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1,582 results for “manuscript”
SHAPE datasets from manuscript: Modulation of pre-mRNA structure by hnRNP proteins regulates alternative splicing of MALT1
<p>Normalized SHAPE reactivity for the MALT1 M1 minigene RNA constructs (wildtype, variant 1, and variant 2) reported in the manuscript titled 'Modulation of pre-mRNA structure by hnRNP proteins regulates alternative splicing of <em>MALT1'</em> .</p> <p> </p>
Dataset and scripts for manuscript "Using Neural Network Ensembles to Separate Ocean Biogeochemical and Physical Drivers of Phytoplankton Biogeography in Earth System Models"
<p>Please note: The title of this version contains an updated title for the manuscript compared to the previous version of this dataset. This is only due to title updates during the peer review process for the manuscript.</p> <p>The zip file contains the scripts, functions, and source files for the manuscript titled "Using Neural Network Ensembles to Separate Ocean Biogeochemical and Physical Drivers of Phytoplankton Biogeography in Earth System Models." The manuscript has been submitted for peer review.</p> <p>Please consult the README file for information on the specifications of the files.</p> <p>These files may occasionally be updated to add annotations to the scripts to make them more user friendly and to correct any errors.</p>
Processed data and models in support of manuscript "Deciphering the state of the lower crust and upper mantle with multi-physics inversion"
<p>Data and model files in original format used in the manuscript "Deciphering the state of the lower crust and upper mantle with multi-physics inversion". These files are accompanied by a set of python scripts to reproduce several of the figures in the Manuscript. Please refer to the Manuscript and the included files for further information on data origin and how to use the scripts. A link will be added upon acceptance.</p>
Experimental data for the manuscript "Magnetoelectric crankshaft"
<p>Here we provide the experimental data correcponding to Fig. 2 of the manuscript "Magnetoelectric crankshaft".</p>
Data used in manuscript Carbon sequestration potential of street tree plantings in Helsinki
<p>Data and model runs used in manuscript "Carbon sequestration potential of street tree plantings in Helsinki". This data set includes model runs for the Surface Urban Energy and Water balance Scheme (SUEWS) and soil carbon model Yasso.</p> <p><br> The data files are:</p> <p><strong>Met_Gapfilling</strong></p> <ul> <li>ConvertMeteorologyInput.m (MATLAB) is the main file and functions gapfilling.m (with other measurements) and gapfillingfill.m (with interpolations) are used in the gap filling</li> <li>Includes files for meteorological measurement data <ul> <li>Airport: Data from Helsinki-Vantaa airport; airportdata.m, where data is cleaned</li> <li>Precipitation: Data from multiple locations; Pres_Gap.m for gap filling precipitation and function PrecipitationGap.m</li> <li>Roof: Data from rooftop</li> <li>SMEARIII: Monthly meteorological data from Kumpula (2003-2016)</li> </ul> </li> <li>SUEWS_met file for the final gap filled meteorological files for SUEWS </li> </ul> <p><strong>Fits</strong></p> <ul> <li>Includes FitCO2_parameter.m for fitting CO2 parameters for SUEWS</li> <li>Includes functions Pho6.m and Resp0.m that have the function forms</li> <li>Includes data files for measurement data <ul> <li>CO2Data: Canopy photosynthesis and canopy respiration estimated with SPP model (KumpulaX.out for Tilia site and Kumpula2X.out for Alnus site)</li> <li>Met_2016: Meteorology from Kumpula for June to August in 2016</li> <li>SWCdata: Soil water content from two streets and three soil types</li> </ul> </li> </ul> <p><strong>ModelRuns</strong></p> <ul> <li>SUEWS model runs separately for Alnus and Tilia sites <ul> <li>Includes input and output files and model codes</li> <li>Alnus site includes both the Baserun and Finalrun</li> </ul> </li> <li>Yasso model runs <ul> <li>Model run in file yasso.f90</li> <li>Output files: DecRate...txt includes three soil types and values for each month from 2002 to 2016</li> <li>Yasso_meteorology_month.m creates meteorological input files for Yasso (Clim_month_xx.txt) using meteorology from SUEWS</li> <li>Lifetimerun: 30 year simulations that includes estimations for leaves and pruned branches</li> </ul> </li> </ul> <p><strong>FigCodes</strong></p> <ul> <li>Includes MATLAB codes for figures and statistics</li> <li>Includes measurement data for CO2, sap flow and SWC</li> </ul> <p> </p>
