Find research datasets worth reusing

Datasets corresponding to "Direct evaluation of antiplatelet therapy in coronary artery disease by comprehensive image-based profiling of circulating platelets"

Datasets corresponding to "Direct evaluation of antiplatelet therapy in coronary artery disease by comprehensive image-based profiling of circulating platelets" 02_CNN_PhenotypeClassif.7z CNN Phenotype classification. Model was trained using AIDeveloper. using manually labelled data. Labelled Data is contained in folder "03_GatedData". The AIDeveloper session file in "02_Model\M10_Nitta6l_32pix_8class_meta.xlsx" shows, which files correspond to which subpopulation. The final model "M10_Nitta6l_32pix_8class_448.model" and corresponding .pb files are also located in that folder. codeforclassification.zip Code for applying model on unlabelled data. Test data is contained in 'sampledata.zip'

Small orbital forcing changes alter the ocean circulation of Earth's next future supercontinent: Simulations

This dataset contains the simulations from the manuscript "Small orbital forcing changes alter the ocean circulation of Earth's next future supercontinent". From the methods section of the manuscript: The simulations are carried out using the fully-coupled ocean-atmosphere general circulation model ROCKE-3D version Planet 1.0 (R3D1) (Way et al., 2017). The model is run at a horizontal resolution of 4 x 5 degrees and simulations were integrated for 5000 and 7000 years for PD and future forcing, respectively, to ensure they were in equilibrium. The topography and bathymetry is the one used by Way et al. (2021) in their simulation 2 (Aurica). This includes a fully dynamic ocean 4252 m deep and land elevations close to present day mean topography and elevations between 1 and 858 m. Due to high uncertainties in its future evolution, atmospheric composition is kept constant at year 1850 levels, following the setup in Way et al. (2021): the atmosphere is dominated by nitrogen with 21% oxygen, 285 ppmv CO2, 0.3 ppmv N2O and 0.79 ppmv CH4, and no aerosols or ozone are included. Two simulations are presented: PD_Aurica which which has present-day day-length (24 hrs) and insolation (1361 Wm-2) and F_Aurica where we apply orbital forcing consistent with 250 Ma into the future - day length is increased by 0.5 hrs and insolation is increased by 2.6 Wm-2 (see Way et al., 2021).  PD_Aurica corresponds to the output files with the following names: ANN4500-4999.*F_AURICA_RAND_PD_03.nc F_Aurica corresponds to the output files with the following names: ANN6500-6999.*F_AURICA_RAND_PD_01.nc The diagnostic files including AGC, AIJ, AIJK and AIJL in the filename contain atmospheric diagnostics and outputs, whereas those that include OIJ, OIJL, OJL and OTJ contain ocean diagnostics and outputs. <a href="https://science.gsfc.nasa.gov/author/533569006/35432">Way M. J.</a>, <a href="https://science.gsfc.nasa.gov/author/830545035/35432">I. Aleinov</a>, D. S. Amundsen, <a title="See all authors for this publication">et al.</a> 2017. "Resolving Orbital and Climate Keys of Earth and Extraterrestrial Environments with Dynamics (ROCKE-3D) 1.0: A General Circulation Model for Simulating the Climates of Rocky Planets." The Astrophysical Journal Supplement Series 231 (1): 12 [<a href="http://dx.doi.org/10.3847/1538-4365/aa7a06">10.3847/1538-4365/aa7a06</a>] <a href="https://science.gsfc.nasa.gov/author/533569006/42520">Way M. J.</a>, H. S. Davies, J. C. Duarte, <a title="See all authors for this publication">et al.</a> 2021. "The Climates of Earth’s Next Supercontinent: Effects of Tectonics, Rotation Rate, and Insolation." Geochemistry, Geophysics, Geosystems 22 (8): [<a href="http://dx.doi.org/10.1029/2021gc009983">10.1029/2021gc009983</a>]

Genome-wide association study for circulating metabolites in 619,372 individuals

<h2>Genome-wide association study for circulating metabolites in 619,372 individuals</h2> Preprint:  <a href="https://doi.org/10.1101/2024.10.15.24315557">https://doi.org/10.1101/2024.10.15.24315557</a> meta_ALL - meta-analysis across Estonian Biobank and six genetic ancestry groups of the UK Biobank meta_EUR - meta-analysis across Estonian Biobank and EUR genetic acestry group of the UK Biobank *_all_lead_varaints.tsv - all genome-wide significant lead variants detected for each of the 249 tested metabolites *_independent_lead_variants.tsv - indepedendent lead variants that were in high LD with each other (r2 > 0.8).

