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7,327 results for “pathways”
Research data supporting "Localized and controlled delivery of nitric oxide to the conventional outflow pathway via enzyme biocatalysis: towards therapy for glaucoma"
<p>Research data supporting the paper above published at DOI: 10.1002/adma.201604932</p>
10 eADAGE models for the PAO1 KEGG pathways case study in PathCORE
<p>ensemble Analysis using Denoising Autoencoders for Gene Expression<strong> </strong>(<strong>eADAGE</strong>) is an unsupervised feature construction algorithm developed by Tan et al. that uses an ensemble of neural networks (an ensemble of ADAGE models) to capture biological signatures embedded in the expression compendium. By initializing eADAGE with different random seeds, Tan et al. produced 10 eADAGE models that each extracted k=300 features from the compendium of genome-scale <em>P. aeruginosa</em> data.</p> <p>eADAGE is described in Tan et al.'s "System-wide automatic extraction of functional signatures in <em>Pseudomonas aeruginosa</em> with eADAGE" (https://doi.org/10.1101/078659).</p> <p>The code to construct these 10 models is available in this repository: https://bitbucket.org/greenelab/eadage (see eADAGE_construction.sh). </p>
P. aeruginosa expression compendium for the PAO1 KEGG pathways case study in PathCORE.
<p>The normalized P. aeruginosa (PAO1) gene expression compendium uses datasets from ArrayExpress. Each gene expression vector is linearly normalized to the range between 0 and 1.</p> <p>The script used to download the PAO1 datasets and process all samples into a single expression compendium is available here: https://bitbucket.org/greenelab/eadage/src/d8a98586e0f448a5b7d497f5516cc4e241635361/data_collection/data_collection.sh</p>
Dataset for "Mapping Water Flow Pathways in the Fengjiaping Landslide Using Self-Potential and Electrical Resistivity Tomography"
<p>This dataset includes soil temperature, moisture, and electrical conductivity measurements taken at a depth of approximately 50 cm, as well as the digital elevation model, electrical resistivity tomography, and self-potential data used in the manuscript "Mapping Water Flow Pathways in the Fengjiaping Landslide Using Self-Potential and Electrical Resistivity Tomography" submitted to <em>Comptes Rendus Geoscience</em>.</p>
A cohort-based study of host gene expression: tumor suppressor and innate immune/inflammatory pathways associated with the HIV reservoir size
<p>The major barrier to an HIV cure is the HIV reservoir: latently-infected cells that persist despite effective antiretroviral therapy (ART). Most prior studies of host genetic predictors of HIV control have focused on "elite controllers," rare individuals able to control virus in the absence of ART. However, there have been few genetic studies among ART-suppressed non-controllers, who make up the majority of people living with HIV (PLWH). We performed host RNA sequencing and HIV reservoir quantification (total DNA [tDNA], unspliced RNA [usRNA], intact DNA) from peripheral CD4+ T cells from 191 HIV+ ART-suppressed non-controllers. After adjusting for nadir CD4+ count, timing of ART initiation, and genetic ancestry, we identified two host genes for which higher expression was significantly associated with smaller total DNA viral reservoir size, <em>P3H3</em> and <em>NBL1</em>, both known tumor suppressor genes. We then identified 17 host genes for which lower expression was associated with higher residual transcription (HIV usRNA). These included novel associations with membrane channel (<em>KCNJ2</em>, <em>GJB2</em>), inflammasome (<em>IL1A, CSF3, TNFAIP5, TNFAIP6, TNFAIP9, CXCL3, CXCL10</em>), and innate immunity (TLR7) genes (FDR-adjusted q<0.05). Gene set enrichment analyses further identified significant associations of HIV usRNA with TLR4/microbial translocation (q=0.006), IL-1/NRLP3 inflammasome (q=0.008), and IL-10 (q=0.037) signaling. Protein validation assays using ELISA and multiplex cytokine assays supported these observed inverse host gene correlations, with P3H3, IL-10, and TNF-a protein associations achieving statistical significance (p<0.05). Of note, plasma IL-10 was also significantly inversely associated with HIV DNA (p=0.016). HIV intact DNA was not associated with differential host gene expression, although this may have been due to a large number of undetectable values in our study. Further data are needed to validate these findings, including functional genomic studies, larger cohorts including underrepresented PLWH in research, and those including dedicated assays to measure the replication-competent HIV reservoir.</p>
Simulations for "Molecular Dynamics-Based Identification of Binding Pathways and Two Distinct High-Affinity Sites for Succinate in the Succinate Receptor 1 SUCNR1/GPR91"
Open the record for dataset details and reuse information.
