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4,017 results for “Reduction”
Original data for article "Is Unsupervised Dimensionality Reduction Sufficient to Decode the Complexities of Electrochemical Impedance Spectra?"
<p>The uploaded Jupyter notebooks contain original data generation and processing methods used in the article "Is Unsupervised Dimensionality Reduction Sufficient to Decode the Complexities of Electrochemical Impedance Spectra?" by A. Makogon, F. Kanoufi, and V. Shkirskiy</p>
Dataset - Uncertainty Reduction in Biochemical Kinetic Models: Enforcing Desired Model Properties
<p>Data needed to reproduce the results from the manuscript “Uncertainty Reduction in Biochemical Kinetic Models: Enforcing Desired Model Properties" by L. Miskovic, J. Beal, M. Moret, and V. Hatzimanikatis</p> <p>1. Data generated with the ORACLE workflow that was used in the iSCHRUNK training:</p> <ul> <li>Classification label vectors for the three analyzed metabolic concentration cases: <ul> <li>Reference case: class_vector_train_ref.mat</li> <li>Extreme1 case: class_vector_train_ex1.mat</li> <li>Extreme2 case: class_vector_train_ex2.mat</li> </ul> </li> <li>Parameter sets used for training for the three analyzed metabolite concentration cases. As parameters, we used the degree of saturation of the enzyme active site, σ<sub>A</sub>, which is constrained between 0 and 1.<sub> </sub> <ul> <li>Reference case: training_set_ref.mat</li> <li>Extreme1 case: training_set_ex1.mat</li> <li>Extreme2 case: training_set_ex2.mat</li> </ul> </li> <li>Flux control coefficients of the xylose uptake rate (XTR) with respect to the network enzymes for the three cases. For the statistics and the figures we have used the population with removed outliers. <ul> <li>Reference case: ccXTR_ref.mat</li> <li>Extreme1 case: ccXTR_ex1.mat</li> <li>Extreme2 case: ccXTR_ex2.mat</li> </ul> </li> <li>Thermodynamics-based Flux Analysis (TFA) models for the three cases: <ul> <li>Reference case: tfa_ref.mat</li> <li>Extreme1 case: tfa_ex1.mat</li> <li>Extreme2 case: tfa_ex2.mat</li> </ul> </li> <li>Parameter names identical for the three cases <ul> <li>parameterNames.mat</li> </ul> </li> </ul> <p>2. Validation data generated with the ORACLE workflow with the parameters constrained using the information obtained with the iSCHRUNK (Figure 4).</p> <ul> <li>Flux control coefficients of the xylose uptake rate (XTR) with respect to the network enzymes for the three cases. For the statistics and the figures we have used the population with removed outliers. <ul> <li>ccXTR_ValidNeg.mat</li> </ul> </li> <li>Parameter sets used in validation <ul> <li>validation_set_neg.mat</li> </ul> </li> </ul> <p>3. Validation data generated with the ORACLE workflow with the parameters constrained using the information obtained with the iSCHRUNK (Table 3).</p> <ul> <li>Negative control: <ul> <li>Flux control coefficients of the xylose uptake rate (XTR) with respect to the network enzymes for the three cases. For the statistics and the figures we have used the population with removed outliers. <ul> <li>Reference case: ccXTR_ValidRef_neg_agg.mat</li> <li>Extreme1 case: ccXTR_ValidEx1_neg_agg.mat</li> <li>Extreme2 case: ccXTR_ValidEx2_neg_agg.mat</li> </ul> </li> <li>Parameter sets used for training for the three analyzed metabolite concentration cases. As parameters, we used the degree of saturation of the enzyme active site, σ<sub>A</sub>, which is constrained between 0 and 1.<sub> </sub> <ul> <li>Reference case: validation_set_ref_neg_agg.mat</li> <li>Extreme1 case: validation_set_ref_neg_agg.mat</li> <li>Extreme2 case: tvalidation_set_ref_neg_agg.mat</li> </ul> </li> </ul> </li> </ul> <ul> <li>Positive control: <ul> <li>Flux control coefficients of the xylose uptake rate (XTR) with respect to the network enzymes for the three cases. For the statistics and the figures we have used the population with removed outliers. <ul> <li>Reference case: ccXTR_ValidRef_pos_agg.mat</li> <li>Extreme1 case: ccXTR_ValidEx1_pos_agg.mat</li> <li>Extreme2 case: ccXTR_ValidEx2_pos_agg.mat</li> </ul> </li> <li>Parameter sets used for training for the three analyzed metabolite concentration cases. As parameters, we used the degree of saturation of the enzyme active site, σ<sub>A</sub>, which is constrained between 0 and 1.