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Dataset related to article "SMA-miRs (miR-181a-5p, -324-5p, and -451a) are overexpressed in spinal muscular atrophy skeletal muscle and serum samples"

mice survival after treatment with anti-miR-181a-5p; mice weight after treatment with anti-miR-324-5p

Dataset related to article "Complement activation promoted by the lectin pathway mediates C3aR-dependent sarcoma progression and immunosuppression"

This record contains raw data related to article “Complement activation promoted by the lectin pathway mediates C3aR-dependent sarcoma progression and immunosuppression" Complement has emerged as a component of tumor promoting inflammation. We conducted a systematic assessment of the role of complement activation and effector pathways in sarcomas. C3 -/-, MBL1/2 -/- and C4 -/- mice showed reduced susceptibility to 3-methylcholanthrene sarcomagenesis and transplanted sarcomas, whereas C1q and factor B deficiency had marginal effects. Complement 3a receptor (C3aR), but not C5aR1 and C5aR2, deficiency mirrored the phenotype of C3 -/- mice. C3 and C3aR deficiency were associated with reduced accumulation and functional skewing of tumor-associated macrophages, increased T cell activation and response to anti-PD-1 therapy. Transcriptional profiling of sarcoma infiltrating macrophages and monocytes revealed the enrichment of MHC II-dependent antigen presentation pathway in C3-deficient cells. In patients, C3aR expression correlated with a macrophage population signature and C3 deficiency-associated signatures predicted better clinical outcome. These results suggest that the lectin pathway and C3a/C3aR axis are key components of complement and macrophage-mediated sarcoma promotion and immunosuppression.

Data and codes related to the article: Horner et al. Streamflow uncertainty due to the limited sensitivity of controls at hydrometric stations

The data files and R code files are related to the article Horner et al. "Streamflow uncertainty due to the limited sensitivity of controls at hydrometric stations" published in Hydrological Processes. Data: 1/ Q_Craponne.txt Original streamflow time series of Craponne hydrometric station which was used to generate the synthetic stage time series using the theoretical equations of the 5 fictive hydrometric stations. Column separator: semi-colon (;) Column 1 ==> Time (%Y-%m-%d %H:%M) Column 2 ==> Streamflow (in m3/s) 2/ h_Mercier.txt Original stage time series for Mercier hydrometric station Column separator: semi-colon (;) Column 1 ==> Time (%Y-%m-%d %H:%M) Column 2 ==> Stage(in mm) Missing value code: NA 3/ Gaugings_Mercier.txt Gaugings (date, stage, streamflow and associated uncertainty) of the Mercier hydrometric station before and after hydraulic control change which occured in November 2013. Column separator: semi-colon (;) Column 1 ==> Date (%Y-%m-%d) Column 2 ==> Stage_m (in m) Column 3 ==> Streamflow_m3_per_s (in m3/s) Column 3 ==> Uncertainty (unitless) R codes: 0/ other ressources: All the ressources related to the bayesian estimation of the rating curve can be found on github: <a href="https://github.com/BaM-tools">https://github.com/BaM-tools</a> Time aggregation of time series was done using the tAgg R package available on github: <a href="https://github.com/IvanHeriver/tAgg">https://github.com/IvanHeriver/tAgg</a> 1/ functions.R This files contains several functions. Comments within the file explains each of the function: <ul> <li>hydraulicEquations(): returns a list of the theoretical equations for the rating curves of the five fictive cases</li> <li>hydraulicEquationsInverter(): inverts of a theoretical rating curve (given a function Q=f(h), it returns a function h=f(Q))</li> <li>computeAM30(): computes the AM30</li> <li>generate_nonsyst_errors(): generates a matrix of non systematic errors</li> <li>generate_syst_errors(): generates a matrix of systematic errors</li> <li>get_resampling_indices_from_periodicity(): returns the indices of the resampling time steps used to generate systematic errors given a time vector and a periodicity</li> </ul> Some of the code require the following packages: dplyr and RcppRoll 2/ examples.R This file contains some code illustrating the usage of the functions in the "functions.R" file.

Selected articles from the scoping review on the study designs for clinical trials applied to personalised medicine

The dataset provides the data extracted for the scoping review of the literature on the study designs for clinical trials applied to personalised medicine, as part of the EU project on “Personalised Medicine Trials” (PERMIT). The dataset reports the references for all articles selected as part of the scoping review, as well as information on the general study characteristics and definition, methodology, statistical considerations, and examples of each study design referred to in each included paper.

opencc-by-sa-4.0Oct 2021View details →

Dataset of first appearances of the scholarly bibliographic references on English Wikipedia articles as of 1 March 2017 and as of 1 October 2021

