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1,025 results for “encoder”
Annotation of genes encoding enzymes across marine phytoplankton genomes
<p>Phytoplankton cells span a large size range, from picoplankton (<2µm), nanoplankton (2 to 20µm), microplankton (20 to 200µm) to macroplankton (200 to <2000µm). Cell size interacts with multiple selective pressures, including cellular metabolic rate, light absorption, nutrient uptake, cell nutrient quotas, trophic interactions and diffusional exchanges with the environment. Beyond simple size, cells of different shapes differ in surface area to volume ratio. For example, more elongated cells, such as pennate diatoms, have a larger surface area to volume ratio compared to more rounded cells, such as centric diatoms, of equivalent biovolume, which can in turn influence diffusional exchanges between cells and their environment. We assembled metadata on diverse marine phytoplankters, in parallel with genomic or transcriptomic data annotations to identify genes encoding enzymes, to facilitate analyses of genomic patterns of encoded enzymes across diverse taxa, sizes, growth forms and origins of strains.</p>
3D Golden radial phase encoding MR raw data
<p>MR raw dataset in ISMRMRD format acquired with a 3D Golden radial phase encoding trajectory. One data set is of a static phantom, the other data set is of a moving phantom. For details about how to reconstruct this data sets please have a look at: <a href="https://github.com/SyneRBI/SIRF-Exercises/tree/master/notebooks/MR">SyneRBI/SIRF-Exercises</a></p>
Growing Arabidopsis pollen tubes expressing genetically encoded reporters for calcium and pH
<p>Spatiotemporal dynamics of intracellular pH (H+) and calcium (Ca2+) in growing Arabidopsis pollen tubes. Fluorescence time-lapses of pollen tubes expressing ratiometric sensors under the pollen-specific LAT52 promoter, namely CaMeleon (Ca2+) [Damineli et al., 2017; DOI: 10.1093/jxb/erx032] and pHluorin (pH) [Hoffmann et al., 2020; DOI: 10.1038/s41467-020-16253-1], were acquired every 4 seconds with an inverted microscope equipped with a front-illuminated camera (2560 × 2160, pixel size 6.45 μm), a fluorescence illuminator, and a ×63 1.2NA water immersion objective lens. The CaMeleon filters were set as follows: excitation 426-450 nm (CFP) and 505-515 nm (YFP), emission 458-487 nm (CFP) and 520-550 nm (YFP). As for pHluorin, the filter settings were: excitation 318-390 nm (DAPI) and 428-475 nm (FITC), emission 435-448 nm (DAPI) and 523-536 nm (FITC) [from Damineli et al., 2017; Hoffmann et al., 2020].</p>
childTale-A: A corpus of eighty fairy tales from the 7th edition by the Brothers Grimm, manually annotated for textually encoded emotions
<p>The childTale-A corpus is a collection of eighty fairy tales, a core set of the Grimms’ Children's and Household Tales as introduced in Herrmann & Lüdtke (2023). Within the CHYLSA project, textually encoded emotions were annotated in each sentence in each of the eighty fairy tales. Annotations were collected for the dimensions <em>valence</em> and <em>arousal</em>, as well as for the six basic emotions <em>anger</em>, <em>disgust</em>, <em>fear</em>, <em>joy</em>, <em>sadness</em>, and <em>surprise</em>. Each fairy tale was annotated by two persons (for details see Hermann & Lüdtke, 2023).</p> <p>In detail, this dataset contains:</p> <ul> <li>instructions and texts used for annotation (zip-files): <ul> <li>all N=80 fairy tales as txt-files (with normalised orthography)</li> <li>instructions (in German) for the valence and arousal annotation as well as for the annotation of the six basic emotions</li> </ul> </li> <li>scripts for preparing and analysing annotations for textually encoded emotions: <ul> <li>Python scripts to prepare Excel files for annotation (including a script to separate texts into individual sentences)</li> <li>R-scripts for data preparation, calculation of inter-rater reliability and smoothing of the valence annotations (discrete cosine transformation (DCT) with length normalisation) <ul> </ul> </li> </ul> </li> <li>sentence-level data (for each sentence in each of the eighty fairy tales): <ul> <li>annotations for the dimensions valence and arousal (continuous values)</li> <li>categorisation of each sentence (as negative, neutral or positive) based on the continuous valence annotation</li> <li>annotations on the occurrence of the six basic emotions anger, disgust, fear, joy, sadness, and surprise</li> </ul> </li> <li>transformed and length-normalised valence annotations as basis for the <em>Emotional Arcs</em> (DCT and length normalisation results in one hundred data points for each fairy tale, saved in a separate data file)</li> <li>text-level data (for each of the eighty fairy tales): <ul> <li>general information, for example title in German and English, number of sentences, Kinder- und Hausmärchen-ID (KMH-ID), corpus ID</li> <li>results of the analysis of the annotated data with values for: <ul> <li><em>Average Valence</em> and <em>Average Arousal</em></li> <li>inter-rater reliability index (Krippendorff's alpha coefficient) for the valence and arousal annotations</li> <li>proportions of positive, negative and neutral sentences</li> <li><em>Emotion Potential</em> (percent of both positive and negative sentences)</li> <li><em>Valence Span</em>, <em>Arousal Span</em> and range of the <em>Emotional Arc</em></li> <li><em>Emotion Profile</em> (relative frequency for each of the six basic emotions <em>anger</em>, <em>disgust</em>, <em>fear</em>, <em>joy</em>, <em>sadness</em>, and <em>surprise)</em></li> <li>inter-rater reliability indices (Krippendorff's alpha coefficient and the percentage of agreement) for each of the six basic emotions</li> </ul> </li> </ul> </li> </ul> <p>Reference: <br> Herrmann, Berenike & Lüdtke, Jana (2023). A Fairy Tale Gold Standard. Annotation and Analysis of Emotions in the Children's and Household Tales by the Brothers Grimm.<em> </em>Zeitschrift für digitale Geisteswissenschaften (ZfdG). DOI: 10.17175/2023_005.</p> <p> </p> <p>DFG Schwerpunktprogramm SPP 2207 “Computational Literary Studies“<br> Online:</p> <ol> <li><a href="https://gepris.dfg.de/gepris/projekt/402743989">https://gepris.dfg.de/gepris/projekt/402743989</a></li> <li><a href="https://dfg-spp-cls.github.io/">https://dfg-spp-cls.github.io<em>/</em></a></li> </ol> <p>Teilprojekt: „CHYLSA - Children’s and Youth Literature Sentiment Analysis“</p> <p>Online:</p> <ol> <li><a href="https://gepris.dfg.de/gepris/projekt/424250469">https://gepris.dfg.de/gepris/projekt/424250469</a></li> <li><a href="https://dfg-spp-cls.github.io/projects_en/2020/01/24/TP-CHYLSA/">https://dfg-spp-cls.github.io/projects_en/2020/01/24/TP-CHYLSA/</a></li> </ol>
Expression of mgtA encoding a magnesium transporter is activated in the absence of the main Mg2+ transporter CorA in Salmonella
<p><i>Salmonella</i> imports magnesium via three known transporters, the widely conserved CorA transporter and the MgtA and MgtB P-type ATPases. CorA is expressed under various growth conditions whereas the other two magnesium transporters, MgtA and MgtB, are expressed under conditions of magnesium starvation under the positive control of the PhoP-PhoQ regulatory system. <br>Our recent results suggest that production of MgtA, but not that of MgtB, is activated in the absence of the main Mg2+ transporter CorA (Metaane <i>et al </i>2022, 2023 ) <br>This hypothesis was further validated in this study by using transcriptional and translational <i>lacZ </i>fusions in the <i>mgtA </i>and <i>mgtB</i> genes. In addition, our data suggest that regulation of expression of MgtA in the absence of CorA is post-transcriptional . </p><p><strong>This work was supported by the French National Research Agency (ANR-19-CE44-0005-01, PERIOMET project).</strong> </p><p>Metaane S, Monteil V, Ayrault S, Bordier L, Levi-Meyreuis C, Norel F. The stress sigma factor sigmaS/RpoS counteracts Fur repression of genes involved in iron and manganese metabolism and modulates the ionome of <i>Salmonella enterica </i>serovar Typhimurium. PLoS One 2022;17(3):e0265511.</p><p>Metaane S, Monteil V, Douché T, Giai Gianetto Q, Matondo M, Maufrais C, Norel F. Loss of CorA, the primary magnesium transporter of <i>Salmonella, </i>is alleviated by MgtA and PhoP-dependent compensatory mechanisms. PLoS One 2023;18(9):e0291736.</p><p> </p>
Global effects of deletion of the sdh genes, encoding succinate dehydrogenase, and of cobalt on protein abundance in stationary phase Salmonella enterica serovar Typhimurium.
