-acceptor type series of Triphenylamine-dicyanovinylene based chromophores (<b>DPMN1-DPMN11</b>) was designed theoretically by the structural tailoring of π-linkers to exploit changes in the optical properties and their NLO behaviour. Density functional theory (DFT) computations were employed to understand the electronic structures, absorption spectra, charge transfer phenomena and the influence of these structural modifications on NLO properties. Interestingly, all investigated chromophores exhibited lower band gap (2.22-2.60 <i>eV</i>) with broad absorption spectra in the visible region, reflecting the remarkable NLO response. Furthermore, natural Bond Orbital (NBO) findings revealed a strong push-pull mechanism in <b>DPMN1-DPMN11 </b>as donor and π-conjugates exhibited positive, while all acceptors showed negative values. Examination of electronic transitions from donor to acceptor moieties via π-conjugated linkers revealed greater linear (<<i>α</i>>=526.536-641.756 <i>a.u</i>) and non-linear (<i>β</i><sub>tot</sub> =51313.8-314412.661 <i>a.u</i>) response. It was noted that the chromophores containing imidazole in 2<sup>nd</sup> p-linker expressed greater hyperpolarizability when compared with the ones containing pyrrole. This study reveals that by controlling the type of π-spacers, interesting metal-free NLO materials can be designed, which can be valuable for the hi-tech NLO applications.</p>
MITgcm model setup and output for "Antarctic Slope Current modulates ocean heat intrusions towards Totten Glacier"
<p>MITgcm model setup and output for "Antarctic Slope Current modulates ocean heat intrusions towards Totten Glacier</p> <p>Here, it contains the results of the East Antarctic simulation from 1992-2016. Model grid is lat-lon similar to LLC1080 grid resolution roughly 3-4 km in the region. See Nakayama et al., submitted to GRL for detail. </p> <p><strong>(Contents)</strong><br> code.zip (code to run this simulation)<br> input.zip (input file required for this simulation)<br> results_zenodo.zip (due to size limit of 50GB, please check <a href="https://ecco.jpl.nasa.gov/drive/files/ECCO2/LatLon_East_Antartic">https://ecco.jpl.nasa.gov/drive/files/ECCO2/LatLon_East_Antarctic</a> for complete model output. Complete datasets can also be obtained by rerunning the simulation.)</p> <p><strong>(How to build and run)</strong><br> mkdir build<br> ./../../tools/genmake2 -of ../../../tools/build_options/linux_amd64_ifort+mpi_ice_nas -mpi -mods ../code/<br> make depend<br> make -j 16<br> cd ..<br> mkdir test<br> cd test<br> ln -sf ../input/* .<br> ln -sf /nobackup/hzhang1/forcing/era_xx/ .<br> cp ../build/mitgcm_uv .<br> qsub run_omp_high_t1.pbs</p>
Data from: The intraspecific variation of functional traits modulates drought resilience of European beech and pubescent oak
<p>A higher frequency and intensity of droughts will impair forest productivity. Therefore, improving our understanding of which factors enhance tree growth resilience against drought has become a crucial issue, but we lack information at the intraspecific level.</p> <p>In this study, we investigate the role played by climatic conditions and tree characteristics in the growth response to severe droughts in two deciduous Fagaceae species near their southern distribution limit: the temperate European beech (Fagus sylvatica) and the Mediterranean pubescent oak (Quercus pubescens). The study area is located in Catalonia, NE Spain, where 149 trees were cored covering the water availability gradient of the species in the region. In addition, tree size (diameter and height) and an ensemble of stem, leaf and hydraulic traits were collected for each tree. Growth responses to extreme droughts during the period 1980-2015 were assessed using resilience indicators based on residual basal area increment series predicted by a model including growing-season water balance.</p> <p>Although resistance was unrelated to drought intensity, higher water availability improved recovery and reduced drought legacy effects. Taller trees showed higher resilience against drought, which could be explained by the relationship between the variation in tree height and functional traits, such as leaf nitrogen concentration, leaf turgor loss point and resistance to xylem embolism. For both species, trees with lower cavitation resistance, higher leaf nitrogen concentration and tighter stomatal regulation (suggested by less negative turgor loss point and carbon isotope composition) displayed better performance during and after severe droughts. Both species showed a progressive decrease in resilience and increase of legacy effects.</p> <p><em>Synthesis</em>. This study highlights the relevance of analyzing intraspecific variation of functional traits involved in tree water and carbon balance to improve our understanding of the resilience and variability of growth responses to drought within species. </p>
