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7,327 results for “pathways”
Supplemetary data for the paper "Knockdown of circular RNA hsa_circ_0003307 inhibits synovial inflammation in ankylosing spondylitis by regulating the PI3K/AKT pathway" by Yanyan Fang, Jian Liu*, Yan Long, Jianting Wen, Dan Huang, Ling Xin
<p>Statistical analyses and graphs were performed using Prism 8 software (GraphPad, La Jolla, USA). Age was analyzed using Student's t test (Supplementary Table 1A,B). Expression of circRNA_0003307 in PBMCs was analyzed using Welch's t-test (Supplementary Table 2A,B). CircRNA_0003307 expression in AS-FLS was analyzed using a one-way analysis of variance, then Games-Howell test (Supplementary Table 4A–C). The p-PI3K protein expression in AS-FLS was analyzed using a one-way analysis of variance, then Games-Howell test (Supplementary Table 5A–C). The p-AKT protein expression in AS-FLS was analyzed using a one-way analysis of variance, then Games-Howell test (Supplementary Table 6A–C). The TNF-α levels in AS-FLS was analyzed using a one-way analysis of variance, then Games-Howell test (Supplementary Table 7A–C). The TNFAIP2 levels in AS-FLS was analyzed using a one-way analysis of variance, then Games-Howell test (Supplementary Table 8A–C). Categorical variables were compared using chi-square test. Correlations were assessed using Spearman’s analysis because clinical characteristics were not normally distributed (Supplementary Table 3). A receiver operating characteristic (ROC) curve analysis was performed to judge whether circRNA_0003307 can be used as a diagnostic indicator for AS. P <0.05 indicates that the difference was statistically significant.</p>
First-order visual interneurons distribute distinct contrast and luminance information across ON and OFF pathways to achieve stable behavior
<p>Source data of the paper Ketkar, Gür, Molina-Obando et al. 2022, eLife.<br> We analyzed the behavioral contribution and physiological response properties of first order interneurons L1, L2 and L3 in the <em>Drosophila melanogaster </em>visual system. Data are sorted by figures and comprise either behavioral measurements of flies walking on an air-cushioned ball while being shown visual stimuli, or <em>in vivo </em>two photon microscopy recordings of L1-L3 calcium responses. </p> <p>Please find all relevant information to use the data in the README file.<br> The code to analyze the data, either written in Matlab or Python, is found at <a href="https://github.com/silieslab/Ketkar-Gur-MolinaObando-etal2022">https://github.com/silieslab/Ketkar-Gur-MolinaObando-etal2022</a></p>
Fig. 5 in Circulation Pathways Of Trematodes Of Freshwater Gastropod Mollusks In Forest Biocenoses Of The Ukrainian Polissia
Fig. 5. The ratio of studied trematode species according to the classes of definitive hosts.
Fig. 4 in Circulation Pathways Of Trematodes Of Freshwater Gastropod Mollusks In Forest Biocenoses Of The Ukrainian Polissia
Fig. 4. Four-host life cycles of trematodes.
Fig. 1 in Circulation Pathways Of Trematodes Of Freshwater Gastropod Mollusks In Forest Biocenoses Of The Ukrainian Polissia
Fig. 1. Points — location of mollusc collection sites (ponds of Ukrainian Polissia).
GEOS-Chem 2015 Speciated PM2.5 Outputs for "Impact of circular- and single-sector waste-heat reuse pathways on PM2.5-air quality, CO2 emissions, and human health in India; material exchanges more viable to achieve sustainability targets"
<p>Daily PM2.5 and species outputs from GEOS-Chem Modeling over India (0.5° x 0.625°) </p>
Supplementary data as part of the article "The role of carbon capture, utilization and storage for economic pathways that limit global warming to below 1.5 °C" (https://doi.org/10.1016/j.isci.2022.104237).