All data of the manuscript "A self-sustained charge neutrality lightning model containing the channel decay and reactivation process" submitted to Geophysical Research Letters
<p>The data supports the manuscript entitled "A self-sustained charge neutrality lightning model containing the channel decay and reactivation process”. Microsoft Notepad can open the *.txt files, they contain the channel information of two intracloud flashes (IC1 and IC2) and the channel elctrical parameters at the first fork of positive or negative leader channels. A normal video player software can open Movies S1.avi, and it shows the entire development process of IC1 discharge.</p> <p>The data can be used freely for scientific purposes with the appropriate citation.</p>
Dataset accompanying manuscript "Correlative imaging of spatio-angular dynamics of biological systems with multimodal instant polarization microscope"
<p>Raw images and microscope calibration metadata for reconstruction of datasets presented in Fig. 1 and Fig. 3 of "Correlative imaging of spatio-angular dynamics of biological systems with multimodal instant polarization microscope". Notebooks demonstrating steps in the label-free and fluorescence anisotropy reconstruction pipelines can be found at https://github.com/mehta-lab/miPolScope.</p>
Datasets and code for manuscript: Age, breed, sex, and diet influence serum metabolite profiles of 2000 pet dogs
<p>Physiology affects metabolism, but there is a lack of large-scale studies investigating the effects of different physiological factors on canine metabolism. We utilised generalised linear models to study how age, breed, sex, sterilisation status, size, diet type, and fasting time before blood sampling affect serum concentrations of 119 metabolite measurands in over 2000 pet dogs. This dataset contains input files and code for the analyses. </p>
Data files for manuscript "A novel syndrome caused by the constitutional gain-of-function variant p.Glu1099Lys in NSD2"
<p>#2022-02-21<br> #Summary<br> This ZIP-file contains the data files used for all analyses for the manuscript "A novel syndrome caused by the constitutional gain-of-function variant p.Glu1099Lys in NSD2".</p> <p><br> #File structure<br> README.txt This README file.<br> File S02 ("FileS02_NSD2-clinical-information-and-variants.xlsx") Clinical data of GoF and LoF inidviduals used for Table 1 and Table 2 and genetic variant data used for Figure 2.<br> File S03 ("FileS03_NSD2-CCLE-analyses.xlsx") Tables containing information of the CCLE analyses and depmap results used for Figure 3A-D.<br> File S04 ("FileS04_humanbase_global_1642958821189.tar.gz") Tar.gz file of the downlaoded humanbase result files used for Figure 3E.</p> <p><br> #Files and checksums<br> 5FE613FC7646419C20153068E8D5F463 ./FileS02_NSD2-clinical-information-and-variants.xlsx<br> AC53634E6044469BE42DBBE8F7503275 ./FileS03_NSD2-CCLE-analyses.xlsx<br> 7AE58A28A4D1E1462521A37522BB78B6 ./FileS04_humanbase_global_1642958821189.tar.gz</p>
Project files provided as supporting information to the manuscript "Making sense of complex systems through resolution, relevance, and mapping entropy"
<p>README file to the project files provided as supporting information to the manuscript “Making sense of complex systems through resolution, relevance, and mapping entropy”</p> <p>Feb. 25, 2022</p> <p>Authors: Roi Holtzman, Marco Giulini and Raffaello Potestio</p> <p>==================================</p> <p>The dataset contains the following files:</p> <p>- A README file with the description of the pymap program for describing how different selections of *N* out of *n* degrees of freedom (mappings) affect the amount of information retained about a full data set.<br> - The pymap.py program<br> - The pymap.yml support file<br> - The data.tar tarball with the setup data<br> - The results.tar tarball with the output data<br> ===</p>
