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zenodo40/100

Dataset and code for article "Explicit description of viral capsid subunit shapes by unfolding dihedrons"

<p>This repository contains data and codes used in a paper "Explicit description of viral capsid subunit shapes by expanding dihedrons" by Toyooka et al.</p> <p>- [grasshopper/] contains a GH file used in the 3D CAD Rhinoceros/Grasshopper.<br>- [docking_axes_viper/] contains notebooks for aligning the subunit coordinates with the VIPER coordinate system (Z-axis is the 2-fold axis, 3-fold axis is on the X-axis, and 5-fold axis is on the Y-axis)</p> <p>- [docking_pairwise/] contains input scipts and analysis notebooks for pairwise docking simulations for subunits<br>&nbsp; - [1stm_zdock_iter/df.jld2] data containing top docking scores and poses, and screw motion parameters<br>&nbsp; - [1stm_zdock_iter/rmsd.jld2] RMSD data of docking poses with regard to the experimental structure &nbsp;- [1stm_zdock_iter/run.sh] is a batch script for conducting docking simulations with ZDOCK<br>&nbsp; - [1stm_zdock_iter/run_each.sh] is a script for a single docking simulation with a specified random seed. Called from `run.sh`<br>&nbsp; - [1stm_zdock_iter/skrew_parameters.ipynb] analyzes the result of docking simulations. Sort the results accoring to docking scores and find the skrew axis of each docking pose<br>&nbsp; - [1stm_zdock_iter/visualize.ipynb] plots the docking score and the screw axis parameters, and also calculates and plots RMSDs from the reference structure (whole-shell structure)<br>&nbsp; - [1stm_zdock_iter/ref.pdb] is a sympolic link to a refrence structure (whole-shell structure)<br>&nbsp; - [4v4m_zdock_iter/] PDB ID: 4V4M<br>&nbsp; - [6s44_zdock_iter/] PDB ID: 6S44<br>&nbsp; - [7odw_zdock_iter/] PDB ID: 7ODW<br>&nbsp; - [3r0r_zdock_iter/] PDB ID: 3R0R<br>&nbsp; - [5zju_zdock_iter/] PDB ID: 5ZJU<br>&nbsp; - [1vb4_zdock_iter/] PDB ID: 1VB4<br>&nbsp; - [1m1c_zdock_iter/] PDB ID: 1M1C<br>&nbsp; - [6r7m_zdock_iter/] PDB ID: 6R7M<br>&nbsp; - [2m99_zdock_iter/] PDB ID: 2M99</p>

opencc-by-4.0Oct 2024View details →
zenodo40/100

Supporting dataset for the article 'Unique structural attributes of the PSI-NDH supercomplex in Physcomitrium patens'

