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7,327 results for “pathways”
Revised supplementary material to "Fumarolic pathways were structurally controlled by a strike-slip fault system beneath the Bishop Tuff, Bishop, California"
<p>Revised supplementary material to "<em>Fumarolic pathways were structurally controlled by a strike-slip fault system beneath the Bishop Tuff, Bishop, California</em>":</p> <p>Figure S1 Supplementary Images V.2.kmz</p> <p>Table S1 Fault Measurements V.2.csv</p> <p>Table S2 Joint Measurements.csv</p> <p>Table S3 Optimal Joints Model Solution.csv</p> <p> </p> <p>Figure S1 Supplementary Images.kmz for use in Google Earth showing field photographs in geographic context. Figure S1 Supplementary Images.kmz contains all supplementary images (S1 to S12), locations and additional images of field photographs of the figures in the main text of the publication (Figures 3,5,7), additional photographs of fault kinematic indicators, sample localities, and some additional photographs. The order of figures in the manuscript changed, so figure numbers differ from the originally published version.</p> <p>Table S1 Fault Measurements.csv contains all measured fault surface orientations (strike and dip), their corresponding slickenline orientations (trend and plunge) and their locations (latitude and longitude in decimal degrees). Fault types were added to the data.</p> <p>Table S2 Joint Measurements.csv contains all measured orientations of joints as measured on a preserved joint wall (strike and dip), their locations (easting and northing in meters), and whether the joint was mineralized or not. No changes were made from the originally published version.</p> <p>Table S3 Optimal Joints Model Solution.csv contains the output to the model presented in the paper. This table was newly added to the revised version of the paper.</p>
GPML files for Caulobacter vibrioides pathways
Monthly data release from WikiPathways.org
GMT file for Zea mays pathways
Monthly data release from WikiPathways.org
Data from: Pathways to global-change effects on biodiversity: New opportunities for dynamically forecasting demography and species interactions
<p>In structured populations, persistence under environmental change is threatened when abiotic factors simultaneously negatively affect survival and reproduction of several life-cycle stages. Such effects can then be exacerbated when species interactions generate reciprocal feedbacks between the demographic rates of the different species. Despite the importance of such demographic feedbacks, forecasts that account for them are severely limited as individual-based data on interacting species are perceived to be essential for such mechanistic forecasting - but are rarely available. This dataset is the input to showcase a state-of-the-art Bayesian method to infer and project stage-specific survival and reproduction from abundance data for several interacting species in a Mediterranean shrub community.</p>
An analgesic pathway from parvocellular oxytocin neurons to the periaqueductal gray in rats
<p>Raw data set related to the publication "An analgesic pathway from parvocellular oxytocin neurons to the periaqueductal gray in rats". It includes ex vivo electrophysiology, ex vivo GRAB recordings, and neuroanatomy data.</p>
VIGET: A web portal for study of vaccine-induced host responses based on Reactome pathways and ImmPort data
<p>Host responses to vaccines are complex but important to investigate. To facilitate the study, we have developed a tool called Vaccine Induced Gene Expression Analysis Tool (VIGET), with the aim to provide an interactive online tool for users to efficiently and robustly analyze the host immune response gene expression data collected in the ImmPort database. VIGET allows users to select vaccines, choose ImmPort studies, set up analysis models by choosing confounding variables and two groups of samples having different vaccination times, and then perform differential expression analysis to select genes for pathway enrichment analysis and functional interaction network construction using the Reactome’s web services. VIGET provides features for users to compare results from two analyses, facilitating comparative response analysis across different demographic groups. VIGET uses the Vaccine Ontology (VO) to classify various types of vaccines such as live or inactivated flu vaccines, yellow fever vaccines, etc. Different variables are classified using our Vaccine Investigation Ontology (VIO). To showcase the utilities of VIGET, we conducted a longitudinal analysis of immune responses to yellow fever vaccines and found an intriguing complex activity response pattern of pathways in the immune system annotated in Reactome, demonstrating that VIGET is a valuable web portal that supports effective vaccine response studies using Reactome pathways and ImmPort data. The portal has been deployed at <a href="https://viget.violinet.org/">https://viget.violinet.org/</a>.</p>
Dataset: 1H NMR metabolomic study of auxotrophic starvation in yeast using Multivariate Curve Resolution-Alternating Least Squares for Pathway Analysis
