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7,228 results for “Modules”
Dataset (Part I) accompanying the paper "In the brain of the beholder: bi-stable motion reveals mesoscopic-scale feedback modulation in V1"
<p><strong>This is Part I of the dataset (from sub-01 to sub-05).</strong> Due to size constraints, the remaining subjects can be found in the following records: <em>Dataset (Part II) accompanying the paper 'In the Brain of the Beholder: Bi-Stable Motion Reveals Mesoscopic-Scale Feedback Modulation in V1'</em> (from sub-06 to sub-09) and <em>Dataset (Part III) accompanying the paper 'In the Brain of the Beholder: Bi-Stable Motion Reveals Mesoscopic-Scale Feedback Modulation in V1'</em> (sub-10)</p>
Constant plane shift model: structure analysis of martensitic phases in Ni50Mn27Ga22Fe1 beyond non-modulated building blocks
<p>Difraction data for lattice parameter calculation, Origin files</p>
Modulation of gene expression in immune related organs by in-ovo stimulation with probiotics and prophybiotics in broiler chickens
<p><span>The current study was performed to further investigate the tissue specific immune modulation and metabolic gene regulation of these <em>in-ovo</em> stimulated chickens. Accordingly, the expression of immune related genes was determined in the secondary immune organs, cecal tonsils and the spleen as well as the liver which is an important organ for both the immune system and metabolism. Additionally, the expression of the genes related to metabolism was also analyzed in the liver.</span></p>
SCHOOL Climate and Agriculture Module and Lesson Review
<p>In this meeting, the TOPSTSCHOOL team meets with Jacob Orser, Jorge Celis, and Michael Humber to discuss the incoming Climate and Agriculture module. We discuss the datasets we have identified for using, the upcoming topics, and hear about everyones background.</p>
Idiothetic representations are modulated by availability of sensory inputs and task-demands in hippocampal-septal circuit
<p>This is the dataset underlying the results presented in the article titled: "Idiothetic representations are modulated by availability of sensory inputs and task-demands in hippocampal-septal circuit". Data is sub-divided per brain regions: CA1, CA3, and lateral septum (LS). Then each region is subdivided by mouse number, and finally by experiment (day). Each experiment contains two main files: ms.mat (miniscope data) and behav.mat (behavior data). These two streams are not sampled at the same frequency and should thus be interpolated during analysis (timestamps are available for both streams). Each .mat files can be opened with Matlab or with any HDF5 reader (e.g. in H5py Python).</p>
Data from: Protection of pepper plants from drought by microbacterium sp. 3J1 by modulation of the plant's glutamine and α-ketoglutarate content: a comparative metabolomics approach
<p><span>Desiccation-tolerant plants are able to survive for extended periods of time in the absence of water. The molecular understanding of the mechanisms used by these plants to resist droughts can be of great value for improving drought tolerance in crops. This understanding is especially relevant in an environment that tends to increase the number and intensity of droughts. The combination of certain microorganisms with drought-sensitive plants can improve their tolerance to water scarcity. One of these bacteria is <i>Microbacterium </i>sp. 3J1, an actinobacteria able to protect pepper plants from drought. In this study, we supplemented drought-tolerant and drought-sensitive plant rhizospheres with <i>Microbacterium</i> sp. 3J1 and analyzed their proteomes under drought to investigate the plant-microbe interaction. We also compare this root proteome with the proteome found in desiccation-tolerant plants. In addition, we studied the proteome of <i>Microbacterium</i> sp. 3J1 subjected to drought to analyze its contribution to the plant-microbe interaction. We describe those mechanisms shared by desiccation-tolerant plants and sensitive plants protected by microorganisms focusing on protection against oxidative stress, and production of compatible solutes, plant hormones, and other more specific proteins.</span></p>
