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21,320 results for “Transcription”
Data from: Gene transcription in sea otters (Enhydra lutris): development of a diagnostic tool for sea otter and ecosystem health
Gene transcription analysis for diagnosing or monitoring wildlife health requires the ability to distinguish pathophysiological change from natural variation. Herein we describe methodology for the development of quantitative real time polymerase chain reaction (qPCR) assays to measure differential transcript levels of multiple immune-function genes in the sea otter (Enhydra lutris); sea otter specific, qPCR primer sequences for the genes of interest are defined. We establish a "reference" range of transcripts for each gene in a group of clinically healthy captive and free-ranging sea otters. The 10 genes of interest represent multiple physiological systems that play a role in immuno-modulation, inflammation, cell protection, tumor suppression, cellular stress-response, xenobiotic metabolizing enzymes, antioxidant enzymes, and cell-cell adhesion. The cycle threshold (CT) measures for most genes were normally distributed; the complement cytolysis inhibitor was the exception. The relative enumeration of multiple gene transcripts in simple peripheral blood samples expands the diagnostic capability currently available to assess the health of sea otters in situ and provides a better understanding of the state of their environment.
Data from: Gene duplication and co-evolution of G1/S transcription factors specificity in fungi are essential for optimizing cell fitness
Transcriptional regulatory networks play a central role in optimizing cell survival. How DNA binding domains and cis-regulatory DNA binding sequences have co-evolved to allow the expansion of transcriptional networks and how this contributes to cellular fitness remains unclear. Here we experimentally explore how the complex G1/S transcriptional network evolved in the budding yeast Saccharomyces cerevisiae by examining different chimeric transcription factor (TF) complexes. Over 300 G1/S genes are regulated by either one of the two TF complexes, SBF and MBF, which bind to specific DNA binding sequences, SCB and MCB, respectively. Our data suggests that whilst SBF is the likely ancestral regulatory complex, the ancestral DNA binding element is more MCB-like. G1/S network expansion took place by both cis- and trans- co-evolutionary changes in closely related but distinct regulatory sequences. Replacement of the endogenous SBF DNA-binding domain (DBD) with that from more distantly related fungi leads to a contraction of the G1/S network in budding yeast, which also correlates with increased defects in cell growth, cell size, and proliferation. This indicates that expansion of the G1/S network in budding yeast may represent an evolutionary product of selection for cell cycle fitness.
ArsR transcriptional regulator mediated attenuated mechanism by regulating self and outer membrane protein in Brucella
<p><span>The ArsR family transcriptional regulators are widely distributed in microorganisms, including in the important intracellular pathogen <i>Brucella</i>. ArsR proteins are implicated in numerous biological processes. However, the specific roles of ArsR family members in <i>Brucella</i> remain obscure. Here we show that ArsR3 (BSS2_RS07325) is required for <i>Brucella</i> survival both under stress <i>in vitro</i> conditions and in a murine infection model<i> in vivo</i>. ArsR3 autoregulate its own expression to maintain metal ion homeostasis to benefit bacterial survival. Moreover, ArsR3 also regulates the production of virulence factor outer membrane protein 25D (Omp25D) which is key for the survival of <i>Brucella</i> under stress conditions. Significantly, ArsR3 deletion strain attenuated in a murine infection model<i> in vivo</i>. Altogether, our findings reveal a unique mechanism in which the ArsR family member ArsR3 autoregulates its expression and also modulates Omp25D expression to maintain metal ion homeostasis and virulence in <i>Brucella</i>.</span></p>
Piecemeal regulation of convergent neuronal lineages by bHLH transcription factors in Caenorhabditis elegans
<p>Image volumes and annotations for lin-32; NeuroPAL mutants.</p> <p>The following image volumes and their annotations are provided for:<br> "Piecemeal regulation of convergent neuronal lineages by bHLH transcription factors in Caenorhabditis elegans".</p> <p>The publication is available here:<br> https://journals.biologists.com/dev/article-abstract/148/11/dev199224/269057/Piecemeal-regulation-of-convergent-neuronal</p> <p>These image files can be viewed with the NeuroPAL ID software, available at:<br> https://www.hobertlab.org/neuropal/<br> OR<br> https://github.com/amin-nejat/CELL_ID</p> <p>This software was provided for the NeuroPAL publication, "NeuroPAL: A Multicolor Atlas for Whole-Brain Neuronal Identification in C. elegans".<br> The publication is available here:<br> https://www.cell.com/cell/fulltext/S0092-8674(20)31682-2</p> <p>Please cite the NeuroPAL publication when using the software.</p>