Data for BY-COVID Pathways to MINERVA Analysis Workflow
<p>Source data (<a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE182152">GSE182152</a>) was analysed with <a href="https://workflowhub.eu/workflows/688">WFHub:688</a> to generate these datasets</p>
Pathformer: a biological pathway informed Transformer for disease diagnosis and prognosis using multi-omics data
<p>Integrating multi-omics data offers a more comprehensive view of gene regulation, which would be helpful in achieving accurate diagnosis of diseases like cancer. To improve the accuracy of disease diagnosis and prognosis, we developed Pathformer, a multi-omics integration method for both tissue and liquid biopsy data. We implemented Pathformer's network architecture using the “PyTorch” package in Python v3.6.9, and our codes can be found in the GitHub repository (https://github.com/lulab/Pathformer). This repository contains preprocessed TCGA dataset data, preprocessedliquid biopsy dataset data, result of Pathformer and comparison_methods, mentioned in GitHub project and article.</p>
Reactivating PTEN to impair glioma stem cells by inhibiting cytosolic iron-sulfur assembly pathway
<p>Glioblastoma (GBM), the most lethal primary brain tumor, harbors glioma stem cells (GSCs) that not only initiate and maintain malignant phenotypes but also enhance therapeutic resistance. Although frequently mutated in GBMs, the function and regulation of PTEN in PTEN-intact GSCs are unknown. Here we found that PTEN directly interacts with MMS19 and competitively disrupts MMS19-based cytosolic iron-sulfur (Fe-S) cluster assembly (CIA) machinery in the differentiated glioma cells (DGCs). Interrogation of GSCs, when compared with their matched DGCs, revealed that PTEN is specifically succinated at cysteine (C) 211 in GSCs. Isotope tracing coupled with mass spectrometry analysis confirmed that fumarate, generated by adenylosuccinate lyase (ADSL) in <em>de novo</em> purine synthesis pathway which is highly activated in GSCs, promotes PTEN C211 succination. This modification abrogates the interaction between PTEN and MMS19, thereby reactivating CIA machinery pathway in GSCs. Functionally, inhibiting PTEN C211 succination through re-expressing PTEN C211S mutant, depleting ADSL, or consuming fumarate by N-acetylcysteine (NAC), an FDA-approved prescription drug, impairs GSC maintenance. Importantly, re-expressing PTEN C211S or treating with NAC sensitizes GSC-derived brain tumors to temozolomide and irradiation, the standard-of-care treatments for GBM patients, by retarding CIA machinery-mediated DNA damage repair. These findings reveal an immediately practicable strategy to target GSCs for treating GBMs by combined therapy with repurposing NAC.</p>
Code and Dataset used for assessment of key variables in manuscript titled "Equity Assessment of Global Mitigation Pathways in the IPCC Sixth Assessment Report".
