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7,327 results for “pathways”
Data for the paper: "Formation and new Transport pathways of the Global Tropopause Dust Layer"
<p>Model simulation output used for "Formation and new Transport pathways of the Global Tropopause Dust Layer" submitted to Geophysical Research Letters (GRL).</p>
Targeted lipidomics yields changes in both arachidonic acid and linoleic acid pathways observed in C57BL/6J mice compared to KitW-sh mice after nitrogen mustard exposure
<p>Sulfur mustard (SM) has been widely used as a chemical warfare agent including most recently in Syria. Mice exposed to SM exhibit an increase in pro-inflammatory cytokines followed by immune cell infiltration in the lung, however, the mechanisms leading to these inflammatory responses has not been completely elucidated. Mast cells are one of the first responding innate immune cells found at the mucosal surfaces of the lung and have been reported to be activated by SM in the skin. Therefore, we hypothesized that nitrogen mustard (NM: a surrogate for SM) exposure promotes activation of mast cells causing chronic respiratory inflammation. To assess the role of mast cells in NM-mediated pulmonary toxicity, we compared the effects of NM exposure between C57BL/6 and B6.Cg-KitW-sh/HNihrJaeBsmJ (Kit<sup><em>W-s</em></sup><sup>h</sup>; mast cell deficient) mice. Lung injury was observed in C57BL/6J mice following NM exposure (0.125 mg/kg) at 72 h, which was significantly abrogated in Kit<sup><em>W-s</em></sup><sup>h</sup> mice. Although both strains exhibited damage from NM, C57BL/6J mice had higher inflammatory cell infiltration and more elevated prostaglandin D<sub>2</sub> (PGD<sub>2</sub>) present in bronchoalveolar lavage fluid compared with Kit<sup><em>W-s</em></sup><sup>h</sup> mice. Additionally, we utilized murine bone marrow-derived mast cells to assess NM-inducedearly and late activation. Although NM exposure did not result in mast cell degranulation, we observed an upregulation in PGD<sub>2</sub> and IL-6 levels following exposure to NM. Results suggest that mast cells play a prominent role in lung injury induced by NM and may contribute to the acute and potentially long-term lung injury observed caused by SM.</p>
Variation in the modality of a yeast signaling pathway is mediated by a single regulator
<p>Bimodal gene expression by genetically identical cells is a pervasive feature of signaling networks, and has been suggested to allow organisms to hedge their "bets" in uncertain conditions. In the galactose-utilization (GAL) pathway of Saccharomyces cerevisiae, gene induction is unimodal or bimodal depending on natural genetic variation and pre-induction conditions. Here, we find that this variation in modality arises from regulation of two features of the pathway response: the fraction of cells that show induction, and their level of expression. GAL3, the galactose sensor, controls the fraction of induced cells, and titrating its expression is sufficient to control modality; moreover, all the observed differences in modality between different pre-induction conditions and amongst natural isolates can be explained by changes in GAL3's regulation and activity. The ability to switch modality by tuning the activity of a single protein may allow rapid adaptation of bet hedging to maximize fitness in complex environments.</p>
Idealized GCM dataset for "Different Pathways to an Early Eocene Climate" by Matthew Henry and Geoffrey K. Vallis
<p>Idealized GCM dataset for "Different Pathways to an Early Eocene Climate" by Matthew Henry and Geoffrey K. Vallis</p> <p>See https://github.com/matthewjhenry/eocene for code to reproduce the figures.</p>
GPML files for Vitis vinifera pathways
Monthly data release from WikiPathways.org
Supplementary files for the article entitled: PIEZO2 promotes cell proliferation and metastasis in colon carcinoma through the SLIT2/ROBO1/VEGFC pathway
<p>All results were analyzed using the Statistical Package for the Social Sciences version 20.0 (IBM Corporation, Armonk, NY, USA). The results of Schoenfeld residuals method were analyzed using the R 4.2.2 software and survminer package.</p>
Postprocessed data for "Tracing the rain formation pathways in numerical simulations of deep convection"
<p>This dataset is associated with the journal paper "Tracing the rain formation pathways in numerical simulations of deep convection".</p> <p>There are six .npz files containing data for the 5 simulations (CTRL, CTRLrfix, K13, CTRL800, K13800)<br> and one npz file containing data for constructing the rain pdfs of simulation CTRL (Figure 6).</p> <p>This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52‐07NA27344 IM Release number LLNL-MI-843623</p>
Datasets associated with "A hypothalamic pathway that suppresses aggression towards superior opponents".