How to assess similarities and differences between mantle circulation models and Earth using disparate independent observations: Data and Analysis

Dataset includes simulation output produced by a TERRA simulation for `How to assess similarities and differences between mantle circulation models and Earth using disparate independent observations'.    <h3>Description of data file contents</h3> <ul> <li>NC*comp.tar.gz - compressed archives containing NetCDF files (file-per-process) with TERRA grid data including temperature, velocity, interpolated bulk composition, denisty, and voscosity fields. Can be read using <a title="terratools" href="https://github.com/mantle-convection-constrained/terratools" target="_blank" rel="noopener">terratools</a>. *dump number</li> <li>NC_seis_037.tar.gz - compressed archive containing NetCDF files (file-per-process) with predicted seismic properties at the resolution of the TERRA grid generated from the present day state of the simulated mantle, including elastic and anelastic Vs and Vp, bulk sound velocity, and predicted density from mineral phyiscs tables. Can be read using <a title="terratools" href="https://github.com/mantle-convection-constrained/terratools" target="_blank" rel="noopener">terratools</a>.</li> <li>NC_hpes_037.tar.gz - compressed archive containing NetCDF files (file-per-process) with interpolated abundances at the resolution of the TERRA grid for isotopes including the heat-producing elements ^40^K, ^232^Th, ^235^U and ^238^U. Can be read using <a title="terratools" href="https://github.com/mantle-convection-constrained/terratools" target="_blank" rel="noopener">terratools</a>.</li> <li>P_files_037.tar.gz - compressed archive of TERRA P-files (particle files).</li> <li>C_files_037.tar.gz - compressed archive of TERRA C-files (grid state files) - together with the P-files describe the full present day state of the simulation. </li> <li>seis_filtered_037.tar.gz - compressed archive (file-per-layer) with reparameterised and seismically filtered (against S40RTS) present day Vs field.</li> <li>seis_tables.tar.gz - compressed archive contianing lookup tables of seismic properties for the 3 principal lithologies assumed in the TERRA simulation (harzburgite, lherzolite and basaltic crust).</li> <li>density_037.sph - Spherical harmonic coefficients for the density field in format to be read by the <a title="propagator" href="https://zenodo.org/records/12696774" target="_blank" rel="noopener">propagator matrix code.</a></li> <li>plumes.pkl, ridges.pkl - Files containing tracer particle information for particles associated with plumes and ridges. </li> <li>plumes_ridges.py - Python script containing example code for reading and plotting plumes.pkl and ridges.pkl files. </li> <li>ptcls_rdgs_plms.py, interrogate_particles.py - Python script and module containing required functions for carrying out post processing routine generating the plumes.pkl and ridges.pkl files. Requires <a title="terratools" href="https://github.com/mantle-convection-constrained/terratools" target="_blank" rel="noopener">terratools</a>.</li> <li>hst.dat - Time series of key simulation properties including mantle temperature profile used for calcualting CMB heat flux. </li> <li>terra, interra - TERRA executable and input parameter file.</li> <li>pyflowng.zip - Compressed directory containing version of the `pyflowng` code used in this work.</li> <li>mode_splitting_methods.zip - Compressed directory contianing synthetic splitting function predictions and maps.</li> </ul>   <h3>Dump Numbers</h3> Below is a table of dump numbers (final three digits of file names) and the corresponding model times. <table> <tbody> <tr> <td>Dump number </td> <td>Model time (Ma)</td> </tr> <tr> <td>037</td> <td>0 (present day)</td> </tr> <tr> <td>027</td> <td>10</td> </tr> <tr> <td>026</td> <td>20</td> </tr> <tr> <td>025</td> <td>30</td> </tr> <tr> <td>024</td> <td>40</td> </tr> <tr> <td>023</td> <td>50</td> </tr> <tr> <td>022</td> <td>60</td> </tr> <tr> <td>021</td> <td>70 </td> </tr> <tr> <td>020</td> <td>80</td> </tr> <tr> <td>019</td> <td>90</td> </tr> <tr> <td>018</td> <td>100</td> </tr> </tbody> </table>