<sub> </sub> <ul> <li>Reference case: validation_set_ref_pos_agg.mat</li> <li>Extreme1 case: validation_set_ex1_pos_agg.mat</li> <li>Extreme2 case: validation_set_ex2_pos_agg.mat</li> </ul> </li> </ul> </li> </ul> <p>4. Reassignment study: validation data generated with the ORACLE workflow with the parameters constrained using the information obtained with the iSCHRUNK (Figure 6 and Table 4).</p> <ul> <li>Negative control: <ul> <li>Flux control coefficients of the xylose uptake rate (XTR) with respect to the network enzymes. For the statistics and the figures we have used the population with removed outliers. <ul> <li>Reference case: ccXTR_Valid_reassignment_neg.mat</li> </ul> </li> <li>Parameter sets used for training for the three analyzed metabolite concentration cases. As parameters, we used the degree of saturation of the enzyme active site, σ<sub>A</sub>, which is constrained between 0 and 1.<sub> </sub> <ul> <li>Reference case: validation_set_neg_reassignment.mat</li> </ul> </li> </ul> </li> <li>Positive control: <ul> <li>Flux control coefficients of the xylose uptake rate (XTR) with respect to the network enzymes. For the statistics and the figures we have used the population with removed outliers. <ul> <li>Reference case: ccXTR_Valid_reassignment_pos.mat</li> </ul> </li> <li>Parameter sets used for training for the three analyzed metabolite concentration cases. As parameters, we used the degree of saturation of the enzyme active site, σ<sub>A</sub>, which is constrained between 0 and 1.<sub> </sub> <ul> <li>Reference case: validation_set_pos_reassignment.mat</li> </ul> </li> </ul> </li> </ul> <p> </p> <p> </p>
Data archive for: Resting cells of Skeletonema marinoi assimilate organic compounds and respire by dissimilatory nitrate reduction to ammonium in dark, anoxic conditions
<p>Data archive for: “Resting cells of <em>Skeletonema marinoi</em> assimilate organic compounds and respire by dissimilatory nitrate reduction to ammonium in dark, anoxic conditions” <a href="https://doi.org/10.1111/1462-2920.16625">https://doi.org/10.1111/1462-2920.16625</a></p> <p> </p> <p>Dataset of single cell assimilation of organic/inorganic C/N by resting cells of the marine diatom <em>Skeletonema marinoi</em> captured using secondary ion mass spectrometry (SIMS) and stable isotopic tracers. The dataset also contains POC/PON changes over time during dormancy, DNRA (<sup>15</sup>N-NH<sub>4</sub><sup>+</sup> production), denitrification (<sup>15</sup>N-N<sub>2</sub> production) and a germination assay to determine survival rate, most probable number analysis (MPN). </p> <p>Two strains (GF04 and R05) were incubated in dark and anoxic conditions in two different incubation experiments.</p> <p>Incubation 1: Diatoms treated with antibiotics before entering dormancy compared to a control not treated with antibiotics then given <sup>15</sup>N-NO<sub>3</sub><sup>-</sup> in dark anoxic conditions.</p> <p>Incubation 2: Diatoms treated with antibiotics given, <sup>15</sup>N & <sup>13</sup>C urea, <sup>15</sup>N & <sup>13</sup>C urea + <sup>14</sup>N-NO<sub>3</sub><sup>-</sup>, <sup>13</sup>C-acetate, <sup>13</sup>C-acetate + <sup>15</sup>N-NO<sub>3</sub><sup>-</sup>, or <sup>15</sup>N-NO<sub>3</sub><sup>-</sup>.</p> <p>See the main manuscript for a extensive experimental setup.</p> <p> </p> <p><strong>Each file is uploaded as both a .CSV and .XLSX, so that you can choose which you prefer.</strong></p> <p><strong>DNRA_and_denitrification.csv/xlsx:</strong> DRNA and denitrification depending on volume (Incubation 1)</p> <p><strong>DNRA_per_cell.csv/xlsx:</strong> DNRA per cell (Incubation 1 & 2)</p> <p><strong>MPN_data.csv/xlsx:</strong> Most probable number analysis (Incubation 1 & 2)</p> <p><strong>POC_PON.csv/xlsx:</strong> POC and PON per cell and volume (Incubation 1 & 2)</p> <p><strong>SIMS_data.csv/xlsx:</strong> SIMS data (Incubation 1 & 2)</p> <p> </p> <p> </p>
