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22,597 results for “Regulation”
Model output from "Potential impacts of marine fuel regulations on an Arctic stratocumulus case and its radiative response"
<p>Model output from "Potential impacts of marine fuel regulations on an Arctic stratocumulus case and its radiative response", in review at Atmospheric Chemistry and Physics, 2024, same authors.<br>The simulations were done using MIMICA version 4 (Savre at el., 2014) and the data includes all model output presented in the publication.</p>
Data from: Repairing a deleterious domestication variant in a floral regulator of tomato by base editing
<p>This repository contains the data necessary to run the analysis described in the publication "Repairing a deleterious domestication variant in a floral regulator of tomato by base editing" by Glaus et al., 2024. A preprint is available on bioRxiv (doi: <a href="https://doi.org/10.1101/2024.01.29.577624" rel="nofollow">https://doi.org/10.1101/2024.01.29.577624</a>)</p> <p> </p> <p>82_acc_Spim0.1_filtered.vcf.gz -- variant call results for 82 genomes with LA1589 as reference</p> <p>82_acc_Spim0.1_filtered_SIFT_out.tar.gz -- sift4g prediction results for 82 genomes with LA1589 as reference (SIFTannotations.xls and SIFTpredictions.list)</p> <p>sift_lib_LA1589.tar.gz -- sift4g library for the LA1589 genome</p> <p>SolpimLA1589_liftoff.tar.gz -- liftoff annotation of LA1589 genome</p> <p> </p> <p>In case of any questions, please contact Sebastian Soyk (sebastian.soyk@unil.ch)</p>
Phosphorylation regulated conformational diversity and topological dynamics of an intrinsically disordered nuclear receptor
<p>Molecular dynamics simulations of AF1c region of human glucocorticoid receptor and its phosphovariants as described in the below paper: </p> <p>Phosphorylation regulated conformational diversity and topological dynamics of an intrinsically disordered nuclear receptor</p> <p>Vasily Akulov, Alba Jiménez Panizo, Eva Estébanez-Perpiñá, John van Noort, Alireza Mashaghi</p> <p> </p> <p>The data related to this project has been deposited in two repositories. This repository contains the second part of the data; the first part can be found at DOI: 10.5281/zenodo.13820169</p>
Hepatic transcriptomic analysis reveals differential regulation of metabolic and immune pathways in three strains of chickens with distinct growth rate exposed to mixed parasites infections
<p><span>This dataset was generated from the study investigating hepatic gene expression in three strains of chickens: Ross-308 (R), Lohmann Brown Plus (LB), and Lohmann Dual (LD), 2 weeks after either an experimental infection (n = 18) with both <em>A. galli</em> and <em>H. gallinarum or kept as uninfected control (n = 12)</em>. </span></p>
Supplemental Data to PhD Dissertation entitled "Non-Coding and Epigenetic Regulators of Ambient Temperature Sensitive Flowering"
<p>Supplemental Data to the PhD dissertation entitled "Non-Coding and Epigenetic Regulators of Ambient Temperature Sensitive Flowering" from Suze Blom, Wageningen University & Research (doi:10.18174/670822). Supplementary data to the chapter entitled "Ambient temperature dependent changes in DNA methylation in Arabidopsis thaliana Col-0 and the decrease in DNA methylation 1 mutant" [manuscript in preparation]</p> <p>Includes Supplemental Data:</p> <p>Supplementary Data 1: Significantly differently expressed (DE) genes in Col-0 after the 24 hour ambient temperature switch from 16°C to 25°C. padj value of 0.05 was set as the cutoff value for statistical significance.</p> <p>Supplementary Data 2: Significantly differently expressed (DE) genes in ddm1-10 after the 24 hour ambient temperature switch from 16°C to 25°C. padj value of 0.05 was set as the cutoff value for statistical significance.</p> <p>Supplementary Data 3: Alternative splicing (AS) of transcripts after an ambient temperature change from 16°C to 25°C in Col-0. Gene ID, splicing event, genomic location, AS frequency and padj values are indicated.</p> <p>Supplementary Data 4: Alternative splicing (AS) of transcripts after an ambient temperature change from 16°C to 25°C in ddm1-10. Gene ID, splicing event, genomic location, AS frequency and padj values are indicated.</p> <p>Supplementary Data 5: List of genes in Col-0 (sheet 1) and ddm1-10 (sheet 2) with both significant AS and DMC associated with them. Gene ID and number of DMCs associated with the gene are indicated.</p>
Supplementary movies for: "The mammalian membrane microenvironment regulates the sequential attachment of bacteria to host cells"