Data from: Positive allosteric modulation of the α7 nicotinic acetylcholine receptor as a treatment for cognitive deficits after traumatic brain injury
<p><span>Cognitive impairments are a common consequence of traumatic brain injury (TBI). The hippocampus is a subcortical structure that plays a key role in the formation of declarative memories and is highly vulnerable to TBI. The α7 nicotinic acetylcholine receptor (nAChR) is highly expressed in the hippocampus and reduced expression and function of this receptor are linked with cognitive impairments in Alzheimer's disease and schizophrenia. Positive allosteric modulation of α7 nAChRs with AVL-3288 enhances receptor currents and improves cognitive functioning in naïve animals and healthy human subjects. Therefore, we hypothesized that targeting the α7 nAChR with the positive allosteric modulator AVL-3288 would enhance cognitive functioning in the chronic recovery period of TBI. To test this hypothesis, adult male Sprague Dawley rats received moderate parasagittal fluid-percussion brain injury or sham surgery. At 3 months after recovery, animals were treated with vehicle or AVL-3288 at 30 min prior to cue and contextual fear conditioning and the water maze task. Treatment of TBI animals with AVL-3288 rescued learning and memory deficits in water maze retention and working memory. AVL-3288 treatment also improved cue and contextual fear memory when tested at 24 hr and 1 month after training, when TBI animals were treated acutely just during fear conditioning at 3 months post-TBI. Hippocampal atrophy but not cortical atrophy was reduced with AVL-3288 treatment in the chronic recovery phase of TBI. AVL-3288 application to acute hippocampal slices from animals at 3 months after TBI rescued basal synaptic transmission deficits and long-term potentiation (LTP) in area CA1. Our results demonstrate that AVL-3288 improves hippocampal synaptic plasticity, and learning and memory performance after TBI in the chronic recovery period. Enhancing cholinergic transmission through positive allosteric modulation of the α7 nAChR may be a novel therapeutic to improve cognition after TBI.</span></p>
The heavy chain 4F2hc modulates the substrate affinity and specificity of the light chains LAT1 and LAT2
<p>Data to Kantipudi S., Jeckelmann J.-M., Ucurum Z., Bosshart P.D. and Fotiadis D. <em>Int. J. Mol. Sci. </em>(2020) <strong>21</strong>, 7573.</p>
Data from: Modulation of yaw stability with an unstable rigid body and a stabilising caudal fin in the yellow boxfish (Ostracion cubicus)
<p>Despite that boxfishes have a rigid carapace that restricts body undulation, they are highly manoeuvrable and manage to swim with remarkably dynamic stability. Recent research has indicated that the rigid body shape of boxfishes shows an inherently unstable response in its rotations caused by course-disturbing flows. Hence, any net stabilising effect should come from the fish's fins. The aim of the current study was to determine the effect of the surface area and orientation of the caudal fin on the yaw torque exerted on the yellow boxfish, <i>Ostracion cubicus</i>, a square cross-sectional shaped species of boxfish. Yaw torques quantified in a flow tank using a physical model with an attachable closed or open caudal fin at different body and tail angles and at different water flow speeds showed that the caudal fin is crucial for controlling yaw. These flow tank results were confirmed by computational fluid dynamics simulations. The caudal fin therefore acts as both a stabiliser and rudder for the naturally unstable rigid body with regard to yaw. Boxfishes seem to use the interaction of the unstable body and active changes in the shape and orientation of the caudal fin to modulate manoeuvrability and stability.</p>
Appendix II for: Social context modulates scale-free walks in a social insect
<p>Plots from the MLE (Maximum likelihood estimation) analysis for the step-lengths of the focal termite workers. Two competing models were tested: Truncated Pareto Lévy (TP - red line) vs exponential (EX - blue dashed line) for both (X and Y) axis. Data series are identified with "S" plus a number from 1 to 75). The Lévy exponent ($1 < \mu \leq 3.0$) and the Akaike weights (wAIC) for the competing models (1 for full support, 0 for not support) are shown in the plots. </p>