<p><strong>Figure </strong><strong>1</strong><strong>:</strong> <strong>Separation and identification of pigment-protein complexes from </strong><strong>Physcomitrium patens</strong><strong> and structural characterization of PSI-NDH/NDH by single particle electron microscopy. a</strong><strong>) </strong>CN-PAGE separation of pigment-protein complexes from the TM from Pp solubilised by 0.5%&nbsp;&beta;-DDM. The image shows the selected gel line scanned at room temperature in transmission mode (colour image) and in fluorescence mode (black and white image). <strong>b)</strong> Immunoblot identification of the NdhH subunit on a PVDF membrane with transferred proteins from the second-dimension denaturing PAGE. Two horizontal bands of the marker (blue colour) designate the molecular weight of proteins at these positions. <strong>c</strong><strong>&ndash;</strong><strong>e</strong>) Electron density maps of two forms of PSI-NDH sc and NDH monomer from Pp revealed by single particle electron microscopy (stromal view). The 2D class average of (<strong>c</strong>) the typical form of PSI-NDH sc consisting of 2566 particles, (<strong>d</strong>) the shifted form consisting of 1098 particles, and (<strong>e</strong>) the NDH monomer composed of 2725 particles. Abbreviations: PSII - photosystem II, PSI - photosystem I, LHCII - light-harvesting complex of photosystem II, mc - megacomplex, cc - core complex, mono - monomer, trim &ndash; trimer, B1 - C<sub>2</sub>S<sub>2</sub>M<sub>2</sub> band, B2 &ndash; C<sub>2</sub>S<sub>2</sub>M band, B3 &ndash; C<sub>2</sub>S<sub>2</sub>/C<sub>2</sub>SM band, B4 &ndash; PSII cc + PSI band.</p> <p><strong>Figure </strong><strong>2</strong><strong>:</strong> <strong>Structural characterisation of PSI-NDH supercomplex and NDH monomer in </strong><strong>Physcomitrium patens</strong><strong>. a) </strong>Structural model of the PSI-NDH sc in Pp, which corresponds to the arrangements in the PSI-NDH sc from At. <strong>b) </strong>Structural model of the PSI-NDH sc, where PSI is rotated clockwise by 35&deg; in comparison to its position in 2a). <strong>c) </strong>Superposition of the Pp PSI-NDH model with the rotated PSI from image 2b) (in colour) over its un-rotated form from 2a) (grey colour) with pictorial color-coded legend of individual LHCA antennae. <strong>d)</strong> Structural model of the NDH monomer fitted by the truncated At NDH. <strong>e)</strong> Comparison of the Pp NDH model (in colour) versus the complete At NDH model (grey) with highlighted subunits absent in Pp NDH (limon). Structural models of PSI-NDH scs viewed from the stromal side were obtained by a fit of the NDH monomer from At (PDB ID: 7WG5, Su et al., 2022) and PSI complex from Pp (PDB ID: 7KSQ, Gorski et al., 2022). Prior to fitting, the subunits of NDH unencoded in Pp genome were removed from the At NDH structure, namely the PnsB2, PnsB3, and the subunits of SubL. PSI subunits and NDH subcomplexes and selected subunits are color-coded. PSI: forest green - core; pink, white, chocolate, yellow and magenta &ndash; LHCA1, LHCA2a, LHCA2b, LHCA5 and LHCA3, respectively. NDH: orange &ndash; SubM, cyan &ndash; SubB (PnsB1, PnsB4, PnsB5), blue &ndash; SubA and NdhT, lime &ndash; SubB (PnsB2, PnsB3) and SubL.</p> <p><strong>Supporting Figure S1: Single particle electron microscopy analysis of PSI-NDH supercomplex in <em>Physcomitrium patens</em>. </strong>Representative transmission EM micrographs of the <strong>a)</strong> B1, <strong>b)</strong> B2 and <strong>c)</strong> B3 band containing PSII scs (un-circled particles), PSI-NDH scs (in blue circles) and NDH monomers (in yellow circles); <strong>d)</strong> 2D classification of the PSI-NDH and NDH particles extracted from all micrographs of B1 and B2 bands with the given numbers of particles in each class. The 2478 and 20&nbsp;454 particles were extracted for B1 and B2 band, respectively, and were further classified into 15 classes.</p> <p><a name="_Hlk177648374"></a><strong>Supporting Figure S</strong><strong>2</strong><strong>: <a name="_Hlk174966851"></a>Relative content of selected proteins in analysed bands (B1&ndash;B3). </strong><strong>a) </strong>Relative protein abundance of individual LHCI proteins (including LHCB9) evaluated to the protein content of PSI core (represented by the sum of PsaA and PsaB) in three different bands: B1, B2, and B3.