Transcription of Physical Properties Data Compilations Relevant to Energy Storage: I. Molten Salts: Eutectic Data
<p>Transcription of Physical Properties Data Compilations Relevant to Energy Storage: I. Molten Salts: Eutectic Data. This is a large dataset of eutectic mixtures originally compiled and published in 1978. There was not previously a machine-readable version of this dataset. We have transcribed the 2-component mixtures into csv format. We have also included 6 basic features that are widely available on Pubchem for the individual components in the mixtures, and a list of components that were not available via Pubchem.</p>
Japhug for Natural Language Processing: a single-speaker audio corpus with transcriptions
<p><em>(français ci-dessous)</em></p> <p>This archive contains a dataset (audio files and transcriptions) of a minority language, Japhug (Glottocode: japh1234; closest iso 639-3 code: jya). The archive contains a subset of the Japhug corpus of the Pangloss Collection: it is a single-speaker corpus, consisting of all the audio resources transcribed, for the main speaker of this corpus (Ms. Tshendzin).<br> The corpus is versioned, so that the experiments carried out on these resources (for linguistic research or for Natural Language Processing) are fully reproducible. All relevant information is contained in YAML files (.yml extension; one in French, one in English).<br> The data sub-folder contains the converted and demultiplexed audio files, as well as the annotations associated with each channel of the audio files.<br> The summary files contain, among other things, the list of graphemes used in the language (complex graphemes are particularly important), as well as information on the various resources (audio and annotations), such as their identifiers (DOIs) and links to the original files.<br> From a computational point of view, the list of DOIs of the audios and annotations described in this YAML file is sufficient to generate this corpus at a given time. A corpus like the present one can be viewed as the version, at a given time, of a set of documents in the Pangloss collection: a corpus as it stands at a precise version.</p> <p>Further information is available from <a href="https://gitlab.com/lacito/outilspangloss">https://gitlab.com/lacito/outilspangloss</a></p> <p>---------------</p> <p>Cette archive contient un jeu de données (audios et transcriptions) d’une langue à tradition orale, le japhug (Glottocode: japh1234; code iso 639-3 le plus proche : jya). L’archive contient un sous-ensemble du corpus japhug de la collection Pangloss : c’est un corpus monolocuteur, constitué de l’intégralité des ressources audio transcrites pour la locutrice principale de ce corpus (Mme Tshendzin).<br> Le corpus est versionné, de sorte que les expériences menées sur ces ressources (pour la linguistique ou pour le Traitement automatique des langues) soient reproductibles de façon exacte (en pensant bien à joindre l’algorithme : paramètres, répartitions des fichiers dans les différents ensembles, etc.). Toutes les informations pertinentes se trouvent dans les fichiers YAML (extension .yml ; un en français, un autre en anglais).<br> Le sous-dossier des données contient d’une part les audios convertis et démultiplexés et d’autre part les annotations associées à chaque canal desdits audios.<br> Les fichiers récapitulatifs contiennent notamment la liste des graphèmes utilisés dans cette langue (les graphèmes complexes sont particulièrement importants), ainsi que des informations sur les différentes ressources (audios et annotations), comme les identifiants (DOI), les liens vers les fichiers originaux, etc.<br> Au plan informatique, la liste des identifiants DOI des audios et annotations décrits dans ce fichier YAML suffit pour générer ce corpus à un instant t. Un corpus comme celui-ci peut être vu comme la version à l’instant t d’un ensemble de documents de la collection Pangloss : un corpus arrêté à une version précise.<br> Pour plus de précisions : <a href="https://gitlab.com/lacito/outilspangloss">https://gitlab.com/lacito/outilspangloss</a></p>
D2.1 - Demonstrator baseline and market characteristics report - Transcripts of interviews with a German company
<p>This is the transcript of the interviews with a German company for D2.1 "Demonstrator baseline and market characteristics report" defining the current baseline and the target/improved circular business models for two demonstrators and analyzing both demonstrators´ market characteristics and their impact on the target circular business models.</p>
Conserved and cell type-specific transcriptional responses to IFN-γ in the ventral midbrain
<p>FISH image quantification and pSTAT1-Y701 analysis of fig.4 </p>
Supporting Data - Temperature and immunostimulants modulate transcription of the ubiquitin and apoptosis pathways in the Antarctic Harpagifer antarcticus and sub-Antarctic Harpagifer bispinis