Genetic disruption of synthesis pathways of Arabidopsis secondary metabolites dramatically affects root-associated nematode populations directly and via modulation of microbial communities
<p>Dataset of nematode, fungal and bacterial sequence reads of Arabidopsis roots. Dataset of fungal and bacterial sequence reads of Arabidopsis microbial suspension. DNA concentration of Arabidopsis root microbial suspension. Meloidogyne incognita J2 invasion into tomato roots. qPCR dataset of Meloidogyne hapla infection pressure into Arabidopsis roots. </p>
Structures for "Protonation States of Molecular Groups in the Chromophore-Binding Site Modulate Properties of the Reversibly Switchable Fluorescent Protein rsEGFP2"
<p>Files with atomic coordinates of the structures obtained in geometry optimization of molecular systems within the protein and cluster models. Supplementary materials for the paper "Protonation States of Molecular Groups in the Chromophore-Binding Site Modulate Properties of the Reversibly Switchable Fluorescent Protein rsEGFP2"</p>
From individual to population level: Temperature and snow cover modulate fledging success through breeding phenology in Greylag geese (Anser anser)
<p>Local weather conditions may be used as environmental cues by animals to optimize their breeding behaviour, and could be affected by climate change. We measured associations between climate, breeding phenology, and reproductive output in greylag geese (<i>Anser anser</i>) across 29 years (1990-2018). The birds are individually marked, which allows accurate long-term monitoring of life-history parameters for all pairs within the flock. We had three aims: (1) identify climate patterns at a local scale in Upper Austria, (2) measure the association between climate and greylag goose breeding phenology, and (3) measure the relationship between climate and both clutch size and fledging success. Ambient temperature increased 2°C across the 29-years study period, and higher winter temperature was associated with earlier onset of egg-laying. Using the hatch-fledge ratio, average annual temperature was the strongest predictor for the proportion of fledged goslings per season. There is evidence for an optimum time window for egg-laying (the earliest and latest eggs laid had the lowest fledging success). These findings broaden our understanding of environmental effects and population-level shifts which could be associated with increased ambient temperature and can thus inform future research about the ecological consequences of climate changes and reproductive output in avian systems.</p>
Thermal modulation of Zebrafish exploratory statistics reveals constraints on individual behavioral variability
<p><span><strong>Background</strong>: </span>Variability is a hallmark of animal behavior. It contributes to survival by endowing individuals and populations with the capacity to adapt to ever-changing environmental conditions. Intra-individual variability is thought to reflect both endogenous and exogenous modulations of the neural dynamics of the central nervous system. However, how variability is internally regulated and modulated by external cues remains elusive. Here we address this question by analyzing the statistics of spontaneous exploration of freely swimming zebrafish larvae, and by probing how these locomotor patterns are impacted when changing the water temperatures within an ethologically relevant range.<br> <br> <span><strong>Results</strong>: </span>We show that, for this simple animal model, five short-term kinematic parameters - interbout interval, turn amplitude, travelled distance, turn probability and orientational flipping rate - together control the long-term exploratory dynamics. We establish that the bath temperature consistently impacts the means of these parameters, but leave their pairwise covariance unchanged. These results indicate that the temperature merely controls the sampling statistics within a well-defined kinematic space delineated by this robust statistical structure. At a given temperature, individual animals explore the behavioral space over a timescale of tens of minutes, suggestive of a slow internal state modulation that could be externally biased through the bath temperature. By combining these various observations into a minimal stochastic model of navigation, we show that this thermal modulation of locomotor kinematics results in a thermophobic behavior, complementing direct gradient-sensing mechanisms.