fMRI free-viewing data, resting-state and structural in macaques associated with publication 'Social prediction modulates activity of macaque superior temporal cortex'
<p>Using a free-viewing and functional magnetic resonance imaging, we show that activity in a region of the macaque middle superior temporal (midSTS) cortex was specifically modulated by the predictability of social interactions. This region could be distinguished from other temporal regions involved in face processing. Using resting-state fMRI in anesthetized macaques, we showed that the connectivity between the face-responsive areas and the social prediction area was more integrated in macaques than in humans. We reproduce the social prediction results in a replication study and provide a control to rule out oculomotor implication through the FEF in the social prediction activity of the midSTS, using Transcranial Ultrasound Stimulation. Using standard geometric shape movement stimuli, we also show that macaques do not attribute mental state to shapes.</p>
Data and code for figures: Coherent Terahertz-to-Microwave Link Using Electro-Optic-Modulated Turing Rolls
<p>This dataset contains the figures and data presented in the paper <Coherent Terahertz-to-Microwave Link Using Electro-Optic-Modulated Turing Rolls>.</p>
Data from: Ongoing habenular activity is driven by forebrain networks and modulated by olfactory stimuli
<p>The data was collected using volumetric two-photon calcium imaging of the forebrain and habenula of juvenile zebrafish expressing a transgenic calcium indicator. The data provided is organized according to the figures of our manuscript and contains the necessary codes and data to replicate the figures presented. In short, included repository contains 6 datasets of experiments. Data structure includes neuronal data as normalised to the baseline fluorescence for each neuron over time (DF/F), 2 or 3 dimensional coordinates of each cell and information about duration and samplings rate of experiments, and appropriate information about stimulation either microstimulation or odor stimulation (if any was performed within the experiment).</p>
Data for ENSO modulation of summertime surface ozone over China
<p>Data for ENSO modulation of summertime surface ozone over China</p>
Modulation of effective precipitation by temperature in East Asia during Marine Isotope Stage 5
<p>Magnetic susceptibility and microcodium Mg/Ca, Sr/Ca, and <sup>87</sup>Sr/<sup>86</sup>Sr records from the Huanxian section, northern Chinese Loess Plateau.</p>
Data on short-term temperature modulated dilution experiments and summary of dilution experiments in (sub)tropical waters
<p>Two datasets were compiled for estimating and comparted the temperature sensitivity of phytoplankton growth rate within vs across communities.</p> <p>One dataset contains the data of short-term temperature modulated dilution experiments conducted at three subtropical coastal sites for one year. In each experiment, the phytoplankton community growth rates were estimated at five different temperatures via the dilution approach. </p> <p>Another dataset contains the phytoplankton community growth rates in (sub)tropical waters estimated by the dilution approach, collected from related literature. </p> <p> </p>
SARA module 3: NGS epitope sequencing: Illumina FASTQ files
<p>We investigate the accumulated microbial and autoantigen antibody repertoire in adult-onset dermatomyositis patients sero-positive for TIF1γ (TRIM33) autoantibodies. We use an untargeted high-throughput approach which combines immunoglobulin disease-specific epitope-enrichment and identification of microbial and human antigens. We observe antibodies recognizing a wider repertoire of microbial antigens in dermatomyositis. Antibodies recognizing viruses and Poxviridae family species are significantly enriched. The identified autoantibodies recognise a large portion of the human proteome, including interferon regulated proteins; these proteins cluster in specific biological processes. In addition to TRIM33, we identify autoantibodies against eleven further TRIM proteins, including TRIM21. Some of these TRIM proteins share epitope homology with specific viral species including poxviruses. Our data suggest antibody accumulation in dermatomyositis against an expanded diversity of microbial and human proteins and evidence of non-random targeting of specific signalling pathways. Our findings indicate that molecular mimicry and epitope spreading events may play a role in dermatomyositis pathogenesis.</p>