<p>This dataset contains the set of 1H NMR data used in https://doi.org/10.1038/srep30982.</p> <p>Yeast was grown in five different liquid media and their metabolism was characterized at 6 different time-points during 24 h.</p> <p>The media used were YSC (Yeast nitrogen base Synthetic Complete) and four Drop-Out (DM) medium that do not contain one of the following nutrients (L-histidine, L-leucine, L-methionine and uracil). Since the used yeast strain does not encode in its genome some genes relative to the biosynthesis of these four nutrients, some gene de-regulations process will occur, detectable at the metabolome level.</p> <p>In this study, we have characterized the metabolome using <sup>1</sup>H NMR spectroscopy, detecting more than 40 metabolites, and the evolution of this metabolome along the measured time-points was described by application of PCA, ASCA and MCR-ALS chemometric methods.</p>
Dataset related to: Empagliflozin protects glomerular endothelial cell architecture in experimental diabetes through the VEGF-A/caveolin-1/PV-1 signaling pathway
<p>The files contain all the dataset included in the manuscript divided by figures.</p> <p>Abstract<br> In addition to having blood glucose-lowering effects, inhibitors of sodium glucose cotransporter 2 (SGLT2) afford renoprotection in diabetes. We sought to investigate which components of the glomerular filtration barrier could be involved in the antiproteinuric and renoprotective effects of SGLT2 inhibition in diabetes. BTBR (black and tan, brachyuric) <em>ob/ob</em> mice that develop a type 2 diabetic nephropathy received a standard diet with or without empagliflozin for 10 weeks, starting at 8 weeks of age, when animals had developed albuminuria. Empagliflozin caused marked decreases in blood glucose levels and albuminuria but did not correct glomerular hyperfiltration. The protective effect of empagliflozin against albuminuria was not due to a reduction in podocyte damage as empagliflozin did not affect the larger podocyte filtration slit pore size nor the defective expression of nephrin and nestin. Empagliflozin<br> did not reduce the thickening of the glomerular basement membrane. In BTBR <em>ob/ob</em> mice, the most profound abnormality seen using electron microscopy was in the endothelial aspect of the glomerular capillary, with significant loss of endothelial fenestrations. Remarkably, empagliflozin ameliorated the subverted microvascular endothelial ultrastructure. Caveolae and bridging diaphragms between adjacent endothelial fenestrae were seen in diabetic mice and associated with increased expression of caveolin-1 and the appearance of PV-1. These endothelial abnormalities were limited by the SGLT2 inhibitor. Although no expression of SGLT2 was found in glomerular endothelial cells, SGLT2 was expressed in the podocytes of diabetic mice. VEGF-A, which is a known stimulus for endothelial caveolin-1 and PV-1, was increased in podocytes of BTBR <em>ob/ob</em> mice and normalized by SGLT2 inhibitor treatment.<br> Thus, empagliflozin’s protective effect on the glomerular endothelium of diabetic mice could be due to a limitation of the paracrine signaling of podocyte-derived VEGF-A that resulted in a reduction of the abnormal endothelial caveolin-1 and PV-1, with the consequent preservation of glomerular endothelial function and permeability.</p>
GMT file for melanogaster pathways
Monthly data release from WikiPathways.org
When the practice does not meet the theory: results from an Italian survey on the clini-cal and pathway management of inpatients with decompressive craniectomy or cranioplasty admitted to rehabilitation
<p>Cranioplasty (CP) is supposed to improve the functional outcome of severe acquired brain injury (sABI) patients with decompressive craniectomy (DC). However, ongoing controversies exist regarding its indications, optimum materials, timing, complications, and relationships with hydrocephalus (HC). For these reasons, an International Consensus Conference (ICC) on CP in traumatic brain injury (TBI) was held in June 2018 to issue some recommendations.</p> <p>AIM: To investigate cross-sectionally before the ICC the prevalence of DC/CP in sABI inpatients admitted to neurorehabilitation units in Italy; to assess the perception of Italian clinicians working in the sABI neurorehabilitation settings on the management of inpatients with DC/CP during their rehabilitation stay.</p> <p>DESIGN: Cross-sectional.</p> <p>SETTING AND POPULATION: Physiatrists or neurologists working in 38 Italian rehabilitation centers involved in the care of sABI, giving a pooled sample of 599 inpatients.</p> <p>METHODS: Survey questionnaire consisting of 21 closed-ended questions with multiple-choice answers. Sixteen questions regarded the respondents' opinions and experiences regarding the clinical and management aspects of patients. Survey data were collected via e-mail between April and May 2018.</p>
Rps19 R67∆ mutation creates a model of Diamond-Blackfan anemia and reveals downstream mediators of p53 pathway.