Data for the Manuscript 'Phenotypic Variation from Waterlogging in Multiple Perennial Ryegrass Varieties under Climate Change Conditions'
<p>Experimental data supporting the findings of the manuscript 'Phenotypic Variation from Waterlogging in Multiple Perennial Ryegrass Varieties under Climate Change Conditions'. This dataset will be made publicly available when the manuscript has been accepted for journal publication unless exceptional conditions become apparent. </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>
Data for manuscript: Ecological lags govern the pace and outcome of plant community responses to 21st century climate change
<p>These data were used in the analyses reported in Block et al. "Ecological lags govern the pace and outcome of plant community responses to 21st century climate change".</p>
Data supporting the manuscript "Sexually divergent development of depression-related brain networks during healthy human adolescence"
<p>This data supports the manuscript "Sexually divergent development of depression-related brain networks during healthy human adolescence" by Dorfschmidt et al. Part of these <a href="https://doi.org/10.6084/m9.figshare.11551602">data</a> were initially released by Váša et al. (2020) as part of their <a href="https://doi.org/10.1073/pnas.1906144117">manuscript</a>. Please cite them when using these data. </p> <p> </p>
Dataset of the manuscript "Problems and Solutions in Applying Continuous Integration and Delivery to 20 Open-Source Cyber-Physical Systems"
<p>This archive contains the artifacts (datasets) for the manuscript "Problems and Solutions in Applying Continuous Integration and Delivery to 20 Open-Source Cyber-Physical Systems"</p>
SWMF/CIMI outputs used in Holappa and Buzulukova (2022) manuscript submitted to Geophys. Res. Lett.
<p>These data files and Python scripts are used to produce Figures 1 and 2 in Holappa and Buzulukova, Explicit IMF By-dependence of energetic protons and the ring current, submitted to Geophys. Res. Lett. (2022).</p> <p>PARAM.in.PosTilt and gitinfo.txt contain the settings and Git version references used to setup the SWMF model.</p> <p>Figure 1: PosBy_CimiFlux_n00000046_h.fls, NegBy_CimiFlux_n00000046_h.fls are CIMI output files containing proton fluxes for different energies and pitch angles. These data can be read with CIMIreader.py. Figures in the manuscript can be produced by Run_CIMI_reader.py. Files PosBy_CimiFlux_n00000046_e.fls, NegBy_CimiFlux_n00000046_e.fls can be used to produce corresponding figures for electrons.</p> <p>Figure 2: Data files CIMI_log_NegBy_PosTilt.dat and CIMI_log_PosBy_PosTilt.dat are CIMI output files containing the ring current energy and other variables. Figures can be produced by Plot_CIMI_Dst.py. </p> <p> </p>
Additional files for manuscript titled 'The double round-robin population unravels the genetic architecture of grain size in barley'
<p>Additional file 1: Parental allele for barley orthologs of genes controlling grain size in rice</p> <p>Additional file 2: Cross-validation of quantitative trait loci (QTLs) detected for grain size characters in rice</p> <p>Additional file 3: Adjusted entry means of recombinant inbred lines of 45 HvDRR sub-populations</p>
Dataset supporting manuscript entitled 'Partitioning of Small Hydrophobic Molecules into Polydimethylsiloxane in Microfluidic Analytical Devices'
<p>This is the dataset supporting the manuscript 'Surface and bulk modifications of polydimethylsiloxane to reduce absorption/adsorption of small molecules in lab-on-a-chip' published in Micromachines</p>
Dated and Datable Manuscripts: dataset