<p><strong>Supplementary Movie 1: Live visualization of bacterial attachment to host cells. </strong></p> <p>Microscopic visualizations of <em>E. coli</em> VHH adhesion to HeLa GFP. Maximum intensity projection of a 1-hour confocal microscopy time-lapse at 0.1 fps accelerated 100x. Overlay of bacteria (red) location of initial contact (circles) and their corresponding tracks (colored lines). Scale bar: 50 µm.</p> <p> </p> <p><strong>Supplementary Movie 2: High-speed visualization of bacterial attachment to host cells upon contact.</strong></p> <p>Close-up on microscopic visualizations of <em>E. coli</em> VHH <em>E. coli</em> adhesion to HeLa GFP. Maximum intensity projection of 5-minutes confocal microscopy time-lapses at 1 fps accelerated 10x. Overlay of bacteria (red) location of initial contact (circles) and their corresponding tracks (colored lines).</p> <p> </p> <p><strong>Supplementary Movie 3: Attachment of <em>E. coli</em> VHH to GFP-coated coverslips. </strong></p> <p><em>E. coli</em> VHH in flow binding to the edge of a GFP-functionalized coverslip used as a substrate for a microfluidic channel. Maximum intensity projection of 5-minutes confocal microscopy time-lapse at 1 fps accelerated 10x. Scale bar: 50 µm.</p> <p> </p> <p><strong>Supplementary Movie 4: HeLa GFP cells actively pull bacteria towards their cell body. </strong></p> <p>Maximum intensity projection of a confocal time-lapse experiment at 0.1 fps accelerated 100x of <em>E. coli</em> VHH (red), HeLa GFP (CD80) (green) and 3 mm/s flow. Scale bar: 10 µm.</p> <p> </p> <p><strong>Supplementary Movie 5: Bacteria sequester GFP upon attachment. </strong></p> <p>Maximum intensity projection of 20-minutes epifluorescence microscopy time-lapse at 1 frame per minutes accelerated 60x. <em>E. coli</em> VHH were added on HeLa GFP under static conditions at an MOI of 200 for a couple of minutes and washed 3 times before imaging. Scale bar: 10 µm.</p> <p> </p> <p><strong>Supplementary Movie 6: Flagella promote unspecific transient binding. </strong></p> <p>Maximum intensity projection of a confocal time-lapse experiment at 6 frames per minutes accelerated 100x of flagellated <em>E. coli</em> VHH (red), HeLa GFP (CD80) (green) and 3 mm/s flow. Scale bar: 10 µm.</p>
Multi-disciplinary survey data for the assessment of regulating and recreational ecosystem services in urban parks under heat and drought conditions
<p>The research group GreenEquityHEALTH provides quantified knowledge on how urban green spaces contribute to the mitigation of climate change induced challenges and challenges from urbanization to improve health, well-being and environmental justice. The project identifies the mediating pathways or direct effects of divers urban green spaces that act to either promote health, encourage healthy behaviours like social interaction or physical activity, or to decrease risk factors such as air pollution or urban heat.</p> <p>Here we present core data of our interdisciplinary multi-method campaigns that included in-situ stationary and aerial (remote sensing-based) environmental measurements, mobile air quality measurements, and social science-informed surveys, namely, park vistor observations and countings and a questionnaire survey.</p> <p><strong>List of data and content</strong></p> <ul> <li>Aarial_survey: digital surface model, orthophoto and thermal infrared images as raster files (*.tif); flight and processing report (*.pdf)</li> <li>Air_quality: stationary PM measurement data (*.csv); coordinates (*.txt)</li> <li>Meteorology: stationary air temperature and humidity data (*.csv), sensor meta data (*.csv)</li> <li>ParkVisitor_Surveys: survey data and questionnaire replies (*.csv), survey sheets (*.docx), questionnaire form (*.pdf)</li> </ul> <p><strong>Data acquisition and processing</strong></p> <p>For details on the data (e.g. sensors, calibration, survey settings) please refer to the linked publication, incl. Supplementary Material.</p> <p><strong>Acknowledgments</strong><br> We would like to thank the City of Leipzig, Department for Urban Green and Waters, for supporting the project. We would like to thank Henrique Miguel Pereira (Head of Research Group Biodiversity Conservation of the German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig) for providing equipment for the meteorological field campaigns. We also thank Anhalt University of Applied Sciences, Institute of Geoinformation and Surveying with Lutz Bannehr for conducting the airborne campaigns, Marco Pohle and Helko Kotas (both Helmholtz Centre for Environmental Research - UFZ) for technical support, and Judith Rakowski for support during the field surveys. This work was carried out within the research project ‘Environmental-health Interactions in Cities<br> (GreenEquityHEALTH) – Challenges for Human Wellbeing under Global Changes’ (2017 to 2022) funded by the German Federal Ministry of Education and Research (BMBF), funding code: 01LN1705A.</p> <p><strong>Related publication</strong><br> Kabisch, N. et al. (2021). A methodological framework for the assessment of regulating and recreational ecosystem services in urban parks under heat and drought conditions. <em>Ecosystems and People</em>. <a href="https://doi.org/10.1080/26395916.2021.1958062">doi:10.1080/26395916.2021.1958062</a></p>