<p>Data of the plots in Figure 1a and Figure 1b, showing, respectively, the incremental and the integrated global CO<sub>2</sub> emissions for the 1.5 °C-committed decarbonization pathways from IPCC (P1, P2, P3, and P4 pathways) and the one originally obtained in this work (Q pathway).</p>
Pathway2Text: Dataset for Biomedical Pathway Description Generation
<p>This is the dataset of the NAACL 2022 paper:</p> <p>Pathway2Text: Dataset and Method for Biomedical Pathway Description Generation.</p> <p>This dataset contains 2,367 pairs of biomedical pathways and textual descriptions. It can be used for automatic pathway description generation. In our paper, we showed it is also appropriate for Text2Graph and BioNER.</p> <p>Read readme.pdf for detaild information.</p>
Sensitization of FOLFOX-resistant colorectal cancer cells via the modulation of a novel pathway involving protein phosphatase 2A
<p>The treatment of colorectal cancer (CRC) with FOLFOX shows some efficacy, but these tumors quickly develop resistance to this treatment. We have observed an increased phosphorylation of AKT1/mTOR/4EBP1 and levels of p21 in FOLFOX-resistant CRC cells. We have identified a small molecule, NSC49L, that stimulates protein phosphatase 2A (PP2A) activity, downregulates the AKT1/mTOR/4EBP1-axis, and inhibits p21 translation. We have provided evidence that NSC49L- and TRAIL-mediated sensitization is synergistically induced in p21-knockdown CRC cells, which is reversed in p21-overexpressing cells. p21 binds with procaspase 3 and prevents activation of caspase 3. We have shown that TRAIL induces apoptosis through the activation of caspase 3 by NSC49L-mediated downregulation of p21 translation, and thereby cleavage of procaspase 3 into caspase 3. NSC49L does not affect global protein synthesis. These studies provide a mechanistic understanding of NSC49L as a PP2A agonist, and how its combination with TRAIL sensitizes FOLFOX-resistant CRC cells.</p>
Multishell Diffusion MR Tractography Yields Morphological and Microstructural Information of the Anterior Optic Pathway: A Proof-of-Concept Study in Patients with Leber's Hereditary Optic Neuropathy. RAW DATA
<p>Raw data used to prepare Figures and Tables in article "Multishell Diffusion MR Tractography Yields Morphological and Microstructural Information of the Anterior Optic Pathway: A Proof-of-Concept Study in Patients with Leber’s Hereditary Optic Neuropathy", accepted for publication at International Journal of Environmental Research and Public Health, 27 May 2022.</p>
Dataset: 1,000 QM/MM minimum energy pathway conformations for the deacylation reactions of GES-5/imipenem
<p>This dataset consists of 1,000 coordinate files (in the CHARMM psf/cor format) for the QM/MM minimum energy pathways of the deacylation reactions between a Class A beta-lactamases (GES-5) and the imipenem antibiotic molecules.</p> <p>All pathway conformations were optimized at DFTB3/3OB-f/CHARMM36 level with 36 replicas.</p> <p>All single point calculations and charge population analysis were done at B3LYP-D3/6-31+G(d,p)/CHARMM36 level.</p> <ul> <li>0.paths_ges_imi_d1.tar.gz: 500 pathway conformations for GES-5/IPM-Delta1 deacylation reactions.</li> <li>0.paths_ges_imi_d2.tar.gz: 500 pathway conformations for GES-5/IPM-Delta1 deacylation reactions.</li> <li>1.eners.zip: The single point replica energies along all GES-5/IPM pathways.</li> <li>1.chrgs.zip: The NBO charges of the QM region of all replica conformations along all GES-5/IPM pathways.</li> <li>2.datasets.zip: The Python codes to postprocess the molecular data and the featurized the NumPy arrays.</li> <li>3.gnn.zip: The Python codes that implements the edge-conditioned graph convolutional NN to predict the deacylation barriers.</li> <li>5.representative_conf.zip: The pathway conformations of all cluster centroids and an energetic representative (pathway id 22) pathway. Note: This file also serves as a peephole of how the pathway conformations from Reaction Path with Holonomic Constrains calculations looks like.</li> <li>6.benchmark.zip: The benchmark calculations that validates the DFTB3/3OB-f/CHARMM36 against DFTB3/3OB/CHARMM36 and B3LYP/6-31G(d,p)/CHARMM36 level of theory on the energetic representative (pathway id 22) pathway conformations. </li> <li>p.figures.zip: A series of Jupyter Notebooks that produces the visualizations in the work.</li> <li>README.md: A markdown file that contains additional descriptions.</li> <li>environment.yml: The Conda environment used for the graph-learning. </li> </ul> <p>Z. Song and P. Tao, Graph-Learning Guided Mechanistic Insights into Imipenem Hydrolysis in GES Carbapenemases. <strong><em>Electron. Struct.</em></strong> 2022, <strong>4</strong>, 034001. DOI: <a href="https://doi.org/10.1088/2516-1075/ac7993">10.1088/2516-1075/ac7993</a></p>