HDX-MS dataset for: "Glycan-induced structural activation softens the human papillomavirus capsid for entry through reduction of intercapsomere flexibility"
<p>Hydrogen/deuterium exchange mass spectrometry dataset used in: <strong>Glycan-induced structural activation softens the human papillomavirus capsid for entry through reduction of intercapsomere flexibility.</strong> Yuzhen Feng*, Dominik van Bodegraven*, Alan Kádek*, Ignacio L.B. Munguira, Laura Soria-Martinez, Sarah Nentwich, Sreedeepa Saha, Florian Chardon, Daniel Kavan, Charlotte Uetrecht#, Mario Schelhaas#, Wouter H. Roos#. <em>Nature Communications</em> 10076 (2024). doi: 10.1038/s41467-024-54373-0</p> <p>* - authors contributing equally</p> <p># - corresponding authors</p> <p><strong>Description:</strong></p> <p>Hydrogen/deuterium exchange mass spectrometry (HXMS) analysis of the effect of heparin on the conformational dynamics of human papillomavirus 16 pseudovirus (PsV).</p> <p><strong>Sample processing:</strong></p> <p>HPV16 PsV were prepared according to (Buck & Thompson: Current Protocols in Cell Biology 2007). In short, p16Shell and pClneo-EGFP were transfected into HEK293TT cells. After 48 h, cells were harvested and lysed followed by maturation of the virus particles for 24 h. For purification, the particles were purified using a CsCl step gradient (27 % w/V and 38.8 % w/V CsCl in 10 mM Tris-HCl pH 7.4, 207570 x g, 3 h 50 min, 4 °C) followed by dialysis in Float-A-Lyzer devices (1 mL, Spectra/Por) against a total of 3 L HPV virion buffer (1x PBS, 635 mM NaCl, 0.9 mM CaCl2, 0.5 mM MgCl2, 2.1 mM KCl, pH 7.4).</p> <p>PsV were pre-incubated for 1 h either with or without heparin (H4784, Sigma-Aldrich) at room temperature. To initiate deuterium labelling the samples were 6-fold diluted with the virion buffer they were obtained in, only made of 99.9% D2O (150 mM NaCl, 4.8 mM KCl, 10 mM Na2HPO4, 1.8 mM KH2PO4, 0.9 mM CaCl2, 0.5 mM MgCl2, pD 7.2). This resulted in a final concentration of 0.5 µM L1 monomer in the form of PsV with or without 1 mg/ml heparin during deuterium labelling. The exchange reaction was left to proceed at room temperature until aliquots of 45 µl were removed at predetermined time points (1 min, 5 min, 15 min, 1 h and 4 h). In the aliquots, the exchange was immediately stopped by twofold dilution with ice-cold quench buffer (0.25 M glycine, 100 mM TCEP, 8 M urea, indicated pH 2.7), resulting in final pH 2.5. For samples with heparin, the quench buffer additionally contained 1 mg/ml protamine sulphate (P4020, Sigma-Aldrich). After 30 s incubation on ice, the samples were centrifuged at 10.000 x g for 1 min at 0 °C. Each supernatant was transferred to a fresh tube and flash frozen in liquid nitrogen. Low binding microtubes and low binding pipette tips (both Axygen) were used throughout for all handling of viral particles.</p> <p>The frozen samples were quickly thawed and injected into a refrigerated (1°C) HPLC system (Infinity 1260, Agilent Technologies), through a porcine pepsin column (≥ 3200 units/mg, Sigma-Aldrich) in-house immobilized onto POROS-20AL perfusion resin (Thermo Scientific) as described previously (Wang et al.: Molecular & Cellular Proteomics 2002), which was kept at 4°C. Pepsin digestion was performed at isocratic 200 µl/min flow rate (0.4 % formic acid in water). After the digestion, peptides were online desalted for 3 min on a peptide microtrap (OPTI-TRAP, Optimize Technologies) and then eluted on a reversed-phase analytical column (ZORBAX 300SB-C18, 0.5 x 35 mm, 3.5 µm, 300Å, Agilent Technologies). There LC separation proceeded at 25 µl/min flow rate through an 8 min gradient of 8–30% solvent B, followed by a 3 min gradient of 30-90 % solvent B (solvent A: 0.4 % formic acid in water, solvent B: 0.4 % formic acid in acetonitrile). The outlet of the HPLC system was connected to an electrospray ionization (ESI) source of an Orbitrap Fusion Tribrid Mass Spectrometer (Thermo Scientific). The instrument was operated in positive ESI MS-only mode for deuterated samples, scan range 300-2000 m/z, using 4 microscans at resolving power setting 120,000. In a separate measurement on non-deuterated sample, the instrument was used in positive data-dependent ESI MS/MS mode with 30% HCD dissociation, 1 microscan and 240,000 resolving power setting for the identification of all peptides produced by non-specific pepsin cleavage.