Supplementary data and simulation code - "ADCY10 is a key regulator of cell cycle control"
<p>Experimental FACS data of cell cycle analysis: The folder raw_data_FACS contains the FACS data for different concentrations of bicarbonate (hco3-_rawdata_all2.csv) and for the KH7 experiments (kh7_rawdata_all.csv). The folder summarized_data_input4analysis contains the csv-files that where used for the Bayesian analysis of cell cycle control. Details are given in the headings of the files.</p> <p>We also set up a webpage, where simulations of the suggested mathematical model of the cell cycle can be performed:</p> <p><a href="https://cellcycle-simulation2.herokuapp.com/">https://cellcycle-simulation2.herokuapp.com/</a></p> <p>The results may be used for prediction or experimental design.</p> <p> </p>
Fig. 4 in Spatial and temporal distribution patterns of ichthyoplankton in a region affected by water regulation by dams
Fig. 4. Average abundance of fish eggs (a) and larvae (b) in the Ilha Grande National Park, from October 2001 to March 2005.
Fig. 2 in Spatial and temporal distribution patterns of ichthyoplankton in a region affected by water regulation by dams
Fig. 2. Average egg abundances (rectangles) and standard errors (bars) by period (a), month (b) and sampling area (c) in the Ilha Grande National Park, from October 2001 to March 2005.
RNA-seq data of "Transcriptome analyses of leaves reveal that hexanoic acid priming differentially regulate gene expression in contrasting Coffea arabica cultivars"
<p>This dataset represent FASTQ gziped files from the study "Transcriptome analyses of leaves reveal that hexanoic acid priming differentially regulate gene expression in contrasting <em>Coffea arabica</em> cultivars" (<a href="https://doi.org/10.3389/fsufs.2021.735893">https://doi.org/10.3389/fsufs.2021.735893</a>). Sequencing was done using an Illumina Novaseq 6000 instrument, paired-sequencing (2 X150 bp). Sample details are also available at https://www.ebi.ac.uk/ena/browser/view/ERA6282544.</p> <p> </p> <p>All filenames have the following naming scheme:</p> <p>LCS7609_DS_AAA_leafBBB_(R1 or R2).fq.gz</p> <p>AAA stands for the abbreviations:</p> <p>- CC (Coffea arabica cv Catuai control)</p> <p>- CHx (Coffea arabica cv Catuai exposed to Hexanoic acid)</p> <p>- OC (Coffea arabica cv Obatã control)</p> <p>- OHx (Coffea arabica cv Obatã exposed to Hexanoic acid)</p> <p>BBB stands for the number of biological replicate (1, 2 or 3).</p> <p> </p> <p> </p> <p> </p>
Data from: Ecological and social pressures interfere with homeostatic sleep regulation in the wild
<p>Sleep is fundamental to the health and fitness of all animals. The physiological importance of sleep is underscored by the central role of homeostasis in determining sleep investment – following periods of sleep deprivation, individuals experience longer and more intense sleep bouts. Yet, most sleep research has been conducted in highly controlled settings, removed from evolutionarily-relevant contexts that may hinder the maintenance of sleep homeostasis. Using tri-axial accelerometry and GPS to track the sleep patterns of a group of wild baboons (<i>Papio anubis</i>), we found that ecological and social pressures indeed interfere with homeostatic sleep regulation. Baboons sacrificed time spent sleeping when in less familiar locations and when sleeping in proximity to more group-mates, regardless of how long they had slept the prior night or how much they had physically exerted themselves the preceding day. Further, they did not appear to compensate for lost sleep via more intense sleep bouts. We found that the collective dynamics characteristic of social animal groups persist into the sleep period, as baboons exhibited synchronized patterns of waking throughout the night, particularly with nearby group-mates. Thus, for animals whose fitness depends critically on avoiding predation and developing social relationships, maintaining sleep homeostasis may be only secondary to remaining vigilant when sleeping in risky habitats and interacting with group-mates during the night. Our results highlight the importance of studying sleep in ecologically relevant contexts, where the adaptive function of sleep patterns directly reflects the complex trade-offs that have guided its evolution.</p>
