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Datasets related to the manuscript 'Hypothalamic deep brain stimulation augments walking after spinal cord injury'

The deposited datasets consist in the following: Supplementary Table 1: All kinematics data and statistical analyses Supplementary Table 2: All differential analyses and statistics for the quantification of transcriptional activity (cFos) and spinal cord-projecting neurons (Rabies) from the contralesional (right) lateral hypothalamus (n = 3 per group).

Dataset and R-scripts to the manuscript: Beyond salinity: plants show divergent responses to soil ion composition

Dataset and R-scripts to the article: Pätsch R., Midolo G., Dítě Z., Dítě, D., Wagner, V., Pavonič, M., Danihelka, J., Preislerová Z., Ćuk M., Stroh H.G., Tóth T., Chytrá H., Chytrý M. (2024) Beyond salinity: plants show divergent responses to soil ion composition. Global Evology and Biogeography, 00, e13821. <a href="https://doi.org/10.1111/geb.13821%E2%80%8B" target="_blank" rel="noopener">https://doi.org/10.1111/geb.13821</a>

Data set related to the manuscript "Dynamics and energetics of ion adsorption at the interface between a pure ionic liquid and carbon electrodes"

Text files with data for plotting figures in the quoted manuscript. Example input files for simulations.

Source code and data for manuscript "Large-scale deep tissue voltage imaging with targeted illumination confocal microscopy"

Source code and data for manuscript "Large-scale deep tissue voltage imaging with targeted illumination confocal microscopy", Nat Methods (2024), https://doi.org/10.1038/s41592-024-02275-w.

TRIDIS: HTR model for Multilingual Medieval and Early Modern Documentary Manuscripts (11th-16th)

TRIDIS (Tria Digita Scribunt) is a Handwriting Text Recognition model trained on semi-diplomatic transcriptions from medieval and Early Modern Manuscripts. It is suitable for work on documentary manuscripts, that is, manuscripts arising from legal, administrative, and memorial practices more commonly from the Late Middle Ages (13th century and onwards). It can also show good performance on documents from other domains, such as literature books, scholarly treatises and cartularies providing a versatile tool for historians and philologists in transforming and analyzing historical texts. A paper presenting the first version of the model is available here: Sergio Torres Aguilar, Vincent Jolivet. Handwritten Text Recognition for Documentary Medieval Manuscripts. Journal of Data Mining and Digital Humanities. 2023. https://hal.science/hal-03892163   <h3>Transcriptions rules :</h3> Since the majority of the training documents come from diplomatic editions, the transcriptions were normalized to contemporary reading standards, and abbreviations were expanded with the aim of facilitating a more fluid reading of the document. The following rules were applied: <ul> <li>The abbreviations have been expanded, both those by suspension (<code>facimꝰ</code> ---> <code>facimus</code>) and by contraction (<code>dñi</code> --> <code>domini</code>). Likewise, those using conventional signs (<code>⁊</code> --> <code>et</code> ; <code>ꝓ</code> --> <code>pro</code>) have been resolved. </li> <li>The named entities (names of persons, places and institutions) have been <code>capitalized</code>. The beginning of a block of text as well as the original capitals used by the scribe are also capitalized.</li> <li>The consonantal <code>i</code> and <code>u</code> characters have been transcribed as <code>j</code> and <code>v</code> in both French and Latin.</li> <li>The punctuation marks used in the manuscript like: <code>.</code> or <code>/</code> or <code>|</code> have not been systematically transcribed as the transcription has been standardized with modern punctuation.</li> <li>Corrections and words that appear cancelled in the manuscript have been transcribed surrounded by the sign <code>$</code> at the beginning and at the end.</li> </ul>   <h3>Versions :</h3> Version 1 of the model was trained on charters and registers dataset from the Late Medieval period (12th-15th centuries). The training and evaluation involved 1855 pages, 120k lines of text, and almost 1M tokens, conducted using three freely available ground-truth corpora: <ul> <li>The Alcar-HOME database: <a href="../record/5600884" target="_new">https://zenodo.org/record/5600884</a></li> <li>The e-NDP corpus: <a href="../record/7575693" target="_new">https://zenodo.org/record/7575693</a></li> <li>The Himanis project: <a href="../record/5535306" target="_new">https://zenodo.org/record/5535306</a></li> </ul> Version 2 of the model has added new datasets from feudal books and legal proceedings (14th-16th centuries), incorporating an additional 115k lines and more than 1.2M tokens to the previous version using other corpora like: <ul> <li>Königsfelden Abbey corpus: <a href="../record/5179361" target="_new">https://zenodo.org/record/5179361</a></li> <li>Monumenta Luxemburgensia.</li> </ul>   <h3>Accuracy</h3> TRIDIS was trained using a CNN+RNN+CTC architecture within the Kraken suite (https://kraken.re/). This final model operates in a multilingual environment (Latin, Old French, and Old Spanish) and is capable of recognizing several Latin script families (mostly Textualis and Cursiva) in documents produced circa 11th - 16th centuries. During evaluation, the model showed an accuracy of 93.1% on the validation set and a CER (Character Error Ratio) of about 0.11 to 0.15 on four external unseen datasets. Fine-tuning the model with 10 ground-truth pages can improve these results to a CER of between 0.06 to 0.10, respectively. <h3>Other formats</h3> The ground truth used for version 2 was also employed to train a Transformer HTR model that combines TrOCR as the encoder with a RoBERTa medieval model as the decoder. This model exhibits a slighly better performance in terms of CER metrics to the current TRIDIS version and shows an improved WER by about 25%. The model is available on the Hugging Face Hub: <a href="https://huggingface.co/magistermilitum/tridis_HTR">magistermilitum/tridis_HTR</a>