Abstract We developed a methodology to detect the oldest scholarly reference added to Wikipedia articles by which a certain paper is uniquely identifiable as the "first appearance of the scholarly reference." We identified the first appearances of 923,894 scholarly references (611,119 unique DOIs) in180,795 unique pages on English Wikipedia as of March 1, 2017, and stored them in the dataset. Moreover, we assessed the precision of the dataset, which was and it was a high precision regardless of the research field. In this version, it is available not only the dataset of English Wikipedia as of March 1, 2017, but also English Wikipedia as of October 1, 2021, generated by using the same methodology.   Data Records The data format of the dataset is JSON lines, where each line is a single record. In this dataset, we detected the first appearance of each scholarly reference added to Wikipedia articles. If there are multiple references corresponding to the same paper on the same page, only the oldest one is collected. Sample of the record is the following. <ul> <li>doi -- DOI corresponding to the paper (String), e.g., "10.1006/anbe.1996.0497"</li> <li>paper_type -- Document type of the paper (String), e.g., "journal-article"</li> <li>paper_container_title -- Journal title, book title, or proceedings title (Array of String), e.g., ["Animal Behaviour"]</li> <li>paper_publisher -- Publisher name (String), e.g., "Elsevier BV"</li> <li>paper_title -- Paper title (Array of String), e.g., ["Push or pull: an experimental study on imitation in marmosets"]</li> <li>paper_published_year -- Published year (String), e.g., "1997"</li> <li>paper_issue -- Issue number (String), e.g., "4"</li> <li>paper_volume -- Volume number (String), e.g., "54"</li> <li>paper_page -- Page numbers (String), e.g., "817-831"</li> <li>paper_author -- Authors information consisted of given and family names, sequences (order in author names), and affiliations (Array of JSON), e.g., [{"given":"THOMAS", "family":"BUGNYAR", "sequence":"first", "affiliation":[]}, {"given":"LUDWIG", "family":"HUBER", "sequence":"additional", "affiliation":[]}]</li> <li>issn -- ISSN related to the paper (Array of String), e.g., ["0003-3472"]</li> <li>research_field -- Research fields from ESI categories (Array of String), e.g., ["PLANT & ANIMAL SCIENCE"]</li> <li>page_id -- Page id (String), e.g., "577858"</li> <li>page_title -- Page title (String), e.g., "Imitation"</li> <li>revision_id -- Revision id (String), e.g., "203309031"</li> <li>revision_timestamp -- Revision timestamp (String), e.g., "2008-04-04 15:54:09 UTC"</li> <li>revision_comment -- Revision comment (edit summary) (String), e.g., "/* Animal Behaviour */"</li> <li>editor_name -- Wikipedia editor's name (String), e.g., "Nicemr"</li> <li>editor_type -- Type of the editor (String), e.g., "User"</li> </ul> References <ul> <li>Kikkawa, J., Takaku, M. & Yoshikane, F. "Dataset of first appearances of the scholarly bibliographic references on Wikipedia articles", Scientific Data, Vol. 9, Article number 85, pp. 1-11, 2022. <a href="https://doi.org/10.1038/s41597-022-01190-z">https://doi.org/10.1038/s41597-022-01190-z</a>.</li> </ul> FUNDING <ul> <li>JSPS KAKENHI Grant Number <a href="https://kaken.nii.ac.jp/en/grant/KAKENHI-PROJECT-20K12543">JP20K12543</a></li> <li>JSPS KAKENHI Grant Number <a href="https://kaken.nii.ac.jp/en/grant/KAKENHI-PROJECT-21K21303">JP21K21303</a></li> </ul>

Dataset related to article "Plasma Lipid Profiling Contributes to Untangle the Complexity of Moyamoya Arteriopathy"

DATABASE REPORTING CLINICAL, NEURORADIOLOGICAL, DEMOGRAPHICAL AND BIOLOGICAL (“OMICS”)  ANONIMYZED DATA OF A SELECTED SUBGROUP OF PATIENTS AFFECTED BY MOYAMOYA ARTERIOPATHY

opencc-by-4.0Apr 2021View details →

Dataset related to article. "Nonphosphorylated tau slows down Aβ1–42 aggregation, binds to Aβ1–42 oligomers, and reduces Aβ1–42 toxicity"

Figures presented in the paper and their data can be found in the corresponding prism files (www.graphpad.com). The raw data and the picture files for most of the figures can be found in the folder with the corresponding figure name.

Reliability of citations of medRxiv preprints in articles published on COVID-19 in the world leading medical journals

Articles published on COVID in 2020 in the BMJ, The Lancet, the JAMA and the NEJM were manually screened to identify all articles citing at least one preprint from medRxiv. We searched PubMed, Google and Google Scholar to assess if the preprint had been published in a peer-reviewed journal, and when. Published articles were screened to assess if the title, data or conclusions were identical to the preprint version.

