Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
3,484
datasets available to search
ShareScore release 0.9.0
Dataset results
3,484 results for “Plastics”
Quantification of 3D spatial correlations between state variables and distances to the grain boundary network in full-field crystal plasticity spectral method simulations
<p>This repository provides supplementary material to our paper: <a href="https://doi.org/10.1088/1361-651X/ab7f8c">https://doi.org/10.1088/1361-651X/ab7f8c</a></p> <p><strong>DAMASKPhenoPowerLaw75x75x75TestCase.zip</strong><br> An exemplary DAMASK simulation and corresponding output, generated from DAMASK v2.0.3. We used this to debug more productively the implementation of the post-processing tools. Furthermore we employed this simulation in the paper to identify why the graph clustering grain reconstruction method in many cases fuses neighboring grains in similar orientation.</p> <p><strong>DAMASKPhenoPowerLaw256x256x256ProductionRun.zip</strong><br> All input to run the DAMASK simulation that we discussed in the paper.</p> <p><strong>DAMASKPDTSettings256x256x256ProductionRun.zip</strong><br> All damaskpdt settings files to execute the individual post-processing studies of the paper.</p> <p><strong>DAMASKPDTSlurmSubmissionScripts256x256x256ProductionRun.zip</strong><br> All SLURM scripts we used to execute the compilation of damaskpdt and post-processing on TALOS.</p> <p><strong>DAMASKPDTSlurmLogs256x256x256ProductionRun.zip</strong><br> All logs from the SLURM job management system from the individual post-processing runs.</p> <p><strong>DAMASKPDTSourceCode_USedForAnalyticalDistanceToVoronoiCellFacets.zip</strong><br> The source code to the tool we developed during the revision process of our paper to verify the methods<br> via computing analytically exact distances to the facets of the Poisson-Voronoi tessellation from the<br> DAMASK microstructure instantiation.<br> <br> <strong>DAMASKPDTSourceCode_Production.zip</strong><br> The source code we used to post-process all results from the DAMASK simulations.</p> <p><strong>GitHub repository:</strong><br> https://github.com/mkuehbach/damaskpdt</p>
Coevolving plasmids drive gene flow and genome plasticity in host-associated intracellular bacteria
<p>Comparative genomics and modeling of plasmids of the obligate host-associated intracellular phylum chlamydiae. </p>
Network properties data and code used in "Ecological plasticity governs ecosystem services in multilayer networks".
<p>Code and network properties data used in the analyses presented in "Ecological plasticity governs ecosystem services in multilayer networks". Further information can be requested of the author David A. Bohan (David.Bohan@inrae.fr).</p>
Chemicals associated with plastics packaging (CPPdb) for MS-FIDNER
<p>The original chemicals associated with plastic packaging database (CPPdb) was compiled by Ksenia J. Groh, etc., and is downloadable in https://zenodo.org/record/1287773. To make the use of this database for structural elucidation in MS-FINDER, the CPPdb is re-organized to the form that is compatible with MS-FINDER. Vital information, e.g., smiles and InChIKey, which are vital for in-silico fragmentation, are added to the CPPdb. Hope this re-formed database would be helpful for anyone who wants to use it for MS-FINDER.</p>
Data from: Advancement in long-distance bird migration through individual plasticity in departure
<p>Research summary: Globally, bird migration is occurring earlier, consistent with climate-related changes in breeding resources. Although often attributed to phenotypic plasticity, there is no clear demonstration of long-term population advancement in avian migration through individual plasticity. Using direct observations of bar-tailed godwits (<em>Limosa lapponica</em>) departing New Zealand on a 16,000-km journey to Alaska, we show that migration advanced by six days during 2008–2020, and that within-individual advancement was sufficient to explain this population-level change. However, in individuals tracked for the entire migration, earlier departure did not lead to earlier arrival or breeding in Alaska, due to prolonged stopovers in Asia. Moreover, changes in breeding-site phenology varied across Alaska, but were not reflected in within-population differences in advancement of migratory departure. We demonstrate that plastic responses can drive population-level changes in timing of long-distance migration, but also that behavioral and environmental constraints <em>en route</em> may yet limit adaptive responses to global change.