<strong> </strong>The relative protein content of all isoforms representing one LHCA protein (see Table S2) were summarised and subsequently evaluated as one for reducing results complicity. <strong>b)</strong> The relative protein content of PSI (represented by sum of PsaA and PsaB) and PSII (represented by sum of PsbA(D1) and PsbD (D2)) evaluated to the sum of all proteins in specific bands.<strong> c) </strong>The SubA/PSI ratio calculated as the sum of relative protein abundance of SubA NDH subunits divided by the sum of relative protein content of PsaA and PsaB in bands B1 and B2. The relative content (relative PG iBAQ values (riBAQ) in ppm format) of individual LHCA isoforms, LHCB9, SubA subunits, PsaA, PsaB, PsbA (D1) and PsbD (D2) was determined by mass spectrometry in samples prepared from gel bands excised from CN-PAGE (Fig 1a). The presented values are means &plusmn; SD from 3 replicates.<strong>&nbsp;&nbsp; </strong></p> <p><strong>Supporting Figure S2 (xlsx format):&nbsp;</strong>Selected mass spectrometry source data for Figure S2(a-c).</p> <p><strong><a name="_Hlk177648454"></a>Supporting Figure S3: Impact of PSI rotation within Pp PSI-NDH sc on the distance between the putative ferredoxin (Fd)-binding sites in NDH and PSI. </strong>Comparison of the distance between Fd-binding site in NDH and PSI in typical (a) and shifted (b) form of PSI-NDH sc. The subunits forming Fd-binding site in NDH according Laughlin et al. (2020): NdhO, NdhI, NdhH (excluding NdhS and NdhV absent in model) and in PSI according Caspy et al. (2020): stromal PsaC-E (excluding PsaA, PsaF) are labelled and colour coded as follows: NDH: limon, blue, orange &ndash; NdhO, NdhH, NdhI, respectively; PSI: yellow, violet, and firebrick &ndash;PsaC, PsaD, PsaE, respectively, with the rest of the subunits in PSI and NDH in grey colour. The binding positions of the Fd in NDH (O-site) and PSI are illustrated as brown circles. Structural models of PSI-NDH scs viewed from the stromal side were obtained by a fit of the NDH monomer from At (PDB ID: 7WG5, Su et al., 2022) and PSI complex from Pp (PDB ID: 7KSQ, Gorski et al., 2022). Prior to fitting, the subunits of NDH unencoded in Pp genome were removed from the At NDH structure, namely the PnsB2, PnsB3, and the subunits of SubL. Two headed arrows determine the distance between approx. centre of Fd-binding sites in NDH and PSI in two different structures with estimated values in Angstroms. <strong>&nbsp;</strong></p> <p><strong>Supporting Table S1:</strong> <strong>A summary of the identified PSI-NDH supercomplex subunits in </strong><strong>Physcomitrium patens</strong><strong>. </strong>MS analysis of the B2 band (in 3 technical replicates) from CN-PAGE used for transmission EM analysis. The subunits of the PSI and NDH complexes identified in the band after digestion with trypsin and assigned according to UniProt database records are listed. Proteins highlighted in green are not encoded in the Physcomitrium patens genome or do not have any record in the UniProt database, proteins highlighted in orange were not identified in our dataset.</p> <p><a name="_Hlk177048123"></a><strong>Supporting Table S2: The list of all LHCI proteins (including LHCB9) and their isoforms identified in four analysed bands B1, B2, B3 and B4 by mass spectrometry.</strong> Individual rows represent different isoforms of LHCI antennae detected in specific bands by MS, accession numbers according UniProt database in one row represent the same isoform of protein. Letters &ldquo;Y&rdquo; and &ldquo;N&rdquo; indicate whether the specific protein was detected or undetected in MS dataset of individual bands, respectively. The label &ldquo;Low&rdquo; was assigned to those protein that were detected, however, whose abundance was close to the detection limit or they had overall low and negligible abundance relatively to PSI core. For band B1&ndash;B3 and B4 three and four technical replicates were analysed, respectively.&nbsp;</p>