</p> <p>In total 22 pmol and 50 pmol L1 protein were injected per MS and MS/MS analysis, respectively. To minimize sample carry-over on the protease column, two washing solutions were always injected between sample injections modified from Majumdar et al. 69 (wash solution 1: 5% acetonitrile, 5% isopropanol, 20% acetic acid; wash solution 2: 4 M Urea, 1 M glycine, pH 2.5). All HDX samples were analysed in technical triplicates, except for the 15 min time point for PsV without heparin, which was measured in duplicate.</p> <p><br><strong>Data processing:</strong></p> <p>Peptides were identified from the MS/MS data by the Andromeda search algorithm implemented in MaxQuant (version 1.6.5.0) using a custom protein database containing the sequences of HPV16 L1 and L2 proteins. Deuterium uptake for the identified peptides was calculated with DeutEx (in-house developed), manually inspected and the statistical significance of the observed differences in deuteration was evaluated by applying an unpaired two-tailed Student’s T-test with single pooled variance evaluated with alpha ≤ 0.05 using the Holm-Šidák correction for multiple comparisons in Prism 8.0.1 (GraphPad Software). The processed data were visualized using MSTools (https://peterslab.org/MSTools/, Kavan & Man: International Journal of Mass Spectrometry 2011) and open-source PyMol 2.6.0a0 (Schrödinger, Inc).</p> <p>For ZENODO the datafiles were deposited as native Thermo .raw files (including instrumental parameters metadata) while all peaks in the spectra were additionally exported into plain m/z vs intensity .txt files per each scan in the LC-MS analysis as also used for the DeutEx HDX-MS processing.</p>
Post‐processed data and analysis codes for the research "Significant reduction of potential exposure to extreme marine heatwaves by achieving carbon neutrality"
<p>[Earth's Future] Oh et al. "Significant reduction of potential exposure to extreme marine heatwaves by achieving carbon neutrality"</p> <p>1. Information for Raw datasets<br>- The data of eight global climate models from the Coupled Model Intercomparison Project Phase 6 (CMIP6) can be accessed at https://esgf-node.llnl.gov/search/cmip6/, <br> and can also be accessed in Eyring et al. (2016). <br>- The NOAA OISST high resolution dataset can be obtained in Reynolds et al. (2007) or via https://psl.noaa.gov/data/gridded/data.noaa.oisst.v2.highres.html. <br>- The five ocean mask dataset can be obtained from https://reccap2-ocean.github.io/regions/. </p> <p>2. Information for Software<br>- The raw data in this study were analyzed using Fortran 90, R version 4.0.3, and Grads version 2.2.1.<br>- The Fortran 90 can be accessed at https://www.intel.com/content/www/us/en/developer/articles/tool/oneapi-standalone-components.html#fortran. <br>- The R version 4.0.3 is available from https://cran.r-project.org/bin/windows/base/old/4.0.3/. <br>- The Grads version 2.2.1 can be downloaded from http://cola.gmu.edu/grads/downloads.php.</p> <p>3. Information for Post-Processed data and Codes used in this work.<br>Please find each folder and the relevant post-processed dataset and codes.</p>
Data from: Evidence for reductions in physical and chemical plant defense traits in island flora