Minimal dataset for the manuscript "Better together against genetic heterogeneity: a sex-combined joint main and interaction analysis of 290 quantitative traits in the UK Biobank".

Dataset "lin2024-sex_combined_interaction-association_signifincant_in_one_or_more_tests-summary.txt" is a minimal dataset to reproduce the figures and tables in the manuscript "Better together against genetic heterogeneity: a sex-combined joint main and interaction analysis of 290 quantitative traits in the UK Biobank".  To generate this dataset, see "https://github.com/BoxiLin/t2meta" Steps 0, 1. This dataset is the input for Steps 2, 3, 4, 5 to generate Figures 1-3 and Table 2-3.   ##### Column information ######################## The following columns are annotations on each variant in the GWAS, calculated across the analysis subset of 361,194 samples by the Neale lab: code: Phenotype identifier in the form of "[UKB Data field]_raw" variant: Unique variant identifier in the form "chr:pos:ref:alt", where "ref" is aligned to the forward strand. chr: Chromosome of the variant. pos: Position of the variant in GRCh37 coordinates. rsid: rs ID ref: Reference allele on the forward strand. alt: Alternate allele (not necessarily minor allele). p_hwe: Hardy-Weinberg p-value. info: Imputation INFO score as provided by UK Biobank.   The following columns are sex-stratified test statistics calculated by the Neale lab: minor_allele.x: Minor allele (AF < 0.5) in the female GWAS  minor_AF.x: Minor allele frequency in the female GWAS  beta.x: Estimated effect size of alt allele in the female GWAS  se.x: Estimated standard error of beta in the female GWAS tstat.x: t-statistic of beta estimate (= beta/se) in the female GWAS  pval.x: p-value of beta significance test in the female GWAS  minor_allele.y: Minor allele (AF < 0.5) in the male GWAS  minor_AF.y: Minor allele frequency in the male GWAS  beta.y: Estimated effect size of alt allele in the male GWAS  se.y: Estimated standard error of beta in the male GWAS  tstat.y: t-statistic of beta estimate (= beta/se) in the male GWAS  pval.y: p-value of beta significance test in the male GWAS    The following columns are sex-combined test statistics calculated in our analysis: T.I: test statsitic for interaction effect-only  p.T.I:  p-value of the interaction effect-only test  TSG.L:  test statsitic for inverse variance weighted meta-analysis p.TSG.L: p-value of the inverse variance weighted meta-analysis TSG.Q: test statsitic for the omnibus meta-analysis p.TSG.Q: p-value for the omnibus meta-analysis

Data for the manuscript "Correlation between two distant quasiparticles in separate superconducting islands mediated by a single spin"

Data for the manuscript "Correlation between two distant quasiparticles in separate superconducting islands mediated by a single spin", https://doi.org/10.48550/arXiv.2203.00104 The archive contains the experimental data and the results of numerical calculations as well as plotting scripts/notebooks for the figures presented in the manuscript.

opencc-zeroMar 2024View details →

dryad36/100

HIDRA simulations and post-processing scripts for JGR: SP manuscript: characterization of N+ abundances in the terrestrial polar wind using the multiscale atmosphere-geospace environment