The lncRNA TUG1 regulates Smac/DIABLO expression by competitively inhibiting miR-29b and modulates the apoptosis of lens epithelial cells in age-related cataracts
<p>As one of the first discovered lncRNAs, TUG1 has been reported to be widely expressed in a variety of tumours. It promotes cell proliferation, differentiation, apoptosis and migration. However, our understanding of its importance in cataracts is limited. This study aims to explore the mechanism by which TUG1 mediates the apoptosis of lens epithelial cells by regulating the miR-29b/Smac axis in age-related cataracts and to identify more strategies for the nonsurgical treatment of cataracts. In this experiment we found TUG1 and Smac were expressed at high levels in age-related cataract (ARC) samples and HLEB3 cells treated with H2O2, while miR-29b expression was decreased. In vitro cell-based experiments confirmed that the downregulation of TUG1 inhibits lens epithelial cell apoptosis. Mechanistically, Smac expression is negatively regulated by miR-29b. TUG1 competitively inhibits miR-29b expression and causes the release of more Smac. In addition, miR-29b reverses the effect of TUG1 on HLE-B3 cells. In conclusion, lncRNATUG1 increases Smac expression by competitively inhibiting miR-29b and promoting the apoptosis of lens epithelial cells in age-related cataracts. This mechanism is the cytological basis of ARC formation. Based on these results, the TUG1-miR29b-Smac axis may be a new molecular pathway to regulate the development of age-related cataracts.</p>
Data from: Carbon versus nitrogen release from root and leaf litter are modulated by litter position and plant functional type
<p><span>Litters of leaves and roots of different qualities occur naturally above- and belowground, respectively, where they decompose in contrasting </span><span>abiotic and biotic</span><span> environments. Therefore, ecosystem carbon (C) and nitrogen (N) dynamics can be strongly affected by the combination of </span><span>litter </span><span>position and quality. However, it is poorly understood how C versus N turnover of litters depends on the interplay among plant functional type (PFT), organs, traits, and litter position. </span></p> <p><span>In a semi-arid inland dune, soil surface and buried leaf litters and buried fine roots of 25 species across three PFTs (herbs, legume shrubs, and non-legume shrubs) were incubated for 3, 6, 9, 12, 18, and 24 months to investigate litter decomposition and C and N dynamics. Morphological and chemical (nutrient and </span><span>NMR carbon)</span><span> traits of initial litters of leaves and fine roots were determined.</span></p> <p><span>The litter decomposition rates (k values) of surface leaves and buried fine roots did not differ, but buried fine roots and buried leaf litter decomposed faster than surface leaf litter. </span><span>Ratios of <em>k</em> values of surface leaves to buried leaves decreased with the leaf C:N ratio. </span><span>Herbs and legume shrubs decomposed faster than non-legume shrubs for buried fine roots, but not for leaves. </span><span>At given C loss, buried fine roots had higher N loss than leaf litters;</span><span> legume shrubs with relatively higher N or lower C:N ratio had higher N loss than non-legume shrubs.</span><span> Stronger positive relationships between C and N losses were shown in leaves and legume shrubs than in fine roots and non-legume shrubs, respectively.</span></p> <p><span><strong>Synthesis</strong>: The generality of faster N release of legume litters at a given C release highlights the importance of legumes in N cycling in semi-arid ecosystems where N is the limiting factor. The dynamics and coordination of C versus N release as a function of litter quality are modulated by litter position and PFT. These findings have important implications for the development of process-based models on C and N cycles in the context of ongoing global change potentially altering the functional composition of plant communities and the relative quantities and qualities of aboveground versus belowground litter.</span></p>