<p>Diamond-Blackfan anemia (DBA) is a rare bone marrow failure syndrome accompanied by cardiovascular, skeletal, and urogenital abnormalities. Most of the affected individuals carry mutations in ribosomal proteins, including S19 (Rps19), a part of the 40S ribosomal subunit. We developed a transgenic model harboring deletion of conserved Arg 67 in <em>RPS19</em>, which is the site of post-translational modification by protein-arginine methyl transferase family and could show that the defect in Rps19 causes phenotype in perfect overlap with the DBA including hematologic dysfunctions, hypotrophy, intrinsic anemia, severe craniofacial, skeletal, urogenital, cardiovascular, and cerebral abnormalities leading to premature lethality during the adolescence of the mouse. This DBA mouse model exhibited activation of the Trp53 signaling pathway in hematopoietic stem cells (HSCs) leading to reduced erythroid lineage development. Competitive transplantation assays using Rps19-deficient bone marrow cells confirmed that HSCs and their progeny lineages were affected while their differentiation was rescued after inactivation of the tumor suppressor Trp53 showing that the development of the DBA phenotype significantly involves non-canonical components of the p53 signaling pathway in the etiopathogenesis of DBA with the Rps19R67∆ mutation leading to the disrupted hematopoietic hierarchy starting at the stage of short-term repopulating stem cells. The activated p53 pathway was mediated by downstream molecules Zmat3, Phlda3, and Eda2r, whose overall function in the pathology of DBA involve erythroid differentiation blockade coupled with cell proliferation and survival disruption. To conclude, the new DBA model represents a powerful tool for exploring new therapeutic options for DBA.</p>
Dataset of the Article "Reconstruction of the unbinding pathways of new inhibitors of the SARS-CoV-2 Papain-like protease using molecular dynamics simulation"
<p>This dataset contains concatenated trajectory files of the SuMD simulation of the unbinding pathways of the new inhibitors for SARS-CoV-2 papain-like protease. This data will be published in an article titled: "<strong>Reconstruction of the unbinding pathways of new inhibitors of the SARS-CoV-2 Papain-like protease using molecular dynamics simulation".</strong></p>
Dataset for: Intracellular carbon storage by microorganisms is an overlooked pathway of biomass growth
<p>Dataset and code for the publication:</p> <p>Intracellular carbon storage by microorganisms is an overlooked pathway of biomass growth<br> Mason-Jones, K., Breidenbach, A., Dyckmans, J., Banfield, C.C., Dippold, M.A.<br> Nature Communications<br> 2023<br> <br> Article DOI: 10.1038/s41467-023-37713-4</p>
Identifying cost-effective decarbonisation pathways for South Africa's power sector (EMP-A 2023) - Dataset
<p>Dataset of the project "Identifying cost-effective decarbonisation pathways for South Africa's power sector (EMP-A 2023)".</p>
GENeSYS-MOD pathways developed by the openENTRANCE project
<p>This dataset contains quantitative pathways developed with the GENeSYS-MOD 3.1 model in the openENTRANCE project.</p> <p>You can find additional information, including all model results and native input files, at the Supplementary Material for Deliverable D3.2 of the openENTRANCE project at <a href="https://doi.org/10.5281/zenodo.7760651">https://doi.org/10.5281/zenodo.7760651</a>.</p> <p>The data file follows the IAMC data format and the conventions established by the openENTRANCE project. See <a href="https://github.com/openENTRANCE/openentrance">https://github.com/openENTRANCE/openentrance</a> for details.</p> <p>Visit the openENTRANCE Scenario Explorer at <a href="https://data.ene.iiasa.ac.at/openentrance">https://data.ece.iiasa.ac.at/openentrance</a> for more information about the openENTRANCE project and other datasets.</p>