opencc-by-4.0Jun 2021View details →

Neglected effect of continental circulation on paleoclimate reconstruction

Three drilling sediment cores (YC03, YC08, and YC10) and 26 surface grab samples were collected during summer of 2016 in western area of the North Yellow Sea, and another 26 surface samples were supplemented during summer of 2020. The cores were cut length-wise, described, and photographed before subsampling in the laboratory. Sediment cores were sampled at 2 cm intervals for grain size. The samples were soaked in 0.05 mol L-1 of (NaPO3)6 for 24 h before measurement in a laser particle analyzer (Mastersizer 2000, Malvern Panalytical, UK).

opencc-zeroDec 2016View details →

Data from: Isopycnal mixing suppression by the Antarctic Circumpolar Current and the Southern Ocean Meridional Overturning Circulation

The meridional overturning circulation (MOC) in the Southern Ocean is investigated using hydrographic observations combined with satellite measurements of sea surface height. A three-dimensional (spatial and vertical) estimate of the isopycnal eddy diffusivity in the Southern Ocean is obtained using the theory of Ferrari and Nikurashin that includes the influence of suppression of the diffusivity by the strong, time-mean flows. It is found that the eddy diffusivity is enhanced at depth, reaching a maximum at the critical layer near 1000 m. The estimate of diffusivity is used with a simple diffusive parameterization to estimate the meridional eddy volume flux. This estimate of eddy volume flux is combined with an estimate of the Ekman transport to reconstruct the time-mean overturning circulation. By comparing the reconstruction with, and without, suppression of the eddy diffusivity by the mean flow, the influence of the suppression on the overturning is illuminated. It is shown that the suppression of the eddy diffusivity results in a large reduction of interior eddy transports and a more realistic eddy-induced overturning circulation. Finally, a simple conceptual model is used to show that the MOC is influenced not only by the existence of enhanced diffusivity at depth but also by the details of the vertical structure of the eddy diffusivity, such as the depth of the critical layer.

openother-openJun 2021View details →

Atmospheric circulation sensitivity to changes in the vertical structure of polar warming

This is the dataset used to make main figures of Atmospheric circulation sensitivity to changes in the vertical structure of polar warming (2021), GRL (in preparation). Please refer to the method section. 1. The name of GRAM experiments, bot, mid1, mid2, and mid3 indicate L990, L850, L700, and L550 forcing respectively. Depending on the forcing amplitude, it varies 1X to 5.5X. The control run for GRAM is ctl_GRAM.nc. 2. There are additional data for L990 and L650 for AM2 experiments. The control run for AM2 is ctl_AM2.nc. 3. kernel_GRAM.mat = the radiative Kerel which is the OLR response to incremental increases in temperature of 1 K at each vertical level and the surface, based on GRaM (Lowest level is the surface kernel).   Arctic domain averaged monthly temperature kernel data for figure 2d : 1. ERA-Interim (Huang et al. 2017); the original data can be obtained from <a href="https://huanggroup.wordpress.com/research/">https://huanggroup.wordpress.com/research/</a>. 2. GFDL-AM2 Aquaplanet (Feldl et al. 2017); the original data can be obtained from <a href="https://climate.rsmas.miami.edu/data/radiative-kernels">https://climate.rsmas.miami.edu/data/radiative-kernels</a>.

opencc-by-4.0Sep 2021View details →

Changes in the velocity of money circulation

Summary of data from empirical research.

opencc-zeroOct 2021View details →

Relationships between immune gene expression and circulating cytokine levels in wild house mice