opencc-by-4.0Oct 2024View details →
zenodo40/100

Dataset for the article 'Estimating countries' additional carbon accountability for closing the mitigation gap based on past and future emissions'.

<p>Dataset for the article 'Estimating countries&rsquo; additional carbon accountability for closing the mitigation gap based on past and future emissions', published in Nature Communications. DOI: <a href="https://doi.org/10.1038/s41467-024-54039-x">10.1038/s41467-024-54039-x</a></p> <p>TablesInManuscriptandCalculations.xlsx includes a calculations sheet where the main results can be estimated using only Excel, and each respective table found in the article.</p> <p>PlannedEmissions.xlsx includes estimated pathways for all analyzed countries during 2023-2070. Results are given in million tonnes of carbon dioxide (MtCO₂).</p> <p>DataForSensitivityAnalysis.xlsx is a full database with all the results used in the article, both the main approach and sensitivity cases.</p> <p>These files are generated using R-code available at:</p> <p><a href="https://github.com/morfeldt/AdditionalCarbonAccountability">https://github.com/morfeldt/AdditionalCarbonAccountability</a></p> <p>&nbsp;</p>

opencc-by-4.0Nov 2024View details →
zenodo40/100

Dataset for article: Nanostructure Formation in Glycerolipid Films during Enzymatic Hydrolysis: A GISAXS Study

<p><strong>Dataset for publication:</strong></p> <p>Nanostructure Formation in Glycerolipid Films during Enzymatic Hydrolysis: A GISAXS Study<br>Rafael V. M. Freire, Bettina Tran, Meron Debas, Mahsa Zabara, Heinz Amenitsch, and Stefan Salentinig<br>ACS Appl. Mater. Interfaces 2024, 16, 44, 61262&ndash;61271 (DOI 10.1021/acsami.4c12125)</p> <p>Setup and conditions for the experiments are described in the experimental section of the published manuscript.</p> <p>Data description in README.txt file.</p>

opencc-by-4.0Nov 2024View details →
zenodo40/100

OpenCSMap dataset: DBLP articles with affiliations

<p>Dataset contains DBLP articles (journal and conference papers) along with one affiliation found for some of them.</p>

opencc-by-4.0Jun 2021View details →
zenodo40/100

Dataset for the article Development of a Submillimetric GNSS-Based Distance Meter for Length Metrology

<p>The data files contain the GNSS RINEX observation files and the ASCII files of the EDM measurements for the different measurement campaigns used in the article &quot;Development of a Submillimetric GNSS-Based Distance Meter for Length Metrology&quot; by Luis Garc&iacute;a-Asenjo, Sergio Baselga, Chris Atkins and Pascual Garrigues, Sensors 2021, 21, 1145. https://doi.org/10.3390/s21041145.&nbsp;This work was partly performed within the 18SIB01 GeoMetre project of the European<br> Metrology Programme for Innovation and Research (EMPIR). This project has received funding<br> from the EMPIR programme co-financed by the Participating States and from the European Union&rsquo;s<br> Horizon 2020 research and innovation programme, funder ID: 10.13039/100014132. This research was also partly funded by the<br> Spanish Ministry of Education, Culture and Sports (PRX17/00371).</p> <p>All files are ASCII files: RINEX files with standard extension and filename notation, where PL1A indicates pillar 1 GNSS with receiver A, PL3B pillar 3 GNSS with receiver B, (as indicated in the paper&nbsp;two receivers per pillar where used),&nbsp;etc.; and space-separated ASCII files with explanatory headers for the ME5000 EDM observations.</p>

opencc-by-4.0Jul 2021View details →
zenodo40/100

Datasets from the KDD 2021 article "A Semi-Personalized System for User Cold Start Recommendation on Music Streaming Apps"

<p>We publicly release&nbsp;the anonymized&nbsp;<em>song_embeddings.parquet&nbsp; user_embeddings.parquet&nbsp; user_features_test.parquet&nbsp; user_features_train.parquet&nbsp; user_features_validation.parquet</em>&nbsp;datasets, with each of the&nbsp;TT-SVD or UT-ALS versions of embeddings, from the music streaming platform Deezer, as described in the&nbsp;article &quot;<em>A Semi-Personalized System for User Cold Start Recommendation on Music Streaming Apps&quot;</em>&nbsp;published in the proceedings of the 27TH ACM SIGKDD conference on knowledge discovery and data mining&nbsp;(<em>KDD 2021</em>). The paper is available&nbsp;<a href="https://arxiv.org/abs/2106.03819">here</a>.</p> <p>These datasets are used in the&nbsp;GitHub repository&nbsp;<a href="https://github.com/deezer/semi_perso_user_cold_start">deezer/semi_perso_user_cold_start</a>&nbsp;to reproduce experiments from the article.</p> <p>Please cite our paper if you use our code or data in your work.</p>