<div> <div> <div> The High-latitude Ionosphere Dynamics for Research Applications (HIDRA) model is part of the Multiscale Atmosphere-Geospace Environment (MAGE) model under development by the Center for Geospace Storms (CGS) NASA DRIVE Science Center. This study employs HIDRA to simulate upflows of H+, He+, O+, and N+ ions, with a particular focus on the relative N+ concentrations, production and loss mechanisms, and thermal upflow drivers as functions of season, solar activity, and magnetospheric convection. The simulation results demonstrate that N+ densities typically exceed He+ densities, N+ densities are typically ∼ 10% O+ densities, and N+ concentrations at quiet-time are approximately 50-100% of N+ concentrations during storm-time. Furthermore, the N+ and O+ upflow fluxes show similar trends with variations in magnetospheric driving. The inclusion of ion-neutral chemical reactions involving metastable atoms is shown to have significant effects on N+ production rates. With this metastable chemistry included, the simulated ion density profiles compare favorably with satellite measurements from Atmosphere Explorer C (AE-C) and Orbiting Geophysical Observatory 6 (OGO-6). </div> </div> </div>

opencc-by-4.0Jan 2024View details →

Supplementary data files of manuscript

Open the record for dataset details and reuse information.

Supplementary file for the manuscript entitled: Demographic and genetic impacts of powdery mildew in a young oak cohort

Barres et al 2023 Supplementary material-vf.pdf: supplementary material file for the related article

Data used in manuscript Direct CO2 emissions and uptake at neighbourhood scale over the urban area of Beijing

This dataset provides the data used in the manuscript "Direct CO2 emissions and uptake at neighbourhood scale over the urban area of Beijing". The folders are: 1. Modelled_CO2_Flux   This folder contains a portion of modelled CO2 fluxes generated by SUEWS. Fc is the net CO2 flux, FcPhoto the CO2 uptake by vegetation, FcRespi the CO2 release from soil and vegetation respiration, FcMetab the CO2 emissions from human metabolism, FcBuild the CO2 emissions from the local fuel combustion in buildings. Longitudes and latitudes denote the centroid of grid.     1.1 Fc_annual_2016_g_C_m-2_yr-1.nc is the annual CO2 fluxes in g C m-2 year-1.     1.2 Fc_monthly_2016_g_C_m-2_mon-1.nc is the monthly CO2 fluxes in g C m-2 month-1.     1.3 Fc_annual_2016_g_C_m-2_yr-1.tiff is the annual Fc (g C m-2 year-1) provided in GeoTiff format.     1.4 6_ring_EPSG4326 contains the ESRI Shapefile defining the study area (with the 6th Ring Road in Beijing as the boundary). 2. ModelRun   This folder includes SUEWS source code (Järvi et al., 2011; Ward et al., 2016; Järvi et al., 2019) and a model run sample.     2.1 SUEWS_SourceCode is a folder including SUEWS V2020b source Fortran codes. For detailed descriptions, readers are referred to SUEWS webpage (https://suews.readthedocs.io/en/latest/). Enter "make" through the command line and a SUEWS executive will be built under ".../ModelRun/Release".     2.2 EvaluationRun is a folder including the SUEWS run for model performance evaluation. To conduct a quick model run to reproduce the results demonstrated in the manuscript, use command line "./SUEWS_V2020b".  3. Observations   The unit for CO2 flux (Fc) is μmol m-2 s-1 under this folder.     3.1 co2_flux_140m_2016_rm_QC.csv is the Fc observations after quality control and resampled to hourly resolution.     3.2 Fc_gapfilled_with_MeanDC.csv is the Fc time series for the year 2016 gap-filled with the Mean Diurnal Cycle method on a seasonal basis.   Contact information: zhengyingqi@mail.iap.ac.cn [References] Järvi, L., Grimmond, C. S. B., & Christen, A. (2011). The surface urban energy and water balance scheme (SUEWS): Evaluation in Los Angeles and Vancouver. Journal of Hydrology, 411(3-4), 219-237. Ward, H. C., Kotthaus, S., Järvi, L., & Grimmond, C. S. B. (2016). Surface Urban Energy and Water Balance Scheme (SUEWS): development and evaluation at two UK sites. Urban Climate, 18, 1-32. Järvi, L., Havu, M., Ward, H. C., Bellucco, V., McFadden, J. P., Toivonen, T., ... & Grimmond, C. S. B. (2019). Spatial modeling of local‐scale biogenic and anthropogenic carbon dioxide emissions in Helsinki. Journal of Geophysical Research: Atmospheres, 124(15), 8363-8384.