<p>This repository contains the code used for extraction of data from the IPCC scenarios database for key variables that are assessed in the manuscript titled "Equity Assessment of Global Mitigation Pathways in the IPCC Sixth Assessment Report". It also contains data for key variables for scenario categories C1, C2, C3, and C4</p>
Data from: Value-related learning in the olfactory bulb occurs through pathway-dependent peri-somatic inhibition of mitral cells
<p>Associating values to environmental cues is a critical aspect of learning from experiences, allowing animals to predict and maximise future rewards. Value-related signals in the brain were once considered a property of higher sensory regions, but their wide distribution across many brain regions is increasingly recognised. Here, we investigate how reward-related signals begin to be incorporated, mechanistically, at the earliest stage of olfactory processing, namely, in the olfactory bulb. In head-fixed mice performing Go/No-Go discrimination of closely related olfactory mixtures, rewarded odours evoke widespread inhibition in one class of output neurons, that is, in mitral cells but not tufted cells. The temporal characteristics of this reward-related inhibition suggest it is odour-driven, but it is also context-dependent since it is absent during pseudo-conditioning and pharmacological silencing of the piriform cortex. Further, the reward-related modulation is present in the somata but not in the apical dendritic tuft of mitral cells, suggesting an involvement of circuit component located deep in the olfactory bulb. Depth-resolved imaging from granule cell dendritic gemmules suggests that granule cells that target mitral cells receive a reward-related extrinsic drive. Thus, our study supports the notion that value-related modulation of olfactory signals is a characteristic of olfactory processing in the primary olfactory area and narrows down the possible underlying mechanisms to deeper circuit components that contact mitral cells peri-somatically.</p>
Current and Future Flood maps for Flood risk assessment under the Shared Socioeconomic Pathways in the Greater Accra region, Ghana
<p>The study used 15 flood conditioning factors in simulating current and future flood conditions under the SSP scenarios using the Frequency Ratio (FR) model </p>
Appendix 1 to "The Status of Biological Invasions and their Management in South Africa in 2022"—Species level pathway data
<p>SANBI and CIB 2023. Appendix 1 to "The Status of Biological Invasions and their Management in South Africa in 2022"—Species level pathway data. South African National Biodiversity Institute, Kirstenbosch and DSI-NRF Centre of Excellence for Invasion Biology, Stellenbosch. http://dx.doi.org/10.5281/zenodo.8217192</p> <p>For more details see: http://iasreport.sanbi.org.za</p> <p>For the report itself see: http://dx.doi.org/10.5281/zenodo.8217182</p>
End of life (EoL) pathways for the battery lifecycle
<p>A flowchart showing the end of life (EoL) pathways for the battery lifecycle, including decisions which need to be made at specific stages. Qualitative ranges have been selected, as the actual figures may change over time. For example, at present, when deciding which route to choose for an EoL battery pack, based on the State of Health (SoH) check, those which exceed 80 % ("above") are suitable for reuse in another automotive application; those which demonstrate 50 % or less ("below") must be dismantled and those which lie between these limits ("mid-range") can be considered for repurposing.</p>
Data from: Gastrointestinal gd T cells reveal upregulated T-cell transcripts and signaling pathways during peanut oral immunotherapy