Data from: Nitrogen addition and warming modulate the pathogen impact on plant biomass by shifting intraspecific functional traits and reducing species richness
<p><span>1. </span><span>Foliar fungal pathogens can substantially reduce plant biomass. This effect can be modulated by environment conditions, such as soil nitrogen availability and air temperature. The ongoing global changes are altering these variables and thus interact with pathogens to influence plant biomass, but experimental test of their interactions is scarce. </span></p> <p><span>2. </span><span>We conducted a 4-year field experiment in a Tibetan alpine meadow to examine the interactive effects of nitrogen addition, warming and foliar pathogens (via fungicide application) on plant biomass. We also measured plant functional traits, species richness and abundance to test the possible mechanisms underlying these interactions. </span></p> <p><span>3. </span><span>Our results showed that foliar fungal pathogens reduced plant community biomass under nitrogen addition, which in turn weakened the positive nitrogen effect on community biomass. Mechanistically, nitrogen addition shifted the plant communities towards fast-growing traits; this happened predominantly because of changes in within-species trait values, including an increase in specific leaf area and height. These trait changes resulted in greater suppression of plant biomass by pathogens, likely because of the trade-offs associated with the allocation of resources to plant growth and defense. Moreover, the reduction in species richness amplified the pathogen effect under nitrogen addition due to the increased density and susceptibility of the most dominant species (i.e. Kobresia capillifolia). Furthermore, warming did not interact with pathogens and nitrogen addition to influence plant community biomass, but their three-way interaction modified the biomass of K. capillifolia. Specifically, warming enhanced the positive effect of nitrogen addition on the biomass of K. capillifolia in the fungicide, low infection plots, while it weakened the nitrogen effect in the no fungicide, high infection plots.</span></p> <p><span>4. </span><span>Synthesis:</span> <span>Our results demonstrate how pathogens interact with nitrogen addition and warming to influence the biomass of dominant species and the whole plant community. Our study highlights the importance of considering foliar fungal pathogens when assessing ecosystem responses to multiple global change factors.</span></p>
Diazotrophy modulates cyanobacteria stoichiometry through functional traits that determine bloom magnitude and toxin production
<p>Harmful cyanobacterial blooms are an increasing threat to water quality. The interactions between two eco-physiological functional traits of cyanobacteria, diazotrophy (nitrogen (N)-fixation) and N-rich cyanotoxin synthesis, have never been examined in a stoichiometric explicit manner. We explored how a gradient of resource N:phosphorus (P) affects the biomass, N, P stoichiometry, light-harvesting pigments, and cylindrospermopsin production in a N-fixing cyanobacterium, Aphanizomenon. Low N:P Aphanizomenon cultures produced the same biomass as populations grown in high N:P cultures. The biomass accumulation determined by carbon, indicated low N:P Aphanizomenon cultures did not have a N-fixation growth tradeoff, in contrast to some other diazotrophs that maintain stoichiometric N homeostasis at the expense of growth. However, N-fixing Aphanizomenon populations produced less particulate cylindrospermopsin and had undetectable dissolved cylindrospermopsin compared to non-N-fixing populations. The pattern of low to high cyanotoxin cell quotas across an N:P gradient in the diazotrophic cylindrospermopsin producer is similar to the cyanotoxin cell quota response in non-diazotrophic cyanobacteria. We suggest that diazotrophic cyanobacteria may be characterized into two broad functional groups, the N-storage-strategists and the growth-strategists, which use N-fixation differently and may determine patterns of bloom magnitude and toxin production in nature.</p>
Data and code for: Human density modulates spatial associations among tropical forest terrestrial mammal species