Tyrosine-protein kinase Yes controls endothelial junctional plasticity and barrier integrity by regulating VE-cadherin phosphorylation and endocytosis
<p><strong>Abstract</strong></p> <p>Vascular endothelial (VE)-cadherin in endothelial adherens junctions is an essential component of the vascular barrier, critical for tissue homeostasis and implicated in diseases such as cancer and retinopathies. Inhibitors of Src cytoplasmic tyrosine kinase have been applied to suppress VE-cadherin tyrosine phosphorylation and prevent excessive leakage, edema and high interstitial pressure. Here we show that the Src-related Yes tyrosine kinase, rather than Src, is localized at endothelial cell (EC) junctions where it becomes activated in a flow-dependent manner. EC-specific <em>Yes1</em> deletion suppresses VE-cadherin phosphorylation and arrests VE-cadherin at EC junctions. This is accompanied by loss of EC collective migration and exaggerated agonist-induced macromolecular leakage. Overexpression of <em>Yes1</em> causes ectopic VE-cadherin phosphorylation, while vascular leakage is unaffected. In contrast, in EC-specific Src-deficiency, VE-cadherin internalization is maintained, and leakage is suppressed. In conclusion, Yes-mediated phosphorylation regulates constitutive VE-cadherin turnover, thereby maintaining endothelial junction plasticity and vascular integrity.</p> <p><strong>Method for retinal EC distribution analysis</strong></p> <p>Chimeric recombination was induced in iSuRe-Cre+ mice at P3 by i.p. injection of tamoxifen (100 µg/mouse, Sigma). Retinas were taken at P7 and P15, immunostained for CD31 and flat-mounted. Images were taken by z-stack tile scanning using a 10X objective on a confocal microscope (Leica SP8). Maximum intensity projection images of whole retinas were used for image segmentation, which was performed with ImageJ resources. The maximum projection of the MbTomato channel threshold was established to distinguish MbTomato+ cells from the background. Outliers with a radius between 0.2-1.0 µm were removed. The CD31 channel (after maximum projection) was used to define the outlines of veins and arteries; the optic nerve was used as a mask to define a referential system. For computational analysis, a bespoken Python-based workflow was employed, accessible on GitHub (https://github.com/wgiese/retina-vein-artery-cs). For every pixel in the image, three numbers were computed (using the mask as referential): (1) distance to the nearest vein (d<sub>v</sub>), (2) distance to the nearest artery (d<sub>a</sub>) and (3) radial distance to the optic nerve (r). From these measures, the relative distances by ϕ<sub>v-a</sub> = d<sub>v/</sub>(d<sub>v</sub> + d<sub>a</sub>) were obtained. The EC distribution was computed by performing the operation for all YFP-positive pixels, which were used as a proxy for EC distribution. A kernel density estimation was used to approximate the underlying EC distribution in the 2D coordinate system spanned by ϕ<sub>v-a</sub> and r. </p>
Data for: Reciprocal cortico-amygdala connections regulate prosocial and selfish choices in mice
<p><span>Decisions that favor one's own interest versus the interest of another individual depend on context and the relationships between individuals. The neurobiology underlying selfish choices or choices that benefit others is not understood. We developed a two-choice social decision-making task in which mice can decide whether or not to share a reward with their conspecifics. Preference for altruistic choices was modulated by familiarity, sex, social contact, hunger, hierarchical status, and emotional state matching. Fiber photometry recordings and chemogenetic manipulations demonstrated that BLA neurons are involved in the establishment of prosocial decisions. In particular, BLA neurons projecting to the prelimbic region (PL) of the PFC mediated the development of a preference for altruistic choices, whereas PL projections to the BLA modulated self-interest motives on decision-making. This provides a neurobiological model of altruistic and selfish choices with relevance to pathologies associated with dysfunctions in social decision-making.</span></p>
Immune checkpoint molecule TIGIT regulates kidney T cell functions and mediates acute kidney injury