<p>Oral immunotherapy (OIT) has been successful in desensitizing patients to offending food allergens, although identification of tissue-resident T cell subsets and cognate pathways leading to desensitization has been challenging. The T cells are a major T-cell subset of mucosal intraepithelial lymphocytes (IELs) and play a significant role in tissue homeostasis and repair. Studies in mouse models suggested a regulatory role of gd T cells in food allergy (FA). Also, peripheral gd T cells from patients analyzed over 24 weeks of peanut OIT were shown to undergo dynamic changes in expression profiles, implicating pathways involved in immune homeostasis. To our knowledge, the role of gd T cells in the intestinal mucosa of FA patients during immunotherapy has not been examined. To this end, we investigated whether gd T cells in the gastrointestinal (GI) tract are modulated during peanut OIT. We hypothesized that GI-resident gd T cells in FA patients would increase during the course of peanut OIT and reveal transcripts and pathways relevant to the mechanisms of peanut desensitization.</p>
Neutron Star - White Dwarf Binaries: Probing Formation Pathways and Natal Kicks with LISA
<p>We present supplementary datasets accompanying our publication<em> </em><a href="https://arxiv.org/abs/2310.06559">Neutron Star - White Dwarf Binaries: Probing Formation Pathways and Natal Kicks with LISA</a>.<em> </em>These catalogues reperesent the Galactic population of double white dwarf (DWD) and neutron star - white dwarf (NSWD) binaries emitting gravitational waves (GWs) in the <em>Laser Interferometer Space Antenna</em> (LISA) frequency band (0.1 mHz - 1 Hz). The catalogues have been constructed based on binary evolution models <a href="https://arxiv.org/abs/1208.6446">Toonen et al. 2012</a> for DWDs and <a href="https://arxiv.org/abs/1804.01538">Toonen et al. 2018</a> for NSWD binaries, obtained using SeBa binary population synthesis code.</p> <p><strong>Data contents</strong></p> <p>The dataset consists of <strong>12 catalogues </strong>representing Galactic populations of NSWD and/or DWD binaries, which are expected to be the most numerous types of binaries amongt LISA's Galactic sources. Each catalogue is distinguished by its model ID, which specifies the presence of NSWD and/or DWD binaries, the CE model used, CE efficiency values, and the NS natal kick prescription applied (see table below).</p> <p>Each catalogue is structured to describe a binary systems with the following attributes:</p> <ul> <li><strong>Name*</strong>: binary identifier; this consist of a prefix indicating the binary type (<code>'MW_DWD'</code> for a DWD binary, <code>'MW_NSWD_ecc0'</code> for a circular NSWD bianry, or <code>'MW_NSWD_ecc1'</code> for an eccentric NSWD binary) followed by a unique ID number. For example, <code>'MW_DWD 28713637'</code>.</li> <li><strong>Frequency</strong>: present-day GW frequency (Hz).</li> <li><strong>Frequency Derivative</strong>: rate of change of GW frequency over time (Hz^2).</li> <li><strong>Ecliptic Latitude</strong>: in radians (rad).</li> <li><strong>Ecliptic Longitude</strong>: in radians (rad).</li> <li><strong>Amplitude</strong>: GW amplitude (dimensionless).</li> <li><strong>Inclination</strong>: angle between the binary's orbital plane and our line of sight, in radians (rad).</li> <li><strong>Polarization</strong>: Orientation of the GW's polarization, in radians (rad).</li> <li><strong>Initial Phase</strong>: initial phase (rad).</li> <li><strong>Eccentricity</strong>: orbital eccentricity (dimensionless).</li> </ul> <p><strong>*</strong>Note that the <strong>Name </strong>field for eccentric NS+WD binaries (staring with <code>'MW_NSWD_ecc1'</code>) is not unique because these binaries are represented by multiple harmonics sharing the same name ID. The number of harmonics included varies for each binary to ensure that at least 99% of the binary's total GW power is represented. Thus, for each binary, we added harmonics incrementally until this threshold is reached.</p> <table> <tbody> <tr> <td>Model ID</td> <td>WD+WD</td> <td>NS+WD</td> <td>CE model</td> <td>CE efficiency</td> <td>NS natal