<p>Datasets associated with "A hypothalamic pathway that suppresses aggression towards superior opponents" published in Nature Neuroscience 2023. Each file is a compressed folder containing the raw data and MATLAB codes needed for generating the relevant figure (indicated in the name of the folder) in the paper. Additionally, all raw images shown in the paper are stored in the folder named "Representative histology images". </p>
An assessment of energy system transformation pathways to achieve net-zero carbon dioxide emissions in Switzerland. Supplementary Information Assumptions and Results
<p>This dataset accompanies the corresponding article in Communications Earth and Environment. It contains the key assumptions used in the energy system modelling with the Swiss TIMES energy systems model (STEM) for assessing net-zero carbon dioxide emissions scenarios for Switzerland. In addition, contains extensive results from STEM for each one of the core scenarios and variants assessed in the study.</p> <p>The following files are contained in this repository:</p> <ul> <li><strong>Supplementary Data 1</strong>: This is the EXCEL file "Supplementary_Information_Assumptions.xslx" which contains key assumptions of the long-term scenarios assessed with STEM. These include among others: the major energy and climate policies in each scenario, the economic and demographic assumptions, key drivers for the residential energy demand (e.g., floor reference area or appliances), key drivers for the energy demand in the services sectors (e.g., Gross Value Added or floor area), key drivers for the energy demand in industry (e.g., production index or Gross Value Added), mobility demands, energy import prices, hourly electricity import prices, net transfer capacities, domestic sustainable renewable resource potentials, energy supply and demand technologies costs and efficiencies</li> <li><strong>Supplementary Data 2</strong>: This is the EXCEL file "Supplementary_Information_Results.xlsx" which contains energy balances from the baseline and the net-zero CO<sub>2</sub> emissions scenarios. The results for each scenario are: domestic production by fuel, net imports by fuel, primary energy consumption by fuel, input to conversion sectors by fuel, electricity supply and capacities by fuel, district heating supply by fuel, final energy consumption by fuel and sector, CO2 emissions by source, energy system costs, and indicators such as energy consumption per capita, energy intensity of GDP, CO2 emissions per capita and CO2 intensity of GDP. </li> <li><strong>Supplementary Data 3</strong>: The ZIP file "Source_code_and_data_for_charts.zip" contains source codes and data for reproducing the figures in the manuscript. </li> </ul>
Anti-cytokine storm activity of fraxin and quercetin, alone and in combination, and their possible molecular mechanisms via TLR4 and PPARγ signaling pathways in LPS-induced RAW 264.7 cell line article data
<p>Anti-cytokine storm activity of fraxin and quercetin, alone and in combination, and their possible molecular mechanisms via TLR4 and PPARγ signaling pathways in LPS-induced RAW 264.7 cell line article data</p>
Data for Patterns of ontogenetic evolution across extant marsupials reflect different allometric pathways to ecomorphological diversity
<p>Data associated with: Wilson LAB, López-Aguirre C, Archer M, Hand SJ, Flores D, Abdala F, Giannini NP. 2023. Patterns of ontogenetic evolution across extant marsupials reflect different allometric pathways to ecomorphological diversity. Nature Communications</p>
Anti-cytokine storm activity of fraxin and quercetin, alone and in combination, and their possible molecular mechanisms via TLR4 and PPARγ signaling pathways in LPS-induced RAW 264.7 cell line article data
<p>Anti-cytokine storm activity of fraxin and quercetin, alone and in combination, and their possible molecular mechanisms via TLR4 and PPARγ signaling pathways in LPS-induced RAW 264.7 cell line article data</p>
Movies and data to accompany "Single-virus fusion measurements reveal multiple mechanistically equivalent pathways for SARS-CoV-2 entry"
<p>Movies and data to accompany "Single-virus fusion measurements reveal multiple mechanistically equivalent pathways for SARS-CoV-2 entry".</p> <p>AVI files contain movies of video micrographs</p> <p>TIFF files contain primary micrographs for representative experiments</p> <p>XLS file contains analyzed data with individual fusion waiting times (as well as locations of fusion events)</p>
Dataset to article "Distinct traits of structural and regulatory evolutional conser-vation of human genes with specific focus on major cancer mo-lecular pathways"
<p>Abstract: Evolution of protein coding genes has both structural and regulatory components. The first can be assessed by measuring the ratio of non-synonymous to synonymous nucleotide sub-stitutions. The second component can be measured as the normalized proportion of transposable elements that used as the regulatory elements. For the first time, we characterized in parallel the regulatory and structural evolutionary profiles for 10,890 human genes and 2,972 molecular pathways. We observed ~0.1 correlation between the structural and regulatory metrics at the gene level, which appeared much higher (~0.4) at the pathway level. We deposited the data in the publicly available database RetroSpect accessible at https://retrospect.oncobox.com. We also analyzed evolutionary dynamics of six cancer pathways of two major axes: Notch/WNT/Hedgehog and AKT/mTOR/EGFR. The Hedgehog pathway had both components slower, whereas the Akt pathway had clearly accelerated structural evolution. In particular, the major hub nodes Akt and beta-catenin showed both components strongly decreased, whereas two major regulators of Akt TCL1 and CTMP had outstandingly high evolutionary rates. We al-so noticed structural conservation of serine/threonine kinases and the genes related to guanosine metabolism in cancer signaling: GPCRs, G proteins, and small regulatory GTPases (Src, Rac, Ras); however, this was compensated by the accelerated regulatory evolution.</p>