<br> <br> <span><strong>Conclusions</strong>: </span>This study establishes the existence of a well-defined locomotor space accessible to zebrafish larvae during spontaneous exploration, and quantifies self-generated modulation of locomotor patterns. Intra-individual variability reflects a slow diffusive-like probing of this space by the animal. The bath temperature in turn restricts the sampling statistics to sub-regions, endowing the animal with basic thermophobicity. This study suggests that in Zebrafish, as well as in other ectothermic animals, ambient temperature could be used to efficiently manipulate internal states in a simple and ethological way.</p>
Mu-rhythm modulation associated with the observation and execution of a goal-directed action in healthy toddlers estimated using two different baseline conditions
<p>The database includes mu-rhythm ERD/ERS values elicited by the observation and execution of a goal-directed action in healthy toddlers (N=19). ERD/ERS values has been computed using to different baseline conditions: 1) observation of a black and white static image (BL1) and 2) short period of stillness (BL2).</p> <p>The first sheet of the database refers to action execution (AE) data, whereas the second sheet refers to action observation (AO) data. The database table in each sheet includes for each subject single trial ERD/ERS values (table rows) registered in 7 different scalp sites (table columns) for both BL1 and BL2.</p> <p>The database was used for the statistical analysis of the following paper: Piazza, C.; Visintin, E.; Reni, G.; Montirosso, R. The Effect of Baseline on Toddler Event-Related Mu-Rhythm Modulation. <em>Brain Sci.</em> <strong>2021</strong>, <em>11</em>, 1159. https://doi.org/10.3390/brainsci11091159 (<a href="https://www.mdpi.com/2076-3425/11/9/1159/htm">https://www.mdpi.com/2076-3425/11/9/1159/htm</a>)</p> <p>All the details about data acquisition and preprocessing are reported in the above mentioned publication.</p>
Data for Seasonal Modulation of Dissolved Oxygen in the Equatorial Pacific by Tropical Instability Vortices
<p>This repository contains data used for the Analysis of "Seasonal Modulation of Dissolved Oxygen in the Equatorial Pacific by Tropical Instability Vortices" By Eddebbar et al. Submitted to JGR Oceans.</p> <p>Code used for the analysis of CESM-HR and CESM-LR model outputs and running and analyzing the particle tracking simulations are available at Zenodo on https://zenodo.org/record/5266337</p> <p>This repository contains the following items: </p> <ol> <li> Observational datasets used for model validation Figure 1 and 2 (obs.tar.gz) </li> <li>Low Resolution CESM outputs used for model resolution comparison Figure 1-3 (CESM_LR.tar.gz)</li> <li>High resolution CESM climatological output (CESM_HR_CLM.tar.gz and CESM_HR_CLM_all.tar.gz)</li> <li>Physical and BGC outputs from high resolution CESM from snapshot for Oct, 03, 0005 (CESM-HR_BGC.0005-10-03.tar.gz and CESM_HR_0005_10_03.tar.gz) used in Fig 3, 4, 5, 6, and 9 and Supp Fig 3.</li> <li>Outputs for year 5 of simulation for select variables from CESM-HR (CESM_HR_0005.tar.gz)</li> <li>Model Grid file: CESM_HR_grid.tar.gz</li> <li>Output for month 8, 9, 10, and 11 of year 5 of CESM-HR simulation used in figure 10, 11, and 12 for select variables including: CESM_HR_HMXL_08_09.tar.gz, CESM_HR_HMXL_10_11.tar.gz, CESM_HR_O2_08_09.tar.gz, CESM_HR_O2_10_11.tar.gz, CESM_HR_PD_08_09.tar.gz, CESM_HR_PD_10_11.tar.gz, CESM_HR_SSH_08_09.tar.gz, CESM_HR_SSH_10_11.tar.gz, CESM_HR_STF_O2_10_11.tar.gz, CESM_HR_TEMP_08_09.tar.gz, CESM_HR_TEMP_10_11.tar.gz, CESM_HR_UVEL_08_09.tar.gz)</li> <li>Near surface (15m) meridional and zonal velocity for the full CESM-HR simulation (CESM_HR_UV.tar.gz) for Fig 7</li> <li>Integrated O2 budget terms for CESM-HR (CESM_HR_O2_budget.tar.gz) used in figure 8</li> <li>Monthly mean O2 and PD (CESM_HR_O2_mon.tar.gz and CESM_HR_PD_mon.tar.gz) for Fig 7</li> <li>Particle trajectories for forward and backward parcels simulations used in fig 10-12 (particle_tracking_bwd_.tar.gz and particle_tracking_fwd_.tar.gz)</li> </ol>