1. Quantitative PCR (qPCR) has been commonly used to measure gene expression in a number of research contexts, but the measured RNA concentrations do not always represent the concentrations of active proteins which they encode. This can be due to transcriptional regulation or post-translational modifications, or localisation of immune environments, as can occur during infection. However, in studies using free-living non-model species, such as in ecoimmunological research, qPCR may be the only available option to measure a parameter of interest, and so understanding the quantitative link between gene expression and associated effector protein levels is vital. 2. Here we use qPCR to measure concentrations of RNA from mesenteric lymph node (MLN) and spleen tissue, and multiplex ELISA of blood serum to measure circulating cytokine concentrations in a wild population of a model species, Mus musculus domesticus. 3. Few significant correlations were found between gene expression levels and circulating cytokines of the same immune genes or proteins, or related functional groups. Where significant correlations were observed, these were most frequently within the measured tissue (i.e. the expression levels of genes measured from spleen tissue were more likely to correlate with each other rather than with genes measured from MLN tissue, or with cytokine concentrations measured from blood). 4. Potential reasons for discrepancies between measures, including differences in decay rates and transcriptional regulation networks are discussed. We highlight the relative usefulness of different measures under different research questions, and consider what might be inferred from immune assays.

opencc-by-4.0Dec 2022View details →

Appendix of the thesis "Acquisition of new genetic knowledge on strains of Mycobacterium bovis, circulating in France, by the whole genome sequencing approach." Ciriac CHARLES

Appendix 1 Table showing the Mycobacterium bovis genome information used in this study in panel 1 The 87 genomes are from previous work (Hauer et al., 2019). The names of the genomes are highlighted with color to distinguish them within a previously defined M. bovis cluster. In Yellow Cluster I/Clonal Complex Eu3. In orange Cluster G/Family F9. In brown Cluster C/Family SB0134. In purple Cluster D/Clonal Complex Eu1. In pink the Cluster A/Family F4. In blue the Cluster F/Clonal Complex Eu2. In grey, the others. Appendix 2 Table showing the Mycobacterium bovis genome information used in this study in panel 3. The 187 genomes are of genotypes F7 and F15 (SB0821 and SB0832 respectively) which are two closely related genotypes. These genomes had already been sequenced before the start of the thesis work. Some were published with the work of Duault and collaborators and others have not yet been published (noted NA) (Duault et al., 2022). Appendix 3 Table showing the Mycobacterium bovis genome information used in this study in panel 4. The 227 genomes are of genotype SB0120-DHV. These genomes had already been sequenced before the start of the thesis work but are currently unpublished (noted NA in the columns "Date of deposit" and "Genbank biosample"). Appendix 4 Position of IS6110 insertion sites in the panel of Mycobacterium bovis strains from Pyrénées-Atlantiques (SB0821 and SB0832). The position of the start and end of IS6110 are determined with the ISMapper tool and the reference genome AF2122/97. Appendix 5 Position of IS6110 insertion sites in the Mycobacterium bovis strain panel of SB0120-DHV. Position of the start and end of IS6110 are determined with the ISMapper tool and the Mb3601 reference genome. Appendix 6 This figure from the Modenesi internship report represents a circular consensus phylogenetic tree of 300 strains of SB0120-DHV (Modenesi 2019). The strains in panel 3 are part of these 300 strains and were selected according to their sequencing quality, which explains the smaller number of strains retained (227). This tree is divided into 11 different colored clades. The posterior probability values (which correspond to the probability that these clades are true) determined with Beast (Drummond and Rambaut, 2007) are represented inside the tree.

opencc-by-4.0Dec 2022View details →

Appendix of the thesis "Acquisition of new genetic knowledge on Mycobacterium bovis strains, circulating in France, by the whole genome sequencing approach", part "4. Sequencing of new complete genomes", Ciriac CHARLES