<p>The spatial aggregation of species pairs often increases with the ecological similarity of the species involved. However, the way in which environmental conditions and anthropogenic activity affect the relationship between spatial aggregation and ecological similarity remains unknown despite the potential for spatial associations to affect species interactions, ecosystem function, and extinction risk. Given that human disturbance has been shown to both increase and decrease spatial associations among species pairs, ecological similarity may have a role in mediating these patterns. Here, we test the influences of habitat diversity, primary productivity, human population density, and species' ecological similarity based on functional traits (i.e., functional trait similarity) on spatial associations among tropical forest mammals. Large mammals are highly sensitive to anthropogenic change and therefore susceptible to changes in interspecific spatial associations. Using two-species occupancy models and camera trap data, we quantified the spatial overlap of 1,216 species pairs from 13 tropical forest-protected areas around the world. We found that the association between ecological similarity and interspecific species associations depended upon surrounding human density. Specifically, aggregation of ecologically similar species was more than an order of magnitude stronger in landscapes with the highest human density compared to those with the lowest human density, even though all populations occurred within protected areas. Human-induced changes in interspecific spatial associations have been shown to alter top-down control by predators, increase disease transmission and increase local extinction rates. Our results indicate that anthropogenic effects on the distribution of wildlife within protected areas are already occurring and that impacts on species interactions, ecosystem functions, and extinction risk warrant further investigation. </p>
O-GlcNAc transferase OGT-1 and the ubiquitin ligase EEL-1 modulate seizure susceptibility in C. elegans Dataset
<p>Neurodevelopmental disorders such as epilepsy and autism have been linked to an imbalance of excitation and inhibition (E/I) in the central nervous system. The simplicity and tractability of<i> C. elegans</i> allows our electroconvulsive seizure (ES) assay to be used as a behavioral readout of the locomotor circuit and neuronal function. <i>C. elegans</i> possess conserved nervous system features such as gamma-aminobutyric acid (GABA) and GABA receptors in inhibitory neurotransmission, and acetylcholine (Ach) and acetylcholine receptors in excitatory neurotransmission. Our previously published data has shown that decreasing inhibition in the motor circuit, via GABAergic manipulation, will extend the time of locomotor recovery following electroshock. Similarly, mutations in a HECT E3 ubiquitin ligase called EEL-1 leads to impaired GABAergic transmission, E/I imbalance and altered sensitivity to electroshock. Mutations in the human ortholog of EEL-1, called HUWE1, are associated with both syndromic and non-syndromic intellectual disability. Both EEL-1 and its previously established binding protein, OGT-1, are expressed in GABAergic motor neurons, localize to GABAergic presynaptic terminals, and function in parallel to regulate GABA neuron function. In this study, we tested behavioral responses to electroshock in wildtype, <i>ogt-1</i>, <i>eel-1</i> and <i>ogt-1; eel-1</i> double mutants. Both <i>ogt-1 </i>and <i>eel-1 </i>null mutants have decreased inhibitory GABAergic neuron function and increased electroshock sensitivity. Consistent with EEL-1 and OGT-1 functioning in parallel pathways, <i>ogt-1; eel-1 </i>double mutants showed enhanced electroshock susceptibility. Expression of OGT-1 in the <i>C. elegans </i>nervous system rescued enhanced electroshock defects in <i>ogt-1; eel-1 </i>double mutants. Application of a GABA agonist, Baclofen, decreased electroshock susceptibility in all animals. Our <i>C. elegans</i> electroconvulsive seizure assay was the first to model a human X-linked Intellectual Disability (XLID) associated with epilepsy and suggests a potential novel role for the OGT-1/EEL-1 complex in seizure susceptibility.</p>
Supplementary Tables for "Giant virus infection signatures are modulated by euphotic zone depth strata and iron regimes...."
<p>Supplementary Tables S4 and S5</p> <p><strong>Supplementary Table 4.</strong> Project ID's for the individual assemblies available through the JGI data portal</p> <p><strong>Supplementary Table 5</strong>. Overview of giant virus isolate genomes/metagenome-assembled genomes detected across the SOTS in situ dataset</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.