opencc-by-4.0Jul 2021View details →
dryad40/100

Dataset for article: Co-evolutionary landscape at the interface and non-interface regions of protein-protein interaction complexes

<p>Proteins involved in interactions throughout the course of evolution tend to co-evolve and compensatory changes may occur in interacting proteins to main­tain or refine such interactions. However, certain residue pair alterations may prove to be detrimental for functional interactions. Hence, determining co-evolutionary pairings that could be structurally or functionally relevant for maintaining the conservation of an inter-protein interaction is important. Inter-protein co-evolution analysis in several complexes utilizing multiple existing methodologies suggested that co-evolutionary pairings can occur in spatially proximal and distant regions in inter-protein interactions. Subsequently, the Co-Var (<b>Co</b>rrelated <b>Var</b>iation) method based on mutual information and Bhattacharyya coefficient was developed, validated, and found to perform relatively better than CAPS and EV-complex. Interestingly, while applying the Co-Var measure and EV-complex program on a set of protein-protein interaction complexes, co-evolutionary pairings were obtained in interface and non-interface regions in protein complexes. The Co-Var approach involves determining high degree co-evolutionary pairings that include multiple co-evolutionary connections between particular co-evolved residue positions in one protein with multiple residue positions in the binding partner. Detailed analyses of high degree co-evolutionary pairings in protein-protein complexes involved in cancer metastasis suggested that most of the residue positions forming such co-evolutionary connections mainly occurred within functional domains of constituent proteins and substitution mutations were also common among these positions. The physiological relevance of these predictions suggests that Co-Var can predict residues that could be crucial for preserving functional protein-protein interactions. Finally, <b>Co-Var </b>web server (<a href="http://www.hpppi.iicb.res.in/ishi/covar/index.html">http://www.hpppi.iicb.res.in/ishi/covar/index.html</a>) that implements this methodology identifies co-evolutionary pairings in intra and inter-protein interactions.</p>

opencc-zeroJul 2021View details →
zenodo40/100

Reproduction package for the article "Accretion disc cooling and narrow absorption lines in the tidal disruption event AT 2019dsg"

<p>This is the&nbsp;reproduction package for the MNRAS Article &quot;Accretion disc cooling and narrow absorption lines in the tidal disruption event AT 2019dsg&quot; by Cannizzaro et al (2021). It contains the reduced optical data, the scripts used for the emission lines fitting and the code used to perform the host galaxy subtraction.</p>

opencc-by-4.0Jul 2021View details →
zenodo40/100

Reproduction package for the article "Spectroscopic Monitoring of the Candidate Tidal Disruption Event in F01004–2237"

<p>This is the&nbsp;reproduction package for the Article &quot;Spectroscopic Monitoring of the Candidate Tidal Disruption Event in F01004-2237&quot; by Cannizzaro et al (2021). It contains the reduced optical data and&nbsp;the scripts used for the emission lines fitting.</p>

opencc-by-4.0Jul 2021View details →
zenodo40/100

Dataset related to article "Acetaldehyde in polyethylene terephthalate (PET) bottledwater: assessment and mitigation of health risk for consumers"