<p>Reduced defense against large herbivores has been suggested to be part of the "island syndrome" in plants. However, empirical evidence for this pattern is mixed. In this paper, we present two studies that compare putative physical and chemical defense traits from plants on the California Channel Islands and nearby mainland based on sampling of both field and common garden plants. In the first study, we focus on five pairs of woody shrubs from three island and three mainland locations and find evidence for increased leaf area, decreased marginal leaf spines, and decreased concentrations of cyanogenic glycosides in island plants. We observed similar increases in leaf area and decreases in defense traits when comparing island and mainland genotypes grown together in botanic gardens, suggesting that trait differences are not solely driven by abiotic differences between island and mainland sites. In the second study, we conducted a common garden experiment with a perennial herb—<em>Stachys bullata </em>(Lamiaceae)—collected from two island and four mainland locations. Compared to their mainland relatives, island genotypes show highly reduced glandular trichomes and a nearly 100-fold reduction in mono- and sesquiterpene compounds from leaf surfaces. Island genotypes also had significantly higher specific leaf area, somewhat lower rates of gas exchange, and greater aboveground biomass than mainland genotypes across two years of study, potentially reflecting a broader shift in growth habit. Together, our results provide evidence for reduced expression of putative defense traits in island plants, though these results may reflect adaptation to both biotic (i.e., the historical absence of large herbivores) and climatic conditions on islands.</p>
Data of "Recurrent Neural Networks (RNNs) with dimensionality reduction and break down in computational mechanics; application to multi-scale localization step."
<p>Data related to<br> ===========<br> title = "Recurrent Neural Networks (RNNs) with dimensionality reduction and break down in computational mechanics; application to multi-scale localization step.",<br> journal = "Computer Methods in Applied Mechanics and Engineering",<br> volume ="390",<br> year = "2022",<br> doi = "https://doi.org/<a href="http://dx.doi.org/10.1016/j.cma.2021.114476">10.1016/j.cma.2021.114476</a> ",<br> pages = "114476 ",<br> author = "Wu, Ling and Noels, Ludovic"</p> <p>We would be grateful if you could cite the paper in the case in which you are using the data</p> <p> </p> <p>The files replace version 1 whose zip was corrupted.</p> <p> </p>
Reproducibility Package: Automata-Driven Partial Order Reduction and Guided Search for LTL
<p>Reproducibility package for the paper <strong>Automata-Driven Partial Order Reduction and Guided Search for LTL Model Checking</strong> accepted for VMCAI'22.</p> <p>Contains scripts, 64-bit Linux binaries, and the dataset used to run the experiments detailed in the paper, a source code snapshot used to compile those binaries, as well as scripts for processing the results into the tables seen in the paper. The file README.md contains details on running the various parts of the artifacts, assuming a Linux environment.</p>
Data from: The 2018 European heatwave led to stem dehydration but not to consistent growth reductions in forests
<p>Heatwaves exert disproportionately strong and sometimes irreversible impacts on forest ecosystems. These impacts remain poorly understood at the tree and species level and across large spatial scales. Here, we investigate the effects of the record-breaking 2018 European heatwave on tree growth and tree water status using a collection of high-temporal resolution dendrometer data from 21 species across 53 sites. Relative to the two preceding years, annual stem growth was not consistently reduced by the 2018 heatwave but stems experienced twice the temporary shrinkage due to depletion of water reserves. Conifer species were less capable of rehydrating overnight than broadleaves across gradients of soil and atmospheric drought, suggesting less resilience toward transient stress. In particular, Norway spruce and Scots pine experienced extensive stem dehydration. Our high-resolution dendrometer network was suitable to disentangle the effects of a severe heatwave on tree growth and desiccation at large-spatial scales in situ, and provided insights on which species may be more vulnerable to climate extremes.</p>
BeMAGIC_Reduction of coercivity in magnetic materials upon voltage application
<p>BeMAGIC ITN (GA861145) Reduction of coercivity in magnetic materials upon voltage application. Results from UCAM, IFW/TUC and INRIM.</p>