Dataset related to article "PLASMA LIPID PROFILING CONTRIBUTES TO UNTANGLE THE COMPLEXITY OF MOYAMOYA ARTERIOPATHY"

DATABASE REPORTING CLINICAL, NEURORADIOLOGICAL, DEMOGRAPHICAL AND BIOLOGICAL (“OMICS”)  ANONIMYZED DATA OF A SELECTED SUBGROUP OF PATIENTS AFFECTED BY MOYAMOYA ARTERIOPATHY

opencc-by-4.0May 2021View details →

Scenario data for article: Environmental impacts of key metals' supply and low-carbon technologies are likely to decrease in the future

This dataset contains the background scenarios for metal supply used for the publication <a href="https://doi.org/10.1111/jiec.13181">"Environmental impacts of key metals' supply and low-carbon technologies are likely to decrease in the future"</a> in the Journal of Industrial Ecology (2021). Scenario description: These background scenarios comprise five variables for the metals of copper, nickel, zinc, and lead for the time period of 2010-2050. These variables are: V1: ore grade decline and energy requirements V2: market shares of primary production locations V3: energy efficiency improvements during smelting and refining V4: market shares of primary production routes V5: market shares of primary and secondary production. The associated <a href="http://doi.org/10.1111/jiec.13181">article</a> in the Journal of Industrial Ecology describes the modelling assumptions and data sources of the scenarios. It also conducts impact assessments for future metal supply and low-carbon technologies with these metal scenarios as well as additional electricity supply scenarios from the IAM of <a href="https://models.pbl.nl/image/index.php/Download#IMAGE_input_data_for_the_Prospective_Life_Cycle_Assessment_model">IMAGE</a> from <a href="https://doi.org/10.1111/jiec.12825">Mendoza Beltran et al. (2020)</a> in the background . How to use this dataset: The background scenarios are suitable for the life cycle inventory database of ecoinvent version 3.5 or 3.6 (allocation, cut-off by classification). They can be incorporated into ecoinvent either via the brightway-based module of <a href="https://github.com/PascalLesage/presamples">presamples</a> or using the <a href="https://github.com/LCA-ActivityBrowser">activity-browser</a> and its scenario-based calculation set-up. Thereby, they can be used as background scenarios for any other prospective LCA based on ecoinvent 3.5 or 3.6. Moreover, they can be combined with the electricity supply scenarios of the IAM of <a href="https://models.pbl.nl/image/index.php/Download#IMAGE_input_data_for_the_Prospective_Life_Cycle_Assessment_model">IMAGE</a> from <a href="https://doi.org/10.1111/jiec.12825">Mendoza Beltran et al. (2020)</a> using the <a href="https://github.com/LCA-ActivityBrowser/brightway-superstructure">superstructure approach</a> of the activity-browser (<a href="https://doi.org/10.1007/s11367-021-01974-2">de Koning & Steubing 2020</a>). Before using the dataset, please adjust the "database" columns to the name of your database, e.g. "ecoinvent3.5", and potentially also the "key" columns. Versions of the scenarios applicable to ecoinvent 3.7.1 or 3.8 may be added later. License: The metal supply scenario data is licensed under the CC-BY 4.0 license.

Raw Data for the article: Donor Preconditioning with Inhaled Sevoflurane Mitigates the Effects of Ischemia-Reperfusion Injury in a Swine Model of Lung Transplantation

Primary graft dysfunction (PGD) and ischemia-reperfusion injury (IRI) occur in up to 30% of patients undergoing lung transplantation and may impact on the clinical outcome. Several strategies for the prevention and treatment of PGD have been proposed, but with limited use in clinical practice. In this study, we investigate the potential application of sevoflurane (SEV) preconditioning to mitigate IRI after lung transplantation. The study included two groups of swines (preconditioned and not preconditioned with SEV) undergoing left lung transplantation after 24-hour of cold ischemia. Recipients' data was collected for 6 hours after reperfusion. Outcome analysis included assessment of ventilatory, hemodynamic, and hemogasanalytic parameters, evaluation of cellularity and cytokines in BAL samples, and histological analysis of tissue samples. Hemogasanalytic, hemodynamic, and respiratory parameters were significantly favorable, and the histological score showed less inflammatory and fibrotic injury in animals receiving SEV treatment. BAL cellular and cytokine profiling showed an anti-inflammatory pattern in animals receiving SEV compared to controls. In a swine model of lung transplantation after prolonged cold ischemia, SEV showed to mitigate the adverse effects of ischemia/reperfusion and to improve animal survival. Given the low cost and easy applicability, the administration of SEV in lung donors may be more extensively explored in clinical practice.