The corticospinal tract primarily modulates sensory inputs in the mouse lumbar cord (Raw data)
<p>Raw data of the eLife 2021 article</p> <p><strong>The corticospinal tract primarily modulates sensory inputs in the mouse lumbar cord.</strong></p> <p>Authors:</p> <p><strong>Yunuen Moreno-Lopez<sup>1</sup>, Charlotte Bichara<sup>1</sup>, Gilles Delbecq, Philippe Isope, Matilde Cordero-Erausquin</strong></p> <p>Methods are described in the article. Data is organized by figure.</p>
Former au sketchnoting à distance - Modules vidéos
<p>Au second confinement, la perspective de devoir former étudiant.es (du L1 au doctorat) et enseignant.es-chercheur.ses au sketchnoting s'est imposée. Le passage en distanciel d'une formation basée sur un outil analogique, nécessitant démonstrations et partage de contenus sur papier s’est avérée très concluante grâce à quelques ajustement techniques simples et de nouvelles idées d’animation.</p> <p>Ces vidéos ont pour leur part été déposées sur des cours Moodle et sur la chaîne Youtube "Salut, c'est la BU !" et proposées comme ressources complémentaires pour les étudiant.es ayant suivi le cours en direct sur Zoom.</p>
Relatedness modulates density-dependent cannibalism rates in Drosophila
<p>1. Cannibalism is taxonomically widespread, and can have large impacts on individual fitness and population-level processes. As such, identifying how cannibalism rates vary in response to ecological cues is important for predicting species evolution and population dynamics.</p> <p>2. In this study, we aimed to identify several eco-evolutionary factors that affect cannibalism rate and measure how they interacted with one another.</p> <p>3. To do this, we conducted two experiments using complimentary methods to measure how cannibalism rates varied among larval Drosophila melanogaster and Drosophila simulans in response to changes in conspecific relatedness, social familiarity and density.</p> <p>4. We found that larvae were more likely to cannibalise non-related larval victims in both species, and that this effect increased at high densities in D. simulans. We found no evidence that Drosophila larvae use social familiarity to assess relatedness. Finally, in D. melanogaster, cannibalistic larvae prefer to cannibalise larvae that are being attacked by a greater number of conspecifics, implying that cues linked to conspecific abundance encourage cooperative cannibalism.</p> <p>5. By showing that cannibalism frequency in Drosophila spp. is sensitive to relatedness and several other factors, we reveal the complex relationship between cannibalism frequency and species ecology. Also, by showing that the effect of relatedness on cannibalism frequency is density-dependent, we advance the current understanding of how ecological variables interact to affect kin selection.</p> <p>ANALYSIS CODE IS WRITTEN IN R.</p>
A comprehensive evaluation of module detection methods for gene expression data
<p><strong>A critical step in the analysis of large genome-wide gene expression datasets is the use of module detection methods to group genes into co-expression modules. Because of limitations of classical clustering methods, numerous alternative module detection methods have been proposed, which improve upon clustering by handling co-expression in only a subset of samples, modeling the regulatory network, or allowing overlap between modules. In this study we use known regulatory networks to do a comprehensive and robust evaluation of these different methods. Overall, decomposition methods outperform all other strategies, while we could not find any clear advantages of biclustering and network-inference based approaches. Using our evaluation workflow, we also investigate several practical aspects of module detection, such as parameter estimation and the use of alternative similarity measures, and conclude with recommendations for the further development of these methods.</strong></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.