Annex S1: Sequencing metric of the 10 new genomes and obtained with fastqc. A: Metric provide to Illumina metric. B: metric provide to MinION metric. Annex S2: Pan-genomic study performed on 12 M. bovis complete genomes. The table indicates the genes accessory. “1” shows the presence of CDS and “0” his absence. Annex S3: Indels between the ten new complete genomes and Mb3601 using progressiveMauve. Annotation of these indels was performed with reference genome comparison for gap or with the annotation (with Prokka) of the new complete genome studied for insertion. IS6110 is marked in green. "Indel distribution" sheet shows the indel distribution on the M. bovis genome for the ten new complete genomes. Black arrows show the genomic region with the most of indel found. Annex S4: WgSNP analysis performed on 98 M. bovis. SNPs were annotated and selected according to their specificity to an M. bovis group described in Fig 5. The last common give information on the genetic impact of the SNP. The last sheet presents a graph of SNP number in genomic position. Annex S5: Alignments of the 12 M. bovis complete genomes.

opencc-by-4.0Jan 2023View details →

The circulation of relativistic electrons injected by radio galaxies in galaxy groups

Remote talk describing the latest simulations on the injection, propagation and energy evolution of relativistic electrons released into the intracluster/group medium by the activity of radio galaxies. Based on these publications: https://ui.adsabs.harvard.edu/abs/2023A%26A...669A..50V/abstract https://ui.adsabs.harvard.edu/abs/2021A%26A...653A..23V/abstract

opencc-by-4.0Jan 2023View details →

Dataset related to the article "Extraction-Free Absolute Quantification of Circulating miRNAs by Chip-Based Digital PCR"

This record contains raw data related to the article "Extraction-Free Absolute Quantification of Circulating miRNAs by Chip-Based Digital PCR" Circulating microRNAs (miRNA) have been proposed as specific biomarkers for several diseases. Quantitative Real-Time PCR (RT-qPCR) is the gold standard technique currently used to evaluate miRNAs expression from different sources. In the last few years, digital PCR (dPCR) emerged as a complementary and accurate detection method. When dealing with gene expression, the first and most delicate step is nucleic-acid isolation. However, all currently available protocols for RNA extraction suffer from the variable loss of RNA species due to the chemicals and number of steps involved, from sample lysis to nucleic acid elution. Here, we evaluated a new process for the detection of circulating miRNAs, consisting of sample lysis followed by direct evaluation by dPCR in plasma from healthy donors and in the cardiovascular setting. Our results showed that dPCR is able to detect, with high accuracy, low-copy-number as well as highly expressed miRNAs in human plasma samples without the need for RNA extraction. Moreover, we assessed a known myocardial infarction-related miR-133a in acute myocardial infarct patients vs. healthy subjects. In conclusion, our results show the suitability of the extraction-free quantification of circulating miRNAs as disease markers by direct dPCR.

opencc-by-4.0Feb 2023View details →

Replication data for "Increasing northern midlatitude temperatures caused by Hadley circulation expansion and strengthening"

Contained in this dataset are 10 *.npz files (5 each for MERRA-2 and ERA5), two jupyter notebooks, and one python script to replicate the figures and statistics in "Increasing northern midlatitude temperatures caused by Hadley circulation expansion and strengthening."   The *npz files are zonal means of zonal wind (u), meridional wind (v), temperature (t), eddy covariances of u'v' (eddy horizontal momentum flux), eddy covariances of v'T' (eddy horizontal heat flux), and eddy kinetic energy ((u'^2+v'^2)/2).  These covariances are calculated eddies as described in the methods.   To generate all figures in the manuscript, run the two jupyter notebooks.

opencc-by-4.0Feb 2023View details →

Supplemental files for manuscript "The circulating phageome reflects bacterial infections"

These are the supplemental files associated with the manuscript "The circulating phageome reflects bacterial infections". These include: 1. Supplemental File 1 (Phage Dictionary).csv which is a dictionary connecting bacteriophage accession numbers to their known taxonomic data as well as the taxonomic data of their host if known. 2. Supplemental File 2 (Coliphage Characteristics).csv which is a dictionary for phages which infect Escherichia coli including host information to strain if known and characteristics of any known strains. 3. Supplemental File 3 (Metadata).xlsx which includes a metadata table for the plasma cfDNA samples sequenced in the associated study, including infection etiology. 4. Supplemental File 4 (Negative Controls).xlsx which includes the sequences and identities of short reads from our negative sequencing controls (PBS, Water)

opencc-by-4.0Mar 2023View details →

Data from "Enhanced radiative forcing from aerosol-cloud interactions due to large-scale circulation adjustments" by Guy Dagan, Netta Yeheskel and Andrew I. L. Williams.