Microbial iron(III) reduction during palsa collapse promotes greenhouse gas emissions before complete permafrost thaw
<p>Data associated with publication "Microbial iron(III) reduction during palsa collapse promotes greenhouse gas emissions before complete permafrost thaw". The data contained within this data set is arranged according to the main text and the supplementary information of this publication.</p> <p><strong>Background information</strong></p> <p>Field site: Stordalen mire, Abisko, Sweden (68 22ʹ N, 19 03ʹ E)</p> <p>Thaw stages: Palsa, bog and fen</p> <p>Type of samples: Gas samples, porewater samples, soil core samples</p>
Raw and analyzed data for manuscript "Dielectric barrier discharge plasma reduction of oxidized copper surfaces in an Ar/SiH4 atmosphere"
<p><strong>Abstract:</strong></p> <p>Nowadays, cold plasma techniques like dielectric barrier discharge (DBD) plasmas have attracted considerable interest in view of high deoxidation efficiencies as well as relative simplicity of setups. Although DBD plasma deoxidation of copper has been mainly studied in Ar/H<sub>2</sub> mixtures, there is no information on reduction performance of such methods in other protective atmospheres. In this study, the reduction of natively oxidized copper surfaces using a DBD plasma in an Ar/SiH<sub>4</sub> atmosphere at 100 hPa and 20 °C was investigated. The influence of a silane gas on the deoxidation performance was studied by varying the SiH<sub>4</sub> concentration from 0.0 to 0.5 vol%. An addition of a SiH<sub>4</sub> gas to an Ar atmosphere results in the increase of the deoxidation effect of a DBD plasma, so almost all Cu<sub>2</sub>O was reduced after around 10 s of treatment in 0.1 vol% silane. Surface morphology analysis showed formation of particles after Ar/SiH<sub>4</sub> plasma treatments, which can be cleaned from the surfaces by wiping. Additionally, characterization of the plasma phase indicated the presence of SiH<sup>*</sup> radicals, which likely play a role in the deoxidation effect. Moreover, an elimination of residual oxygen and nitrogen species in Ar by addition of SiH<sub>4</sub> was observed.</p>
Supplementary Figures, Files and Datasets: Reduction of Metastasis via Epigenetic Modulation in a Murine Model of Metastatic Triple Negative Breast Cancer (TNBC)
<p>*denotes authors contributed equally to this work</p> <p>FileS1_Figures_Proofread.pdf: (Updated) Supplementary Figures (Figure S1: RNA-sequencing experimental design; Figure S2: Experiments measuring proliferation between drug-treated and control conditions indicate no significant difference 6 hrs. after scratch; Figure S3: Effect of 4SC-202 treatment on 4T1 tumor volume in mice; Figure S4: Differential expression between 4SC-202- and Vorinostat-treated 4T1 tumors; Figure S5: Top underexpressed differentially expressed genes 4SC-202 vs Control; Figure S6: HDACi target genes are not differentially expressed in RNA-sequencing data from 4SC-202-treated mice relative to control mice; Figure S7: Differential expression and expression of genes implicated gene ontology biological processes of interest; Figure S8: IPA visualization of the Regulation of Epithelial Mesenchymal Transition By Growth Factors Pathway emphasizing influence of 4SC-202-induced consensus DEGs; Figure S9: 4SC-202 modulates gene networks related to Cancer, Endocrine System Disorders, and Organismal Injury and Abnormalities; Figure S10: 4SC-202 modulates gene networks related to Cancer, Cellular Movement, and Organismal Injury and Abnormalities; Figure S11: 4SC-202 modulates gene networks related to Cell-mediated Immune Response, Cellular Movement, and Hematological System Development and Function; Figure S12: 4SC-202 differentially modulates gene networks related to Cellular Movement, Hematological System Development and Function, and Immune Cell Trafficking relative to Vorinostat); File S2: DAVID 4SC vs. Control 70DEG results: DAVID Annotation 4SC-202 vs Control 70 DEGs: Full functional annotation clustering results from DAVID