TemoaProject: Databases used in Sinha et al. (2024), Diverse Decarbonization Pathways Under Near Cost-Optimal Futures
<p>Contains modeling to generate alternative databases for the U.S. energy system used as part of the Open Energy Outlook. Databases were created using the logic outlined in: https://github.com/adityasinha1992/temoa/tree/mga_parallelized</p>
Cancer-specific association between Tau (MAPT) and cellular pathways, clinical outcome, and drug response
<p>To bring new evidence that Tau represents a key protein in cancer, we present an <em>in silico</em> pan-cancer analysis of <em>MAPT</em> transcriptomic profile in over 10000 clinical samples and over 1300 pre-clinical samples provided by the TCGA and the DEPMAP datasets respectively.</p>
Data for: Characterization of a sperm motility signaling pathway in a gonochoric coral suggests conservation across sexual systems
<p>Most stony corals liberate their gametes into the water column via broadcast spawning, where fertilization hinges upon the activation of directional sperm motility. Sperm from gonochoric and hermaphroditic corals display distinct morphological and molecular phenotypes, yet it is unknown whether the signaling pathways controlling sperm motility are also distinct between these sexual systems. Here, we addressed this knowledge gap using the gonochoric broadcast spawning coral <em>Astrangia</em> <em>poculata</em>. We found that cytosolic alkalinization of sperm activates the pH-sensing enzyme soluble adenylyl cyclase (sAC), which is required for motility. Additionally, we demonstrate for the first time in any cnidarian that sAC activity is necessary for PKA activation, and PKA activity is also required for motility. Ultrastructures of <em>A. poculata</em> sperm displayed morphological homology with other gonochoric cnidarians, and investigation of cnidarian proteomes revealed that sAC exhibits broad structural and functional conservation across this phylum. These results indicate a conserved role for pH-dependent sAC-PKA signaling in sperm motility across coral sexual systems and suggest that the role of this pathway in sperm motility is likely ancestral in metazoans. Finally, the dynamics of this pH-sensitive pathway may play a critical role in determining the sensitivity of marine invertebrate reproduction to anthropogenic ocean acidification.</p>
Model simulation data used in "The global impact of the transport sectors on the atmospheric aerosol and the resulting climate effects under the Shared Socioeconomic Pathways (SSPs)" (Righi et al., Earth Syst. Dynam., 2023)
<p>This dataset contains the output of the EMAC global model simulations analysed and discussed in Righi et al. (<i>Earth Syst. Dynam.</i>, 2023). For details see the README.md file.</p>
Figure 4 in Pathway Analysis: Likelihood of Coffee Berry Borer (Hypothenemus hampei Ferrari) Introduction into the Hawaiian Islands by Air Passenger Travel
Figure 4. Probability for the estimated annual passenger entries with CBB-infested materials: (a) to Hawaii from CBB-occurring countries; (b) between Hawaii island and Oahu; (c) between Oahu and Maui; (d) between Oahu and Kauai; (e) between Hawaii island and Maui; (f) between Maui and Kauai; (g) between Hawaii island and Kauai; (h) between Oahu and Lanai.
ScienceDex guides
Understand access before you commit
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.