The Jak/Stat pathway mediates disease tolerance during systemic bacterial infection in Drosophila
<p>Data and code for </p> <p>Prakash, A., Bonnet, M., Monteith, K. M., & Vale, P. F. (2021). The Jak/Stat pathway mediates disease tolerance during systemic bacterial infection in Drosophila. <em>bioRxiv</em>.</p>
NGS data from: Predominant HDR-dependent genome editing and prevention of byproducts by DNA repair pathway choice
<p>CRISPR-Cas9 genome editing has been widely adapted to cleave genomic DNA sequences of interest. Cellular repair of the CRISPR induced DNA double-strand breaks is dominated by error prone end joining pathways that outcompete inefficient homology-directed repair (HDR) that would allow precise introduction of a mutation present in a supplied synthetic DNA donor. To achieve predominant HDR, we studied the combinatory effect of inhibitory mutations in genes that are central to competing repair pathways.</p>
BridgeDb: pathway identifier mapping database derived from Wikidata
<p>Release of a BridgeDb gene identifier mapping database between Wikidata and Ensembl.</p> <pre>[INFO]: Database finished. INFO: old database is Wikidata 1.0.0 (build: 20230506) INFO: new database is Wikidata 1.0.0 (build: 20230506) INFO: Number of ids in Wd (Wikidata): 153715 (unchanged) INFO: Number of ids in En (Ensembl): 153637 (unchanged) INFO: new size is 95 Mb (changed +0.0%) INFO: total number of identifiers is 307352 INFO: total number of mappings is 307430 </pre>
Data for manuscript "Wildfire Emissions Transport Pathways in the Global Atmosphere"
<p>Model results and emission dataset that was used to produce the data presented in the manuscript by Daskalakis et al., submitted in GRL in May 2023.</p>
Single-Cell RNA-Seq Identifies Pathways and Genes Contributing to the Hyperandrogenemia Associated with Polycystic Ovary Syndrome
<p>Polycystic ovary syndrome (PCOS) is a common endocrine disorder characterized by hyperandrogenemia of ovarian thecal cell origin, resulting in anovulation/oligo-ovulation and infertility. Our previous studies established that ovarian theca cells isolated and propagated from ovaries of normal ovulatory women and women with PCOS, have distinctive molecular and cellular signatures that underlie the increased androgen biosynthesis in PCOS. To evaluate differences between gene expression in single cells from passaged cultures of theca cells from ovaries of normal ovulatory women and women with PCOS, we performed single-cell RNA sequencing (scRNA-seq). Results from these studies revealed differentially expressed pathways and genes involved in the acquisition of cholesterol, the precursor of steroid hormones, and steroidogenesis. Bulk RNA-seq and microarray studies confirmed the theca cell differential gene expression profiles. The expression profiles appear to be directed largely by increased levels or activity of the transcription factors SREBF1, which regulates genes involved in cholesterol acquisition (<em>LDLR, LIPA, NPC1, CYP11A1, FDX1, FDXR)</em> and GATA6, which regulates expression of genes encoding steroidogenic enzymes (<em>CYP17A1) </em>in concert with other differentially expressed transcription factors (<em>SP1</em>, <em>NR5A2</em>). This study provides insights into the molecular mechanisms underlying the hyperandrogenemia associated with PCOS, and highlights potential targets for molecular diagnosis and therapeutic intervention.</p> <p><strong>scRNA-seq data in the form of 10x Cell Ranger files are available for the following samples:</strong></p> <p>PCOS affected - Mc03, Mc10, Mc16, Mc26, Mc27</p> <p>Normal cycling women - Mc02, Mc06, Mc31, Mc40, Mc50</p> <p>A F in the sample name indicates forskolin treatment and a C indicates untreated control samples.</p> <p> </p>
Pollinator sharing and hybridization in a pair of dioecious figs sheds light on the pathways to speciation
<p>The dynamics and processes underlying the co-diversification of plant–pollinator interactions are of great interest to researchers of biodiversity and evolution. Co-speciation is generally considered to be a key process in generating the diversity of figs and their pollinating wasps. Groups of closely-related figs pollinated by separate wasps occur frequently and represent excellent opportunities to study ongoing diversification in this textbook mutualism. We study two closely-related sympatric dioecious figs (<em>F. heterostyla</em> and <em>F. squamosa</em>) in Xishuangbanna, southwest China, and aim to document what is likely to be the final stages of speciation between these species using a combination of trait data and experimental manipulation. Thirty-seven and 29 floral volatile compounds were identified from receptive <em>F. heterostyla </em>and<em> F. squamosa</em> figs respectively, with 25 compounds shared by both species. Interspecific variation in chemical dissimilarity was significant but relatively low. Ovipositor lengths lie well within the range required for access to heterospecific ovules, facilitating hybridization. Cross-introduction of wasps into figs was conducted and hybrid seeds were generated for all donor/recipient combinations. Wasps of <em>F. heterostyla </em>produce adult offspring in <em>F. squamosa</em> figs, while wasps of <em>F. squamosa</em> induce gall development in <em>F. heterostyla</em> figs and their offspring fail to mature in synchrony with their novel host. We record limited geographic barriers, limited volatile dissimilarity, compatible morphology, complementary reproductive phenologies and the production of hybrid seeds and wasp offspring. We hypothesize that this incomplete wasp specialization and incomplete reproductive isolation may generalize to other closely-related figs.</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.