A feed-forward pathway drives LRRK2 kinase membrane recruitment and apparent activation
<p>Activating mutations in the Leucine Rich Repeat Kinase 2 (LRRK2) cause Parkinson's disease and activated LRRK2 phosphorylates a subset of Rab GTPases. Moreover, Golgi-associated Rab29 can recruit LRRK2 to the surface of the Golgi and activate it there for both auto- and Rab substrate phosphorylation. Here we define the precise Rab29 binding region of the LRRK2 Armadillo domain between residues 360-450 and show that this site, termed "Site #1", can also bind additional LRRK2 substrates, Rab8A and Rab10. Moreover, we identify a distinct, N-terminal, higher affinity interaction interface between LRRK2 phosphorylated Rab8 and Rab10 termed "Site #2", that can retain LRRK2 on membranes in cells to catalyze multiple, subsequent phosphorylation events. Kinase inhibitor washout experiments and mutation analysis demonstrate that rapid recovery of kinase activity in cells depends on the ability of LRRK2 to associate with phosphorylated Rab reaction products. Reconstitution of purified LRRK2 recruitment onto planar lipid bilayers decorated with Rab10 protein demonstrates cooperative association of only active LRRK2 with phospho-Rab10-containing membrane surfaces. These experiments reveal a feed-forward pathway that provides spatial control and apparent membrane activation of LRRK2 kinase activity.</p>
Dataset for Women's Career Pathway in Chemical Sciences; a Multi-stage Investigation in Kerala, India
<p>The dataset for the final report submitted to the Royal Society of Chemistry, as part of the project 'Women’s Career Pathway in Chemical Sciences; a Multi-stage Investigation in Kerala', funded by the Inclusion and Diversity Grant-2020 by the Royal Society of Chemistry (RSC), Cambridge, UK.</p> <p> </p>
The evolution of multi-gene families and metabolic pathways in the evening primroses (Oenothera: Onagraceae): a comparative transcriptomics approach
<p>The plant genus <em>Oenothera</em> has played an important role in the study of genome evolution and plant defense and reproduction. Here, we built on the 1kp transcriptomic dataset and developed a molecular resource of 63 transcriptomes and present a large-scale comparative study across 29 <em>Oenothera</em> species. We produced 2.3 million transcripts and 25.4 Mb of total length assembly per individual. We used this transcriptome resource to examine genome-wide evolutionary patterns and functional diversification by searching for orthologous genes and performed gene family evolution analysis. We found wide heterogeneity in gene family evolution across the genus, with section <em>Oenothera </em>exhibiting the most pronounced evolutionary changes. Overall, more significant expansions occurred than contractions. We also analyzed the molecular evolution of phenolic metabolism by retrieving proteins annotated for phenolic enzymatic complexes. We identified 1,568 phenolic genes arranged into 83 multigene families that varied widely across the genus. All taxa experienced rapid phenolic evolution involving 33 gene families, which exhibited large expansions, gaining about 2-fold more genes than they lost. Upstream enzymes phenylalanine ammonia-lyase (PAL) and 4-coumaroyl: CoA ligase (4CL) accounted for most of the significant expansions and contractions. Our results suggest that adaptive responses to environmental stress coupled with non-adaptive evolutionary forces have contributed to <em>Oenothera </em>diversification and rapid gene family evolution.</p>
Data From: Exploitation of an ancestral pheromone biosynthetic pathway contributes to diversification in Heliconius butterflies