kick</td> </tr> <tr> <td>1_0</td> <td>Yes</td> <td>No</td> <td>αα</td> <td>αλ=2.00</td> <td>N/A</td> </tr> <tr> <td>1_1</td> <td>Yes</td> <td>Yes</td> <td>αα</td> <td>αλ=2.00</td> <td>Verbunt</td> </tr> <tr> <td>1_2</td> <td>Yes</td> <td>Yes</td> <td>αα</td> <td>αλ=2.00</td> <td>Arzoumanian</td> </tr> <tr> <td>1_3</td> <td>Yes</td> <td>Yes</td> <td>αα</td> <td>αλ=2.00</td> <td>Hobbs</td> </tr> <tr> <td>1_4</td> <td>Yes</td> <td>Yes</td> <td>αα</td> <td>αλ=2.00</td> <td>Blaauw</td> </tr> <tr> <td>2_0</td> <td>Yes</td> <td>No</td> <td>αα2</td> <td>αλ=0.25</td> <td>N/A</td> </tr> <tr> <td>2_1</td> <td>Yes</td> <td>Yes</td> <td>αα2</td> <td>αλ=0.25</td> <td>Verbunt</td> </tr> <tr> <td>2_2</td> <td>Yes</td> <td>Yes</td> <td>αα2</td> <td>αλ=0.25</td> <td>Arzoumanian</td> </tr> <tr> <td>2_3</td> <td>Yes</td> <td>Yes</td> <td>αα2</td> <td>αλ=0.25</td> <td>Hobbs</td> </tr> <tr> <td>2_4</td> <td>Yes</td> <td>Yes</td> <td>αα2</td> <td>αλ=0.25</td> <td>Blaauw</td> </tr> <tr> <td>3_0</td> <td>Yes</td> <td>No</td> <td>αγ</td> <td>αλ=2.00, γ=1.75</td> <td>N/A</td> </tr> <tr> <td>3_1</td> <td>Yes</td> <td>Yes</td> <td>αγ</td> <td>αλ=2.00, γ=1.75</td> <td>Verbunt</td> </tr> </tbody> </table> <p> </p> <h4><strong>Citing the Dataset</strong></h4> <p>When utilising these catalogues in your research, please cite <a href="https://arxiv.org/abs/2310.06559">Korol et al. 2024.</a> We also note our companion data-analysis-focused paper <a href="https://arxiv.org/abs/2310.06568">Moore et al. 2024</a>.</p>
Isomerization pathways of a mismatched base pair of A:8OG in free duplex DNA
<p>plumed.dat --> input file for OPES simulation.</p> <p>str0.pdb ~ str19.pdb --> initial structures for OPES simulation.</p> <p>traj.xtc --> sample output trajectory of OPES simulation.</p>
Predicting the pathways of string-like motions in metallic glasses via path featurizing graph neural networks
<p>String-like motions (SLMs) cooperative, "snake"-like movements of particles—are crucial for dynamics in diverse glass formers. Despite their ubiquity, questions persist: do SLMs prefer specific paths? If so, can we predict these paths? Here, in Al-Sm glasses, our iso-configurational ensemble simulations reveal that SLMs indeed follow certain paths. By designing a graph neural network (GNN) to featurize the environment around directional paths, we achieve a high-fidelity prediction of likely SLM pathways solely based on the static structure. GNN gauges a structural measure to assess each path's propensity to engage in SLMs, akin to a "softness" metric, but for paths rather than for atoms. Our GNN interpretation reveals the critical role of the bottleneck zone along paths in steering SLMs. By monitoring "path-softness", we elucidate SLM-favored paths transit from fragmented to interconnected upon glass transition. Our findings reveal that, beyond atoms or clusters, glasses have another dimension of structural heterogeneity: "paths".</p>
Data From: Lighting pathways to success in STEM: A virtual Lab Meeting Program (LaMP) mutually benefits mentees and host labs
<p>Developing robust professional networks can help shape the trajectories of early career scientists. Yet, historical inequities in STEM fields make access to these networks highly variable across academic programs, and senior academics often have little time for mentoring. Here, we illustrate the success of a Virtual Lab Meeting Program (LaMP). In this program, we matched students ("Mentees") with a more experienced researcher ("Mentors") from a research group. The Mentees then attended the Mentors' lab meetings during the academic year with two lab meetings specifically dedicated to the Mentee's professional development. Survey results indicate that Mentees expanded their knowledge of the hidden curriculum as well as their professional network, while only requiring a few extra hours of their Mentor's time over eight months. In addition, host labs benefitted from Mentees sharing new perspectives and knowledge in lab meetings. The diversity of the Mentees was significantly higher than the Mentors, suggesting that the program increased the participation of traditionally underrepresented groups. Finally, we found that providing a stipend was very important to many mentees. We conclude that Virtual Lab Meeting Programs can be an inclusive and cost-effective way to foster trainee development and increase diversity within STEM fields with little additional time commitment.</p>
Pathway-based, reaction-specific annotation of disease variants for elucidation of molecular phenotypes
<p>Supplementary Tables and Supplementary Methods for the research article "Pathway-based, reaction-specific annotation of disease variants for elucidation of molecular phenotypes" published in Database.</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.