Bioinformatics Resource for the 4SC-202-induced, consensus differentially expressed genes.; File S3: DAVID 4SC vs. Vori 33 DEGs results: DAVID Annotation 4SC-202 vs Control 33 DEGs: Full functional annotation clustering results from DAVID Bioinformatics Resource for the 4SC-202 versus Vorinostat consensus differentially expressed genes.; File S4: IPA 70 All Results: IPA Canonical Pathways Enrichment 70 DEGs: Full Ingenuity Pathway Analysis (IPA) canonical pathways enrichment results for the 4SC-202-induced, consensus differentially expressed genes.; File S5: IPA 33 Summary: Ingenuity Pathway Analysis (IPA) summary of the enrichment results for the 4SC-202-induced, consensus differentially expressed genes against Vorinostat.; File S6: Experiment RIN Numbers: RNA extraction quality control step, one of the various steps of quality control within the RNA-sequencing workflow. These RNA Integrity numbers are from the Agilent 2100 Bioanalyzer that looks for RNA contamination and degradation.; File S7: 4SC vs. Control all DEGs: Workflow results including all DEGs for 4SC-202 vs Control: Full excel file that contains all of the DEGs from the results of all workflows for 4SC-202.</p>
Contrasting parasite-mediated reductions in fitness within vs. between patches of a nematode host
<p>Host and parasites interact across spatial scales, but parasite-mediated fitness effects are often measured at local scales only. Recent work suggests that parasites can reduce host fitness during dispersal between patches, highlighting the potential for both within- and between-patch effects to contribute to the net fitness consequences of parasitism. Building on this work, we measured the contribution of the dispersal phase to parasite-mediated reductions in host fitness. We used the nematode <em>Caenorhabditis elegans</em> and its natural microsporidian parasite <em>Nematocida parisii</em> to quantify the fitness consequences of parasitism at the individual, population, and metapopulation level. <em>N. parisii</em> reduced individual fecundity and population growth but had its greatest fitness impact at the dispersal stage: parasitism reduced the fitness of dispersing larvae by 63 – 100%. These results indicate that the cost of parasitism in this system is greatly underestimated if the metapopulation level is not taken into account. We also found that the effects of <em>N. parisii</em> vary with host genotype, and the relative advantage of the most resistant genotype increases with inclusion of the dispersal stage. Taken together, our findings demonstrate that host-parasite interactions at the dispersal stage magnify selection for parasite resistance.</p>
Long-term dynamics of trace elements concentrations in the organism of the shrews (Sorex) during the periods of high and reduction emissions from the copper smelter
<p>Data and code for mixed-model analysis for the article: </p> <p>Mukhacheva S.V. (2022) Long-term dynamics of trace elements concentrations in the organism of the shrews (Sorex) during the periods of high and reduction emissions from the copper smelter" // Russian Journal of Ecology. Vol. 5. </p> <p>Data provided by S.V. Mukhacheva</p> <p>Code provided by A.N. Sozontov</p>
Climate Response to ~23% Albedo Reduction in IPSL-CM5A2-LR
<p>The dataset consists of IPSL-CM5A2-LR outputs from a present-day control (pdControl, Con) and 23% Arctic sea ice albedo reduction experiment (Alb). Both sets of experiments are annual means for 200 years of simulation. The Con has 12 members from two restarts (7 and 5) and the Alb experiment has 14 members from the same restarts (9 and 5). Annual datasets include: Winter (JFM) and summer (JAS) sea ice area fraction (SIA), Atlantic overturning streamfunction (zomsfatl,msftrho), sea level pressure (SLP), sea surface temperature (TOS), sea surface salinity (SOS), barotropic streamfunction (BSF), zonal windstress (TAUX), and meridional windstress (TAUY). Since there are two restarts from different model years, the time axis has been changed to count years of the experiment (i.e. 1,2,3,...200). The anomalies of the Alb experiment are also provided taking into account the respective control. The missing data is recorded as nan.</p> <p>The datasets are created from the IPSL-CM5A-LR output files, using CDO and Python3 commands to combine and create annual averages.</p>