ARCHIMED-φ simulation files for the simulation of Design A from the article "When architectural plasticity fails to counter the light competition imposed by planting design: an in silico approach using a functional-structural model of oil palm"; in silico Plants journal

Input files for the simulation of Design A in ARCHIMED-φ from the article "When architectural plasticity fails to counter the light competition imposed by planting design: an in silico approach using a functional-structural model of oil palm"; in silico Plants journal. See https://archimed-platform.github.io/archimed-phys-user-doc/ for more details on the model. Make a simulation by opening a terminal at the root of the folder and type: `java -jar .\archimed-phys.jar .\DesignA_MockUpA_seed1_MAP_72.yml`.

Dataset related to article"Globus Pallidus Internus Deep Brain Stimulation Using Frame-Based vs. Frameless Stereotaxy in Dystonia: A Single-Center Experience"

Demographic, clinical (BFMDRS at baseline and in follow up), implantation (frame and frameless) data for the sample considered in the study.

dataset related to article "On the evaluation of edgeless diode detectors for patient-specific QA in high-dose stereotactic radiosurgery"

The database contains the comparison table between calculated doses and values actually measured by the edgeless detectors and an example of dose planar distribution as exported from the radiotherapy Treatment Planning System.

Dataset - Classification of abrupt changes along viewing profiles of scientific articles

This is the dataset used to run experiments described in "Classification of abrupt changes along viewing profiles of scientific articles" (more info in https://github.com/carolmb/viewing-profiles-of-scientific-articles). Data original from PlosOne papers views.

Data set figures 1-3 article Reaux et al; Communications Biology 2022

The files attached are : - the manuscript and figures of our article entitled ".." accepted for publication in Communication Biology in February 2022.  - A supplementary material, which is an Excel file is the dataset of the figures 1 to 3. It is composed of two sheets in which the values of cerebral blood volume are given for every single animal included in our study:  before and during each stimulation (been mechanical or chemical stimulation in sheet 1 - figure 2 or mechanical stimulations of either the ophthalmic or maxillary territories - 2d sheet - figure 3).  - A Matlab file with dataset of the figure 4 (ULM of the saggital brain showing the rich and complex vasculature in the trigeminal ganglion)

Supplementary data for article "Small hydropower – small ecological footprint? A multi-annual environmental impact analysis using aquatic macroinvertebrates as bioindicators. Part 2: effects on functional diversity" by Scotti A., et al.

Supplementary data for article "Small hydropower – small ecological footprint? A multi-annual environmental impact analysis using aquatic macroinvertebrates as bioindicators. Part 2: effects on functional diversity" by Scotti A., et al.: - Trait-based distances calculated for each pair of taxa; - CWM, CWM(LN) values, and their difference (CWMDIFF) Refer to the published articles for further details.

Raw Data for the article: Changes in the Transcriptome Profiles of Human Amnion-Derived Mesenchymal Stromal/Stem Cells Induced by Three-Dimensional Culture: A Potential Priming Strategy to Improve Their Properties

Mesenchymal stromal/stem cells (MSCs) are believed to function in vivo as a homeostatic tool that shows therapeutic properties for tissue repair/regeneration. Conventionally, these cells are expanded in two-dimensional (2D) cultures, and, in that case, MSCs undergo genotypic/phenotypic changes resulting in a loss of their therapeutic capabilities. Moreover, several clinical trials using MSCs have shown controversial results with moderate/insufficient therapeutic responses. Different priming methods were tested to improve MSC effects, and three-dimensional (3D) culturing techniques were also examined. MSC spheroids display increased therapeutic properties, and, in this context, it is crucial to understand molecular changes underlying spheroid generation. To address these limitations, we performed RNA-seq on human amnion-derived MSCs (hAMSCs) cultured in both 2D and 3D conditions and examined the transcriptome changes associated with hAMSC spheroid formation. We found a large number of 3D culture-sensitive genes and identified selected genes related to 3D hAMSC therapeutic effects. In particular, we observed that these genes can regulate proliferation/differentiation, as well as immunomodulatory and angiogenic processes. We validated RNA-seq results by qRT-PCR and methylome analysis and investigation of secreted factors. Overall, our results showed that hAMSC spheroid culture represents a promising approach to cell-based therapy that could significantly impact hAMSC application in the field of regenerative medicine.

Nimble Output for MCMC Estimation of Source Apportionment; Accompaniment for Journal Article

Paper A dependent Bayesian Dirichlet Process model for source apportionment of particle number size distribution contributed to the Environmetrics Special Issue on Environmental Data Science. In this paper, a fairly extensive Bayesian model is run using the Nimble probabilistic programming language. To allow for user reproducibility, the output of this model (full, not summary), is provided here.

Dataset Related to article "NEURODEVELOPMENTAL DISORDER AND LATE-ONSET DEGENERATIVE PARKINSONISM IN A PATIENT WITH A WDR45 DEFECT"

NGS data (.vcf; .bam; .bam.bai; .csv; .fastq) of patient analysed and sanger sequencing (.abi) for confirm the mutation.