<p><em>The file contains the raw data related to the manuscript: &quot;Acetaldehyde in Polyethylene Terephthalate (PET) Bottled Water: Assessment and Mitigation of Health Risk for Consumers&quot;</em></p> <p><strong>Abstract</strong>: This study was designed to investigate the levels of acetaldehyde residues in polyethylene terephthalate bottled water and its significance in terms of consumer health. We analyzed 104 samples collected throughout Italy, so as to be representative of the national market. Parameters such as CO<sub>2</sub>&nbsp;level, shelf life, weight of the empty bottle and distance from the production sites to the point of sale were also collected. Although the levels of acetaldehyde complied with the limits established by Italian legislation, they varied widely, with concentrations ranging from 0.41 to 76.2 &micro;g/L. An assessment of safety for human health, using the margin of exposure approach, showed that the amount of acetaldehyde in bottled water is unlikely to be of any safety concern for human health. The acetaldehyde residues were mainly due to CO<sub>2</sub>&nbsp;levels which influence solubility of acetaldehyde in water. They are also related to the size of the bottle and the distance from the store, but not to the shelf life, at least for 40 days. The findings suggest some good practices for a better product from the point of view of public health, like polymer quality and limitation of transport distances.</p> <p><strong>Funding</strong>: This research was funded by Mineracqua.</p> <p>&nbsp;</p>

opencc-by-4.0Jul 2021View details →
zenodo40/100

Disk population synthesis data for the article: "Large gaps and high accretion rates in photoevaporative transition disks with a dead zone"

<p>We make available here the results of our gas evolution simulations for the article &quot;Large gaps and high accretion rates in photoevaporative transition disks with a dead zone&quot;.</p> <p>We include the result of our population synthesis study, consisting in 10 tables corresponding to 9 models including both dead zone and photoevaporation, and 1 control model including photoevaporation only. The results can be plotted using the &quot;Plotting-PopulationSynthesisModels.ipynb&quot; jupyter notebook.</p> <p>The tables including a dead zone are named as: Macc_Rhole_Pop_AD(X)_RD(Y).txt, where (X)*1.e-4 corresponds to the turbulence in the dead zone, and (Y)*AU corresponds to the dead zone radial extent.</p> <p>The tables include the following fields: Simulation ID, Time [Myr] at which the snapshot was taken, Gap size [AU] measured at the outer edge, Accretion rate log[Msun/yr], and Gas disk mass. We also include a table called &quot;LxRc_Distribution.txt&quot;, that indicates the X-ray luminosity log[erg/s] and initial disk characteristic radius [AU] used for the corresponding Simulation ID.</p> <p>&nbsp;</p> <p>We also include the gas surface density evolution of a Control simulation, with photoevaporation only (with Lx = 1.e30 erg/s), and a Dead Zone + Photoevaporation simulation (with dead zone turbulence 1.e-4, and dead zone radial extend 10 AU). These can be plotted using the &quot;Plotting-SingleGasEvolution.ipynb&quot; jupyter notebook.</p>

opencc-by-4.0Dec 2020View details →
zenodo40/100

Dateset related to article "Cytokines as potential biomarkers of disease clinical course in muscular dystrophies "

<p>This database includes a comprehensive profile of circulating pro- and anti-inflammatory molecules (cytokines, chemokines and growth factors) obtained from a group of 53 patients with muscular laminopathy, 10 with non-muscular laminopathy, 22 with other muscular disorders and 35 healthy controls. Data obtained by Luminex multiple immune-assay identify TGF-b2, IL-17 and G-CSF as potential biomarkers in discriminating&nbsp; between muscle-related laminopathy and healthy subjects. The different expression&nbsp; of IL-1b, IL-4 and IL-8 among the different forms of laminopathy provides a new hint for the understanding of the pathogenic mechanisms underlying the diverse phenotypes caused by <em>LMNA</em> mutations.</p>

opencc-by-4.0Aug 2021View details →
zenodo40/100

Data from article "Sea-level rise in Venice: historic and future trends (review article)"

<p>Data from the article Zanchettin D., et al.:&nbsp;Sea-level rise in Venice: historic and future trends (review article),&nbsp;Nat. Hazards Earth Syst. Sci., 21, 1&ndash;35, 2021, https://doi.org/10.5194/nhess-21-1-2021</p> <p>The dataset contains:</p> <p>- Historical tide gauge data for Venice (relative sea level, or RSL, and RSL corrected for vertical land movement) for the winter (JFM) and autumn (OND) seasons.</p> <p>- sea-level projections for Venice for the RCP2.6, the RCP8.5 and a high-end scenario.</p>

opencc-by-4.0Jul 2021View details →
zenodo40/100

Dataset for article "Energy flux paths in lakes and reservoirs" by Guseva et al., 2021