<p>A common strategy that bacteria utilize to increase their survival under stressful conditions in their natural environments, including antibiotic treatment, is the entry into quiescence, a state of reversible cell growth arrest that offers protection against many environmental insults. Understanding quiescence is an important fundamental question, with relevance in the medical and environmental fields. Little is known about the molecular and physiological determinants that orchestrate survival during this temporary arrest of proliferation, or those that allow a rapid transition back to the proliferating state when conditions again become favorable. In the wide host-range pathogen <em>Salmonella enterica</em> serovar Typhimurium (S. Typhimurium) and other Gram-negative bacteria, this temporary arrest of proliferation induces the expression of the alternative sigma subunit of RNA polymerase, σS/RpoS, which remodels global gene expression to reshape the cell physiology and ensure survival under starvation and various stress conditions (<em>i.e</em>., the general stress response). One important aspect of persistence is the phenotypic differentiation of quiescent populations into sub-population(s) of "persisters" that survive in the presence of lethal concentrations of antibiotics. This phenomenon is worsening the worldwide antibiotic crisis, by causing therapy failure and chronic infections and potentially favoring the development of antibiotic resistance. Understanding mechanisms governing bacterial persisters is thus an important topic and a key issue for drug developments. However, despites many studies, the physiological and molecular mechanisms controlling the formation of persisters are poorly understood and controversial.</p> <p>We have recently discovered an unexpected functional interaction between σS and succinate dehydrogenase (Sdh) in the formation of persisters. Succinate dehydrogenase (Sdh), a membrane bound complex that connects the TCA cycle and respiratory chain, is one major target down regulated by σS (Levi-Meyrueis <em>et al</em>. 2014, 2015, Lago <em>et al.</em> 2017). Stationary-phase <em>Salmonella</em> grown in LB rich medium form persisters with a higher frequency than actively growing bacteria, after transfer to fresh LB medium in the presence of lethal concentrations of ampicillin and ciprofloxacin, but not significant effect of the Δ<em>rpoS</em> mutation on this phenomenon was observed. Surprisingly however, the Δ<em>rpoS</em> mutation suppressed the defect in persister formation of a Δ<em>sdh </em>mutant. It is very likely that the Δ<em>rpoS</em> mutation compensates for a metabolic perturbation provoked by the Δ<em>sdh </em>mutation, and key for persister formation.</p> <p>To get further insights into the synthetic rescue process involved in persisters formation, we used a mass spectrometry-based proteomics approach to compare the proteome of the wild-type, Δ<em>rpoS</em>, Δ<em>sdh</em> and Δ<em>sdh</em>Δ<em>rpoS</em> strains grown to late stationary phase in nutrient-rich LB medium. Cells were also grown in LB supplemented with cobalt to pinpoint major changes induced by cobalt on the <em>Salmonella</em> proteome. Indeed, the synthetic rescue process involved in persisters formation in the presence of ampicillin was abolished when the inoculum has been grown in the presence of a non-lethal dose of cobalt (100 μM).</p> <p><strong>Accession number</strong>.The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier <strong>PXD043726.</strong></p> <p><strong>See also:</strong></p> <p>NOREL, F., & MONTEIL, V. (2023). Unraveling a synthetic rescue process involved in persisters formation [Data set]. Zenodo. https://doi.org/10.5281/zenodo.10277562</p> <p>Phégnon, L., Uttenweiler-Joseph, S., & Létisse, F. (2024). <span>Key physiological and metabolic characteristics for the differentiation of quiescent Salmonella's cells into persisters [Data set]. </span>Zenodo. <a href="https://doi.org/10.5281/zenodo.10885905" target="_blank" rel="noopener">https://doi.org/10.5281/zenodo.10885905</a></p> <p><strong>This work was supported by the French National Research Agency (ANR-19-CE44-0005-01, PERIOMET project).</strong></p> <p><strong>References</strong></p> <p>Levi-Meyrueis C, Monteil V, Sismeiro O, Dillies MA, Monot M, Jagla B<em>, et al. </em>Expanding the RpoS/sigmaS-network by RNA sequencing and identification of sigmaS-controlled small RNAs in <em>Salmonella</em>. PloS one. 2014;9(5):e96918.</p> <p>Levi-Meyrueis C, Monteil V, Sismeiro O, Dillies M-A, Kolb A, Monot M <em>et al</em>. Repressor activity of the RpoS/sigmaS-dependent RNA polymerase requires DNA binding. Nucleic Acids Res 2015 43, 1456–1468.</p> <p>Lago M, Monteil V, Douche T, Guglielmini J, Criscuolo A, Maufrais C, <em>et al</em>. Proteome remodelling by the stress sigma factor RpoS/sigma(S) in <em>Salmonella</em>: identification of small proteins and evidence for post-transcriptional regulation. Scientific reports. 2017;7(1):2127.</p> <p> </p>
Depolarization block in olfactory sensory neurons expands the dimensionality of odor encoding
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Enhancing two-dimensional control via single-channel haptic feedback: A multi-dimensional encoding strategy
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Network-level encoding of local neurotransmitters in cortical astrocytes
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Data from: Learning of probabilistic punishment as a model of anxiety produces changes in action but not punisher encoding in the dmPFC and VTA
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Data from: Gesture encoding in human left precentral gyrus neuronal ensembles
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Annotation of genes encoding enzymes across marine phytoplankton genomes
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Sound improves neuronal encoding of visual stimuli in mouse primary visual cortex