<p>This data set encompasses 101 transcriptions of digital images of dated medieval manuscripts</p> <p>The original data set was created as part of the <a href="https://anr.fr/Project-ANR-12-CORP-0010">ANR ORIFLAMMS (ANR-12-CORP-0010)</a> project. Texts were transcribed by Irene Ceccherini in the original TEI-XML format, rendering both abbreviated and expanded forms of the original text. The transcriptions were revised at the end of the project by Dominique Stutzmann, and the alignement data was produced by merging coordinates created through the Oriflamms software and coordinates produced by A2IA for words, and corrected at word level by Dominique Stutzmann.</p> <p> A new version was prepared in March 2022 as part of the research for a joint paper on HTR diversity for the<br> DH 2022 conference (Tokyo). In particular, (1) the coordinates of lines were corrected through a complete new layout segmetation with the Transkribus software; (2) several ALTO files were generated with different versions of the edited text (normalized or not normalized / abbreviations expanded or not).<br> <br> <strong>Folders</strong><br> The present data set gathers different folders with different types of information.<br> The folder schema and file format used in the ORIFLAMMS is described in:</p> <ul> <li>Consortium Oriflamms. « Spécification du format XML-TEI pour l’alignement texte-image. 1. Structure et convention de nommage ». *Écriture médiévale & numérique*, 11 Sept. 2016. [<a href="http://oriflamms.hypotheses.org/1442">http://oriflamms.hypotheses.org/1442</a>].</li> <li>Consortium Oriflamms. « Spécification du format XML-TEI pour l’alignement texte-image. 2. Bonnes pratiques d’encodage ». *Écriture médiévale & numérique*, 12 Sept. 2016. [<a href="http://oriflamms.hypotheses.org/1510">http://oriflamms.hypotheses.org/1510</a>].</li> </ul> <p><br> <strong>img</strong><br> Folder with 101 images.<br> These images are scans of actual printed photographs at scale. The source of the photograph, i.e. the shelfmark<br> of the medieval manuscript and the folio number, is handwritten on the picture. It is also formalized as TEI <msIdentifier/> element in the files of the /texts/ folder.<br> These images are also integrated in the <a href="https://bvmm.irht.cnrs.fr/">BVMM (Bibliothèque Virtuelle des Manuscrits Médiévaux)</a> as IIIF compliant images.</p> <p><strong>texts</strong><br> Original TEI-XML edition with identifiers for all paragraphs, lines, words in the `texts/mss-dates-w.xml` file, and also for characters in the `mss-dates-c.xml` file.<br> The additional file named `texts/mss-dates-w-merged.xml` does not correspond to the ORIFLAMMS specification. It is a XML-TEI file with the same structure as `mss-dates-w.xml` but with following additions:</p> <ol> <li>the zones coordinates are integrated in a `<facsimile/>` element within each concerned `<TEI/>` element;</li> <li>the `@xml:id` attributes within `<milestone/>` elements are renamed to avoid multiple occurrences;</li> <li>he `<lb/>` and `<w/>` elements are enhanced with a `@facs` attribute pointing to the corresponding `<zone/>` element;</li> <li>the `<w/>` elements are enhanced with a `@corresp` attribute containing the string value of the word without expansion nor normalization.</li> </ol> <p><strong>/zones/, /img_links/</strong><br> zones described as coordinates on the images (/img/ folder) and files linking between the edition in /texts/ folder and coordinates in the /zones/ folder.</p> <p><strong>/ontologies/, /ontologies_link/, /oriflamms/</strong><br> Here, folders are present, but the data is not created.</p> <p><strong>/alto/</strong><br> ALTO files were created from the preexisting TEI files and combine the coordinates and the text in single files where the text is flat and rendered at a line level, with/without normalization and with/without abbrevations.</p>
Characterization data for the manuscript: "Using genetic algorithms to systematically improve the synthesis conditions of Al-PMOF"
<p>This entry contains characterization data for the manuscript "Using genetic algorithms to systematically improve the synthesis conditions of Al-PMOF", which we exported from the electronic lab notebook (ELN).</p> <p>To visualize the data in this dataset: <a href="https://www.cheminfo.org/flavor/zenodo/index.html?id=6620502">open entry</a></p>
ScienceDex guides
Understand access before you commit
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.