<p class="MsoNormal"><span>During courtship, male butterflies produce androconial secretions containing male sex pheromones (MSPs) that communicate species identity and affect female choice. MSPs are thus likely candidates as reproductive barriers, yet their role in speciation remains poorly studied. Although <em>Heliconius </em>butterflies are a model system in speciation, their MSPs have not been investigated from a macroevolutionary perspective. We use GC-MS to characterise male androconial secretions in 33 of the 69 species in the Heliconiini tribe. We found these blends to be species-specific, consistent with a role in reproductive isolation. We detected a burst in blend diversification rate at the most speciose genus,<em> Heliconius</em>; a consequence of <em>Heliconius</em> and <em>Eueides</em> species using a fatty acid metabolic pathway to unlock more complex blends than basal Heliconiini species, whose secretions are dominated by plant derivatives. A comparison of 10 sister species pairs demonstrates a striking positive correlation between blend dissimilarity and range overlap, consistent with a scenario of character displacement or reinforcement in sympatry. These results demonstrate for the first time that MSP diversification can promote reproductive isolation across this group of butterflies, showcasing how re-activation of an ancestral trait, the co-option of the fatty acid metabolic pathway for pheromone production, can facilitate rapid speciation. </span></p>
More soil organic carbon is sequestered through the mycelium-pathway than through the root-pathway under nitrogen enrichment in an alpine forest
<p><span>Plant roots and associated mycorrhizae exert a large influence on soil carbon (C) cycling. Yet, little was known whether and how roots and </span><span>ectomycorrhizal</span><span> extraradical mycelia differentially contribute to soil organic C (SOC) accumulation in alpine forests under increasing nitrogen (N) deposition. Using ingrowth cores, the relative contributions of the root-pathway (RP) (i.e., roots and rhizosphere processes) and mycelium-pathway (MP) (i.e., extraradical mycelia and hyphosphere processes) to SOC accumulation were distinguished and quantified in an ectomycorrhizal-dominated forest receiving chronic N addition (25 kg N ha<sup>-1</sup> yr<sup>-1</sup>). Under the non-N addition, the RP facilitated SOC accumulation, while the MP reduced SOC accumulation. Nitrogen addition enhanced the positive effect of RP on SOC accumulation from +18.02 mg C g<sup>-1</sup> to +20.55 mg C g<sup>-1</sup> but counteracted the negative effect of MP on SOC accumulation from -5.62 mg C g<sup>-1</sup> to -0.57 mg C g<sup>-1</sup>, as compared to the non-N addition. Compared to the non-N addition, the N-induced SOC accumulation was 1.62~2.21 mg C g<sup>-1</sup> and 3.23~4.74 mg C g<sup>-1</sup>, in the RP and the MP, respectively. The greater contribution of MP to SOC accumulation was mainly attributed to the higher microbial C pump (MCP) efficacy (the proportion of</span><span> increased microbial residual C to the increased SOC under N addition) in the MP (72.5%) relative to the RP (57%). The higher MCP efficacy in the MP was mainly associated with the higher fungal metabolic activity (i.e., the greater fungal biomass and N-acetyl glucosidase activity) and greater binding efficiency of fungal residual C to mineral surfaces than those of RP. Collectively, our findings highlight the indispensable role of mycelia and hyphosphere processes in the formation and accumulation of stable SOC in the context of increasing N deposition.</span></p>
Bacterial-Type Long-Chain Polyphosphates Bind Human Proteins in the Phosphatidylinositol Signaling Pathway
<p>This dataset consists of 2 tabs.<br> Tab 1: Processed full data<br> This contains the full array data (all proteins), with brightest signals sorted to the top. The data was filtered according to the criteria laid out in the report (see column headers, cells formatted in red if criteria not met).<br> The right side of the table displays the raw data of the duplicate spots on the sample array (incubated with polyP-bio + Strept-532) and the control array (incubated with Strept-532 only). "</p> <p>Tab 2: Histone Controls<br> This contains the individual fluorescence values for the histone control spots (which are repeated in duplicate on each of the 48 subarrays, i.e. 96 values total), as well as their averages, side by side for sample and control array.</p> <p> </p>
Additional Data and Code from "Increased energy use for adaptation significantly impacts mitigation pathways".