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Valence and salience encoding in the central amygdala
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Identification of candidate SNPs in the encoding region of two sugarcane cultivars as to resistance to water stress
<p>Identification of candidate SNPs in the encoding region of two sugarcane cultivars as to resistance to water stress</p>
Data from: Zebrafish retinal ganglion cells asymmetrically encode spectral and temporal information across visual space
<p>In vertebrate vision, the tetrachromatic larval zebrafish permits non-invasive monitoring and manipulating of neural activity across the nervous system in vivo during ongoing behaviour. However, despite a perhaps unparalleled understanding of links between zebrafish brain circuits and visual behaviours, comparatively little is known about what their eyes send to the brain via retinal ganglion cells (RGCs). Major gaps in knowledge include any information on spectral coding, and information on potentially critical variations in RGC properties across the retinal surface corresponding with asymmetries in the statistics of natural visual space and behavioural demands. Here, we use in vivo two photon (2P) imaging during hyperspectral visual stimulation as well as photolabeling of RGCs to provide a functional and anatomical census of RGCs in larval zebrafish. We find that RGCs' functional and structural properties differ across the eye and include a notable population of UV-responsive On-sustained RGCs that are only found in the acute zone, likely to support visual prey capture of UV-bright zooplankton. Next, approximately half of RGCs display diverse forms of colour opponency including many that are driven by a pervasive and slow blue-Off system - far in excess of what would be required to satisfy traditional models of colour vision. In addition, most information on spectral contrast was intermixed with temporal information. Taken together, our results suggest that zebrafish RGCs send a diverse and highly regionalised time-colour code to the brain.</p>
Data from: Decoding and encoding models reveal the role of mental simulation in the brain representation of meaning
<p>How the brain representation of conceptual knowledge vary as a function of processing goals, strategies and task-factors remains a key unresolved question in cognitive neuroscience. Here we asked how the brain representation of semantic categories is shaped by the depth of processing during mental simulation. Participants were presented with visual words during functional magnetic resonance imaging (fMRI). During shallow processing, participants had to read the items. During deep processing, they had to mentally simulate the features associated with the words. Multivariate classification, informational connectivity and encoding models were used to reveal how the depth of processing determines the brain representation of word meaning. Decoding accuracy in putative substrates of the semantic network was enhanced when the depth processing was high, and the brain representations were more generalizable in semantic space relative to shallow processing contexts. This pattern was observed even in association areas in inferior frontal and parietal cortex. Deep information processing during mental simulation also increased the informational connectivity within key substrates of the semantic network. To further examine the properties of the words encoded in brain activity, we compared computer vision models - associated with the image referents of the words - and word embedding. Computer vision models explained more variance of the brain responses across multiple areas of the semantic network. These results indicate that the brain representation of word meaning is highly malleable by the depth of processing imposed by the task, relies on access to visual representations and is highly distributed, including prefrontal areas previously implicated in semantic control.</p>
Oral Music of the Maghreb and the Mashriq and the digital encoding of scores / transcriptions
<p>2<sup>nd</sup> Lecture</p>
The encoding of stochastic regularities is facilitated by action-effect predictions
<p>The data represent the raw EEG datasets generated and analysed during the current study, along with the Principal Component Analysis (PCA) solutions computed for the active and passive tasks, respectively. For details regarding the EEG preprocessing, statistical analyses, and results, please refer to the main manuscript body.</p>
Encoding and control of airflow orientation by a set of Drosophila fan-shaped body neurons
<p class="Body"><span><span><span><span><span><span><span><span><span><span>The insect Central Complex (CX) is thought to underlie goal-oriented navigation but its organization is still not fully understood. We recorded from genetically-identified CX cell types in <i>Drosophila</i> and presented directional visual, olfactory, and airflow cues known to elicit orienting behavior. We found that a group of neurons targeting the ventral fan-shaped body (ventral P-FNs) are robustly tuned for airflow direction. Ventral P-FNs did not generate a "map" of airflow direction. Instead, cells in each hemisphere were tuned to 45° ipsilateral, forming a pair of orthogonal bases. Imaging experiments suggest that ventral P-FNs inherit their airflow tuning from neurons that provide input from the lateral accessory lobe (LAL) to the noduli (NO). Silencing ventral P-FNs prevented flies from selecting appropriate corrective turns following changes in airflow direction. Our results identify a group of central complex neurons that robustly encode airflow direction and are required for proper orientation to this stimulus.</span></span></span></span></span></span></span></span></span></span></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.