This is the data presented in "Enhanced radiative forcing from aerosol-cloud interactions due to large-scale circulation adjustments" by Guy Dagan, Netta Yeheskel and Andrew I. L. Williams.   Please read the README file for explanations about the data.

opencc-by-4.0Mar 2023View details →

R scripts for manuscript "The circulating phageome reflects bacterial infections"

These are documents and an R script associated with the manuscript "The circulating phageome reflects bacterial infections". These include: 1. allphagedf_seqids.csv which is a table including number of BLAST hits to unique phage Genbank IDs by sample. The samples used in this table are the 71 (61 septic, 10 asymptomatic controls) sequenced in this study. The rows of this table correspond to samples (rownames are library IDs) and columns correspond to all identified phage Genbank IDs from the blast output. 2. Phageome Summaries.RMD which is an R markdown document which demonstrates i) processing of blast output into a new allphagedf_seqids document, ii) use of the phage dictionary to summarize representation of phage taxonomic families as well as host genuses, and iii) use of the coliphage dictionary to assess how E. coli phages represent known host bacterial characteristics across samples. 3. Readme.txt which summarizes the above as well as provides links to other relevant data.

opencc-zeroMar 2023View details →

Dissimilarity of turbulent transport of momentum and heat under unstable conditions linked to convective circulations

The dissimilarity between the turbulent transport of momentum and heat under unstable conditions and its physical mechanisms are investigated in this study, based on the multiple-level turbulence observation from Tianjin's 255-m meteorological tower. The transport dissimilarity is observed from the surface layer to the lower part of the mixed layer as atmospheric instability increases. Although the transport dissimilarity is accompanied by the development of plumes and thermals under unstable conditions, plumes and thermals can produce intense transport of momentum and heat simultaneously. It is convective circulations related to vigorous thermals that cause transport dissimilarity. The horizontal divergence induced by convective circulations imposes a dominant large-scale reduction in the along-wind velocity component near the surface, while the temporal variations in temperature mainly reflect the role of plumes and thermals. This difference in respective physical processes subsequently leads to dissimilar transport between momentum and heat under unstable conditions. Therefore, the influence of convective circulations on the momentum-flux estimation should be considered in atmospheric numerical models, particularly for the simulation and prediction of severe convective weather.

opencc-zeroApr 2023View details →

Seasonal changes of vomeronasal responses to chemosensory cues associated with circulating estrogen in the female muskrats (Ondatra zibethicus)

In numerous animals, the vomeronasal organ (VNO) is a crucial chemosensory organ that receives chemical signals, which is involved in species-specific behaviors, including social and sexual behaviors. Muskrat (Ondatra zibethicus) has a sensitive VNO system that detects specific chemicals such as pheromones and hormones and induces seasonal breeding behaviors. The purpose of this study is to investigate the distributions and expression patterns of vomeronasal receptor type-1 (V1R), vomeronasal receptor type-2 (V2R), estrogen receptors α and β (ERα and ERβ) in the female muskrats' VNO during the different periods. V1R, V2R, ERα and ERβ were found in sensory epithelial cells, non-sensory epithelial cells and lamina propria cells of the female muskrats' VNO. V2R and ERα mRNA levels in the VNO of the breeding period declined sharply, in comparison to those of the non-breeding period, while V1R and ERβ mRNA levels were detected reversely. Additionally, a transcriptomic study in the VNO identified that differentially expressed genes might be related to estrogen signals and metabolic pathways. These findings suggested that the seasonal structural and functional changes of VNO in the female muskrats within different reproductive statuses, and estrogen regulated its function through binding to ERα and ERβ in the female muskrats' VNO.