<p>Additional Data and Code from: "Increased energy use for adaptation significantly impacts mitigation pathways".</p> <p>Authors: Francesco Pietro Colelli, Johannes Emmerling, Giacomo Marangoni, Malcolm Mistry, Enrica De Cian</p> <p>This repository contains:</p> <p>- The output data and R-scripts to produce the figures of the manuscript.</p> <p>- The code building the additional WITCH modules and input data generated. The results obtained in the study can be replicated by running the additional WITCH modules and input data in combination with the open source WITCH available in the repository: https://github.com/witch-team/witchmodel</p> <p> </p>
Microscopy data from: Identification of genetic interactions with priB links the PriA/PriB DNA replication restart pathway to double-strand DNA break repair in Escherichia coli
<p>Collisions between DNA replication complexes (replisomes) and impediments such as damaged DNA or proteins tightly bound to the chromosome lead to premature dissociation of replisomes at least once per cell cycle in <em>Escherichia coli</em>. Left unrepaired, these events produce incompletely replicated chromosomes that cannot be properly partitioned into daughter cells. DNA replication restart, the process that reloads replisomes at prematurely terminated sites, is therefore essential in <em>E. coli</em> and other bacteria. Three replication restart pathways have been identified in <em>E. coli</em>: PriA/PriB, PriA/PriC, and PriC/Rep. A limited number of genetic interactions between replication restart and other genome maintenance pathways have been defined, but a systematic study placing replication restart reactions in a broader cellular context has not been performed. We have utilized transposon insertion sequencing to identify new genetic interactions between DNA replication restart pathways and other cellular systems. Known genetic interactors with the <em>priB</em> replication restart gene (uniquely involved in the PriA/PriB pathway) were confirmed and several novel <em>priB </em>interactions were discovered. Far fewer connections were found with the PriA/PriC or PriC/Rep pathways, suggesting a primacy role for the PriA/PriB pathway in <em>E. coli</em>. Targeted genetic and imaging-based experiments with <em>priB</em> and its genetic partners revealed significant double-strand DNA break (DSB) accumulation in strains with mutations in <em>dam</em>, <em>rep</em>, <em>rdgC</em>, <em>lexA</em>, or <em>polA</em>. Modulating the activity of the RecA recombinase partially suppressed the detrimental effects of <em>rdgC</em> or <em>lexA</em> mutations in Δ<em>priB</em> cells. Taken together, our results highlight roles for several genes in DSB homeostasis and define a genetic network that facilitates DNA repair/processing upstream of PriA/PriB-mediated DNA replication restart in <em>E. coli</em>.</p>
Tracking Global Invasion Pathways of the Spongy Moth (Lepidoptera: Erebidae) to the U.S. using Stable Isotopes as Endogenous Biomarkers
<p>The spread of invasive insect species causes enormous ecological damage and economic losses worldwide. A reliable method that tracks back an invaded insect's origin would be of great use to entomologists, phytopathologists and pest managers. The spongy moth (Lymantria dispar (L.d.), Linnaeus 1758) is a persistent invasive pest in the north-eastern United States (U.S.) and periodically causes major defoliations in temperate forests. We analysed field-captured (Europe, Asia, U.S.) and lab-reared L.d. specimens for their natal isotopic hydrogen and nitrogen signatures imprinted in their biological tissues (δ2H and δ15N) and compared these values to the long-term mean δ2H of regional precipitation (Global Network of Isotopes in Precipitation) and δ15N of regional plants at the capture site. We established the percentage of hydrogen-deuterium exchange for L.d. tissue (Pex=8.2%) using the comparative equilibration method and two-source-mixing-models, which allowed the extraction of the moth's natal δ2H value. We confirmed that the natal δ2H and δ15N values of our specimens are related to the environmental signatures at their geographic origins. With our regression models, we were able to isolate potentially invasive individuals and give estimations of their geographic origin. To enable the application of these methods on eggs, we established an egg-to-adult fraction factor for L.d. (Δegg-adult = 16.3‰ ± 4.3‰). Our models suggested that around 25% of the field-captured spongy moths worldwide were not native in the investigated capture sites. East Asia was the most frequently identified location of probable origin. Furthermore, our data suggested that eggs found on cargo ships in U.S. harbors in Alaska, California and Louisiana most probably originated from Asian L.d. in East Russia. These findings show that stable isotope biomarkers give a unique insight into invasive insect species pathways and thus, can be an effective tool to monitor the spread of insect pest epidemics.</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.