<p>The dataset includes the measured parameters&nbsp;that have been analyzed in the manuscript &ldquo;Energy flux paths in lakes and reservoirs&rdquo; by Guseva S., Casper P., Sachs T., Spank U. and Lorke A. The manuscript has been submitted to <em>Water</em>.</p>

opencc-by-4.0Aug 2021View details →
zenodo40/100

Images, graphs and tables from the article: Biological performance of a bioabsorbable Poly (L-Lactic Acid) produced in polymerization unit: in vivo studies -

<p>The images, graphs and tables attached correspond to the study performed in the thesis project on the in vivo biocompatibility of the PLLA polymer produced.</p>

opencc-by-4.0Aug 2021View details →
zenodo40/100

Raw data for the article: Human Amnion Epithelial Cells Impair T Cell Proliferation: The Role of HLA-G and HLA-E Molecules

<p>The immunoprivilege status characteristic of human amnion epithelial cells (hAECs) has been recently highlighted in the context of xenogenic transplantation. However, the mechanism(s) involved in such regulatory functions have been so far only partially been clarified. Here, we have analyzed the expression of HLA-Ib molecules in isolated hAEC obtained from full term placentae. Moreover, we asked whether these molecules are involved in the immunoregulatory functions of hAEC. Human amnion-derived cells expressed surface HLA-G and HLA-F at high levels, whereas the commonly expressed HLA-E molecule has been measured at a very low level or null on freshly isolated cells. HLA-Ib molecules can be expressed as membrane-bound and soluble forms, and in all hAEC batches analyzed we measured high levels of sHLA-G and sHLA-E when hAEC were maintained in culture, and such a release was time-dependent. Moreover, HLA-G was present in extracellular vesicles (EVs) released by hAEC. hAEC suppressed T cell proliferation in vitro at different hAEC:T cell ratios, as previously reported. Moreover, inhibition of T cell proliferation was partially reverted by pretreating hAEC with anti-HLA-G, anti-HLA-E and anti-&beta;2 microglobulin, thus suggesting that HLA-G and -E molecules are involved in hAEC-mediated suppression of T cell proliferation. Finally, either large-size EV (lsEV) or small-size EV (ssEV) derived from hAEC significantly modulated T-cell proliferation. In conclusion, we have here characterized one of the mechanism(s) underlying immunomodulatory functions of hAEC, related to the expression and release of HLA-Ib molecules.</p>

opencc-by-4.0Aug 2021View details →
zenodo40/100

Categorization of articles 2017 with authorship of Pontificia Universidad Católica de Chile, through the SDGs

<p>The dataset comprises a single list of publications exported from Web of Science (Clarivate Analytics) and Scopus (Elsevier) databases, to which a process was applied that eliminated duplicate records. 2,379 scientific publications in English or Spanish of the &quot;Article&quot; type from the year 2017, with authorship associated with the Pontificia Universidad Cat&oacute;lica de Chile, were considered.</p> <p>In addition, the classification process carried out by the team of specialists that considered three consecutive milestones is included: establishment of the reading level applied to each publication record; assignment of one of the 18 categories identified in the information analysis, which include the 17 SDGs and the option &quot;Unclassified&quot; and one of the 169 subcategories corresponding to the goals; and, finally, the status of the review process carried out.</p>

opencc-by-4.0Aug 2021View details →
zenodo40/100

Dataset related to article "ANTIHYPERTENSIVE DRUGS FOR SECONDARY PREVENTION AFTER ISCHEMIC STROKE OR TRANSIENT ISCHEMIC ATTACK"