Supplemental Files for manuscript "Prenatal Transmission of Bacteriophage DNA in Humans"

This repository includes the following files: 1) Maternal_UCB_Phage_Analysis.RMD This is an R markdown file to reproduce the analysis in the manuscript “Prenatal Transmission of Bacteriophage DNA in Humans”.  It depends on the following files: 2) BLAST_Processing.R R script used for the processing of BLAST outputs.  The outputs of this analysis for our two cohorts and negative controls with each phage database are provided as R objects.    a. POPE_AllPhage_Stats.RDS  b. POPE_GPD_Stats.RDS  c. Witt_AllPhage_Stats.RDS  d. Witt_GPD_Stats.RDS  e. Neg_AllPhage_Stats.RDS  f. Neg_GPD_Stats.RDS 3) Clean_Data_Structures.R This script includes 3 sections to generate the data structures used in subsequent analyses.  4) Phage_Plots_Tables.R This script includes 3 sections to reproduce the figures and tables from the manuscript “Prenatal Transmission of Bacteriophage DNA in Humans”.  5) POPE_index.csv This CSV file contains the metadata for the POPE cohort. 6) SummaryMetaData.csv This CSV file contains the metadata for the Witt cohort as relayed by the study authors from the original publication of this dataset. 7) README.txt which summarizes the above as well as provides links to other relevant data. These scripts can be used to re-process our sequencing data or to process and interpret additional datasets.

Supporting dataset for manuscript "Role of metabolism, resistance, and/or antagonism as drivers of endomicrobiomes assemblage in Origanum heracleoticum L." by Giulia Semenzato et al. 2024

Raw data used for the analysis presented in the manuscript "Role of metabolism, resistance, and/or antagonism as drivers of endomicrobiomes assemblage in Origanum heracleoticum L." by authors Giulia Semenzato, Francesco Vitali, Arcangela Frascella, Ludovica Lollini, Stefano Mocali, Alessio Papini, Renato Fania, and Giovanni Emiliani  <ul> <li>phenome_combined_normalized_R.csv = activity values (AV) obtained after DuctApe elaboration of phenotype microarray data for carbon sources analysis. Control well signal was substracted.</li> <li>phenome_combined_nonNormalized_R.csv = activity values (AV) obtained after DuctApe elaboration of phenotype microarray data for resistance/sensibility sources analysis. Control well were signal not substracted.</li> <li>Rawdata_cross_streaking.csv = raw data obtained from cross-streaking experiment.</li> <li>Rawdata_MIC.csv = raw data obtained from MIC experiment.</li> <li>Raw_data_BIOLOG.zip = raw data from phenotype microarray readings.</li> </ul>

Supplementary materials for the manuscript entitled: "Impacts of creatine on the health of elderly individuals: a bibliometric study"

These images/figures complement what was presented in the results of the manuscript "Impacts of creatine on the health of elderly individuals: a bibliometric study.

Data associated to the manuscript "Simulating the charging mechanism of a realistic nanoporous carbon-based supercapacitor using a fully polarizable model"

Contains input files and data used to generate the figures of the article: Simulating the charging mechanism of a realistic nanoporous carbon-based supercapacitor using a fully polarizable model Camille Bacon, Patrice Simon, Mathieu Salanne and Alessandra Serva ChemRxiv, 10.26434/chemrxiv-2024-9577m, 2024 The folder input_files contains typical MetalWalls input files used to perform the simulations. The folder raw_data contains the processed data used to plot all the figures of the paper.

Dataset for the manuscript "Observation of time-reversal symmetry breaking in the band structure of altermagnetic RuO2" in Science Advances Vol. 10, No. 5

Dataset for publication "Observation of time-reversal symmetry breaking in the band structure of altermagnetic RuO2" in Science Advances Vol. 10, No. 5, https://doi.org/10.1126/sciadv.adj4883. The details corresponding to the dataset of the figures are given in a readme file in the corresponding folders.

The raw GNSS position time series (raw_time_series.rar) and TDEFNODE models (TDEFNODE_models.rar) related to the manuscript authored by Rui Xu, D. S. Stamps and C. A. Williams

This repository saves the raw GNSS position time series (raw_time_series.rar) and TDEFNODE models (TDEFNODE_models.rar) related to the manuscript authored by Rui Xu, D. S. Stamps and C. A. Williams. For more details, please refer to the NOTES files in each .rar archive.

Raw data for the manuscript: Survival and reproduction effects of microplastics from three agricultural mulching films on Folsomia candida, Sinella curviseta, Heteromurus nitidus and Ceratophysella denticulata (Collembola)

Survival and reproduction data from single species tests involving four Collembola species and three types of plastic materials.

opencc-by-4.0Nov 2024View details →

Data and codes for manuscript "A study on radiative efficiencies and warming effects of halocarbons"

Data and codes for “A study on radiative efficiencies and warming effects of halocarbons”, including the 998-band radiative transfer model for calculating the radiative efficiency, scripts for plotting and corresponding data.