<p>C<sub>t</sub> values obtained from Real-Time PCR (<em>ß-ACTIN</em>, <em>UBE3</em>, <em>SMAC/DIABLO</em> and <em>BAX</em> genes) of cDNA from liver, gills and spleen of <em>Harpagifer antarcticus</em> and <em>Harpagifer bispinis</em> fish stimulated with LPS, Poly I:C or non-stimulated (control, PBS-injected) under three temperatures (2, 5 and 8°C).</p>
Enhancing MovieLens Dataset: Enriching Recommendations with Audio Information, Transcriptions, and Metadata
<p>Nowadays, there are lots of datasets available for training and experimentation in the field of recommender systems. Specifically, in the recommendation of audiovisual content, the MovieLens dataset is a prominent example. It is focused on the user-item relationship, providing actual interaction data between users and movies. However, although movies can be described with several characteristics, this dataset only offers limited information about the movie genres. </p> <p>In this work, we propose enriching the MovieLens dataset by incorporating metadata available on the web (such as cast, description, keywords, etc.) and movie trailers. By leveraging the trailers, we extract audio information and generate transcriptions for each trailer, introducing a crucial textual dimension to the dataset. The audio information was extracted by the waveform and frequency analysis, followed by the application of dimensionality reduction techniques. For the transcription generation, the deep learning model Whisper was used. Finally, metadata was obtained from TMDB, and the BERT model was applied to extract embeddings.</p> <p>These additional attributes enrich the original dataset, providing deeper and more precise analysis. Then, the use of this extended and enhanced dataset could drive significant advancements in recommendation systems, enhancing user experiences by providing more relevant and tailored movie recommendations based on their tastes and preferences. </p>
Genome-wide analysis reveals extensive functional interaction between DNA replication initiation and transcription in the genome of Trypanosoma brucei
<p>Raw ChIP-chip and MFA-seq data from the paper listed above.</p>
Fig. 9. SmbHLH3 binding with the G in SmbHLH3 acts as a transcription repressor for both phenolic acids and tanshinone biosynthesis in Salvia miltiorrhiza hairy roots
Fig. 9. SmbHLH3 binding with the G-box motifs of the TAT, HPPR, KSL1and CYP76AH1.
Molecular mechanisms of regulation by a β-alanine-responsive Lrp-type transcription factor from Acidianus hospitalis
<p>This dataset contains the raw data that lie at the basis of the results discussed in <strong>Chapter 5: Molecular mechanisms of regulation by a β-alanine-responsive Lrp-type transcription factor from Acidianus hospitalis </strong>of the PhD thesis of Amber Bernauw. This chapter is also published as an article at MicrobiologyOpen (<a href="https://doi.org/10.1002/mbo3.1356">https://doi.org/10.1002/mbo3.1356</a>).</p>
Raw data - Digital scans - Sepsis Induces Heterogeneous Transcription of Coagulation- and Inflammation-Associated Genes in Renal Microvasculature
<p>Raw data of the manuscript "<em>Sepsis Induces Heterogeneous Transcription of Coagulation- and Inflammation-Associated Genes in Renal Microvasculature</em><em>"</em> as published in Thrombosis Research (<a href="https://doi.org/10.1016/j.thromres.2024.03.014" target="_blank" rel="noopener">doi.org/10.1016/j.thromres.2024.03.014</a>) is included. Types of included data are:</p> <p> </p> <p>- NDPI files of digital scans showing immunohistochemical (IHC) protein staining in mouse kidney</p> <p>- NDPI files of digital scans showing Martius Scarlet Blue staining (MSB) in mouse kidney</p>
Peripheral and Intrarenal B Cell Study in Antibody Mediated Transplant Rejection : Phenotypic and Transcriptional Study, Study of Reactivity
ClinicalTrials.gov study NCT07134491. IPD Sharing: YES. Countries: 1. Publications: 0.
Effects of the Anti-HIV Pill Truvada on Gene Transcription in the Gastrointestinal Tract of HIV-uninfected Individuals
ClinicalTrials.gov study NCT02621242. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Chronic Obstructive Pulmonary Disease Transcription Factor and Cytokine Study
ClinicalTrials.gov study NCT02557958. IPD Sharing: Not stated. Countries: 0. Publications: 1.
T Cell Receptor (TCR) Sequencing and Transcriptional Profiling in Adult Celiac Disease Patients Undergoing Gluten Challenge
ClinicalTrials.gov study NCT04614571. IPD Sharing: YES. Countries: 1. Publications: 0.
Data from: The contributions of sex, genotype and age to transcriptional variance in Drosophila melanogaster
Open the record for dataset details and reuse information.
Data from: Characterization of Arabidopsis transcriptional responses to different aphid species reveals genes that contribute to host susceptibility and non-host resistance
Open the record for dataset details and reuse information.
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