<p>we performed a systematic review and meta-analysis in order to summarize the current evidence on blood pressure (BP)-lowering drugs for secondary prevention in patients with ischemic stroke or transient ischemic attack. We searched MEDLINE, EMBASE, and the Cochrane Central Register of Controlled Trials up to January 31, 2020. We included randomized controlled trials comparing any specific BP-lowering drug, as monotherapy or combination, with either a control or another BP-lowering drug. Eight studies that enrolled 33 774 patients with ischemic stroke or transient ischemic attack were included in the meta-analysis. Primary outcomes were all-cause mortality and the proportion of patients who developed a stroke following BP-lowering drug use, irrespective of its nature (ischemic or hemorrhagic) and severity. Secondary outcomes included the proportion of patients who developed an ischemic stroke; an ischemic stroke or TIA irrespective of severity; a hemorrhagic stroke, defined as an acute extravasation of blood into and around the brain parenchyma (subdural hematoma and epidural hematoma were excluded); a cardiovascular event defined as any sudden death, fatal or nonfatal acute coronary syndrome, stroke, intracranial hemorrhage, or pulmonary embolism; a fatal cardiovascular event defined as any death due to any vascular cause, including unexplained sudden death; and serious adverse events of hypotension, syncope, injurious falls, electrolyte abnormalities, bradycardia, or acute renal failure. We recorded the outcomes at the longest available follow-up for all analyses. We considered the following potential sources of heterogeneity (effect modifiers): inclusion limited to hypertensive patients (normotensive and hypertensive patients versus hypertensive patients only) or noncardioembolic ischemic strokes (all ischemic strokes versus noncardioembolic ischemic strokes only), time from the index ischemic event to randomization (acute patients treated within the first week versus stabilized patients treated after the first week), and trial risk of bias.</p>

opencc-by-4.0Aug 2021View details →
zenodo40/100

Data related to article 'Thawing Yedoma permafrost is a neglected nitrous oxide source'

<p>Data on nitrous oxide (N<sub>2</sub>O) fluxes with related process, soil and microbial data from two thawing Yedoma exposures in Northeast Siberia.</p> <p>Metadata:</p> <p>Study site 1:Kurungnakh<br> Location 1:N 72&deg;20&#39;, E 126&deg;17&#39;</p> <p>Study site 2:Duvanny Yar<br> Location 2:68&deg;38&#39; N, 159&deg;09&#39; E</p> <p>Contact:Maija Marushchak (maija.marushchak@uef.fi); Christina Biasi (christina.biasi@uef.fi)</p> <p>Ecosystem type:Yedoma exposure; retrogressive permafrost thaw slump</p> <p>Duration:July 2016, July 2017</p> <p>Data creation date:1 September 2021</p> <p>File origin:Created at University of Eastern Finland/University of Jyv&auml;skyl&auml; by Maija Marushchak (maija.marushchak@uef.fi)<br> Data policy:Kindly inform Maija Marushchak and Christina Biasi if you are going to use the data and of any publication plans.<br> If they think that they should be acknowledged or offered participation as authors they will let you know.</p> <p>Questions about this file should be addressed to Maija Marushchak (maija.marushchak@uef.fi).</p> <p>&nbsp;</p>

opencc-by-4.0Aug 2021View details →

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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.

allen-brain-atlas
neuroscienceopenDocumentation, web resources, and API references are available online.
Last verified 2026-04-30Open record

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.

abode-home-cage
behavioral-neuroscienceopenThe DataShare record exposes download links for annotations, documentation, license text, and the zipped per-snippet data directory.
Last verified 2026-04-30Open record

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.

dandi-nwb
electrophysiologyopenPublished Dandiset metadata and archive endpoints are available through the production DANDI API.
Last verified 2026-04-30Open record

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.

ibl
behavioral-neuroscienceopenPublic sessions can be searched and loaded from the IBL public data server through ONE.
Last verified 2026-04-29Open record

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.

openneuro
neuroscienceopenPublished datasets are available on demand over the internet.
Last verified 2026-04-29Open record

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