EPIC: Annotated epileptic EEG independent components for artifact reduction
<p>Scalp electroencephalogram is a non-invasive multi-channel biosignal that records the brain’s electrical activity. It is highly susceptible to noise that might overshadow important data. Independent component analysis is one of the most used artifact removal methods. Independent component analysis separates data into different components, although it can not automatically reject the noisy ones. Therefore, experts are needed to decide which components must be removed before reconstructing the data. To automate this method, researchers have developed classifiers to identify noisy components. However, to build these classifiers, they need annotated data. Manually classifying independent components is a time-consuming task. Furthermore, few labeled data are publicly available. This dataset is composed of a source of annotated electroencephalogram independent components acquired from patients with epilepsy (EPIC Dataset). This dataset contains 77,426 independent components obtained from approximately 613 hours of electroencephalogram, visually inspected by two experts, which was already successfully utilized to develop independent component classifiers.</p>
Dataset to "Hydride Formation Diminishes CO2 Reduction Rate on Palladium"
<p>Dataset to "Hydride Formation Diminishes CO2 Reduction Rate on Palladium" as published in ChemPhysChem, 20 (2019), 1398-1403</p>
Attempting genetic inference from directional asymmetry during convergent hindlimb reduction in squamates
<p>Loss and reduction of paired appendages is common in vertebrate evolution. How often does such convergent evolution depend on similar developmental and genetic pathways? For example, many populations of the Threespine Stickleback and Ninespine Stickleback (Gasterosteidae) have independently evolved pelvic reduction, usually based on independent mutations that caused reduced <em>Pitx1</em> expression. Reduced <em>Pitx1</em> expression has also been implicated in pelvic reduction in manatees. Thus, hind limb reduction stemming from reduced <em>Pitx1</em> expression has arisen independently in groups that diverged tens to hundreds of millions of years ago, suggesting a potential for repeated use of <em>Pitx1</em> across vertebrates. Notably, hindlimb reduction based on reduction of <em>Pitx1</em> expression produces left-larger directional asymmetry in the vestiges. We used this phenotypic signature as a genetic proxy, testing for hindlimb directional asymmetry in six genera of squamate reptiles that independently evolved hindlimb reduction and for which genetic and developmental tools are not yet developed: <em>Agamodon</em> <em>anguliceps</em>, <em>Bachia</em> <em>intermedia</em>, <em>Chalcides</em> <em>sepsoides</em>, <em>Indotyphlops</em> <em>braminus</em>, <em>Ophisaurus</em> <em>attenuatuas</em> and <em>O</em>. <em>ventralis</em>, and <em>Teius</em> <em>teyou</em>. Significant asymmetry occurred in one taxon, <em>Chalcides</em> <em>sepsoides</em>, whose left-side pelvis and femur vestiges were 18% and 64% larger than right-side vestiges, respectively, suggesting modification of <em>Pitx1</em> expression in that species. However, there was either right-larger asymmetry or no directional asymmetry in the other five taxa, suggesting multiple developmental genetic pathways to hindlimb reduction in squamates and vertebrates more generally.</p>
Raw data for "Fluorescence crosstalk reduction by modulated excitation-synchronous acquisition for multispectral analysis in high-throughput droplet microfluidics."
<p>Raw data to quantify the crosstalk reduction and signal resolution improvement by MESA used in Figure 3 and 4.</p> <p><br> </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
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