<p>This dataset includes the single cell RNA-seq data associated with the publication listed in the title (abstract below).<br> <br> CellRanger.zip contains the raw transcript counts as produced by CellRanger. There is one folder per sample. The samples are indicated by the folder name (e.g. KO_Ctrl). <br> <br> We have also included .h5ad files that contain of cells that passed quality control, as described in the manuscript.<br> <br> adTIGIT_raw_031422.h5ad contains all passing cells and the raw counts, as well as cell annotations ('celltype')<br> <br> adTIGIT_Tonly_091421.h5ad contains only T cells, .X contains the normalized data and T-cell sub-type ('cluster').<br> <br> Abstract: T cells mediate pathologic and reparative processes during acute kidney injury (AKI) but exact mechanisms regulating kidney T cell functions are unclear. This study identified upregulation of the novel immune checkpoint molecule, TIGIT, on mouse and human kidney T cells following AKI. TIGIT-expressing kidney T cells produced proinflammatory cytokines and had effector and central memory phenotype. Kidney Tregs were predominantly TIGIT+ and reduced after ischemia reperfusion (IR) injury. TIGIT deficient mice had protection from both ischemic and nephrotoxic AKI. Single cell RNA sequencing led to discovery of possible downstream targets of TIGIT. TIGIT mediates AKI pathophysiology, is a promising target for developing AKI therapy, and is being increasingly studied in human cancer therapy trials.</p>
Real-time Automatic Temperature Regulation During In Vivo MRI-guided Laser Induced Thermotherapy (MR-LITT)
<p>This dataset is associated with the article.</p> <p>For each example (in vitro/in vivo), two matrices are provided, each containing :</p> <p>- coefficients estimation curves ;</p> <p>- automatic regulation curves and recontructed data (thermometry, phase, module) of the MRI sequence.</p>
De novo modelling of HEV replication polyprotein: Five-domain breakdown and involvement of flexibility in functional regulation - DATASET
<p>All models used for the paper "De novo modelling of HEV replication polyprotein: Five-domain breakdown and involvement of flexibility in functional regulation".</p>
Data for: "Market Power and Price Exposure: Learning from Changes in Renewable Energy Regulation"
<p>Given the key role of renewable energies in current and future electricity markets, it is important to understand how they affect firms' pricing incentives in these markets. In this paper, we study whether renewables depress electricity market prices, and how this effect depends on their degree of market price exposure. Our theoretical analysis shows that paying renewables with fixed prices, rather than with market-based prices, is relatively more effective at curbing market power when the dominant electricity firms own large shares of the renewable capacity, and <em>vice-versa</em>. To test this prediction, our empirical analysis leverages several short-lived changes to renewable energy pricing mechanisms in the Spanish electricity market. In this context, we find that the switch from full price exposure to fixed prices caused a 2-4% reduction in the average price-cost markup.</p>
Homeostatic regulation through strengthening of neuronal network correlated synaptic inputs
<p>Data from "Homeostatic regulation through strengthening of neuronal network correlated synaptic inputs" by Barnes SJ, Keller GB & Keck T.</p> <p> </p>
Chromosome-scale genome assembly and insights into the metabolome and gene regulation of leaf color transition in an important oak species, Quercus dentata
<p><em>Quercus dentata</em> Thunb., a dominant forest tree species in northern China, has significant ecological and ornamental value due to its adaptability and beautiful autumn coloration, with color changes from green to yellow into red resulting from the autumnal shifts in leaf pigmentation. However, the key genes and molecular regulatory mechanisms for leaf color transition remain to be investigated. First, we presented a high-quality chromosome-scale assembly for <em>Q. dentata</em>. This 893.54 Mb sized genome (contig N50=4.21 Mb, scaffold N50=75.55 Mb; 2n=24) harbors 31,584 protein-coding genes. Second, our metabolome analyses uncovered pelargonidin-3-O-glucoside, cyanidin-3-O-arabinoside, and cyanidin-3-O-glucoside as the main pigments involved in leaf color transition. Third, gene co-expression further identified the MYB-bHLH-WD40 (MBW) transcription activation complex as central to anthocyanin biosynthesis regulation. Notably, transcription factor (TF) <em>QdNAC </em>(<em>QD08G038820</em>) was highly co-expressed with this MBW complex and may regulate anthocyanin accumulation and chlorophyll degradation during leaf senescence through direct interaction with another TF, <em>QdMYB </em>(<em>QD01G020890</em>), as revealed by our further protein-protein and DNA-protein interaction assays. Our high-quality genome assembly, metabolome and transcriptome resources further enrich <em>Quercus </em>genomics, and will facilitate upcoming exploration of ornamental values and environmental adaptability in this important genus.</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.