</p> <p>The collection of long-term departure data was supported by Chris & Neville Hopkins, David & Lucile Packard Foundation, Dobberke Foundation for Comparative Psychology, Manawatu Estuary Trust, Marsden Fund (Royal Society of New Zealand), Massey University Doctoral Scholarship, New Zealand Department of Conservation, Ornithological Society of New Zealand, Pacific Shorebird Migration Project, Pūkorokoro Miranda Naturalist’s Trust, and Royal Netherlands Academy of Arts & Sciences.</p>
Supporting Data: Complementary Organic Logic Gates on Plastic Formed by Self-Aligned Transistors with Gravure and Inkjet Printed Dielectric and Semiconductors
<p>The file contains the supporting data for the publication:</p> <p>S.G. Higgins, B.V.O. Muir, G. Dell'Erba, A. Perinot, M. Caironi, A.J. Campbell. Complementary Organic Logic Gates on Plastic Formed by Self-Aligned Transistors with Gravure and Inkjet Printed Dielectric and Semiconductors. doi: 10.1002/aelm.201500272. <em>Advanced Electronic Materials </em>(2015)</p> <p>See 'README.txt' for a description of the contents of the compressed file.</p>
Supporting Data: Indacenodithiophene-benzothiadiazole Organic Field-Effect Transistors with Gravure Printed Semiconductor and Dielectric on Plastic
<p>The file contains the supporting data for the publication:</p> <p>S.G. Higgins, B.V.O. Muir, M. Heeney, A.J. Campbell. Indacenodithiophene-benzothiadiazole Organic Field-Effect Transistors with Gravure Printed Semiconductor and Dielectric on Plastic. doi: 10.1557/mrc.2015.66. <em>MRS Communications</em> (2015)</p> <p>See 'README.txt' for a description of the contents of the compressed file.</p>
Supporting Data: Self-Aligned Organic Field-Effect Transistors on Plastic with Picofarad Overlap Capacitances and Megahertz Operating Frequencies
<p>The file contains the supporting data for the publication:</p> <p>S.G. Higgins, B.V.O. Muir, G. Dell'Erba, A. Perinot, M. Caironi, A.J. Campbell. Self-Aligned Organic Field-Effect Transistors on Plastic with Picofarad Overlap Capacitances and Megahertz Operating Frequencies. doi: 10.1063/1.4939045. <em>Applied Physics Letters</em> (2016)</p> <p>See 'README.txt' for a description of the contents of the compressed file.</p>
The gut microbiota of environmentally enriched mice regulates visual cortical plasticity
<p>ABSTRACT</p> <p>The complexity of brain circuits is sculpted both by innate genetic programs and environmental stimuli. Since the 1960s scientists have noticed that raising rodents in an enriched environment (EE) is able to improve all aspects of brain plasticity, from learning and memory to visual plasticity in adult and developing animals. Importantly, EE has also been shown to have beneficial effects on a variety of preclinical models of central nervous system diseases: Alzheimer’s and Parkinson’s disease, Rett syndrome, epilepsy etc, prompting intervention protocols in humans. However, the “enrichment derived key signals” through which this special environment performs its broad positive effects on brain health have not been completely elucidated yet. Here, we focused on signals coming from the body periphery and in particular on the gut microbiota. We found that the intestinal microbiota composition of EE mice is significantly different from the one of standard raised (ST) animals. Treatment of EE mice with an antibiotic cocktail completely prevented the EE-driven enhancement of OD plasticity. Strikingly, the fecal microbiota transplant from EE donors to adult ST mice was able to re-activate OD plasticity in the ST recipients. Thus, taken together our data suggest that experience-dependent changes in gut microbiota regulate brain plasticity.</p> <p>METHODS</p> <p>In the first dataset (Dataset1, files called zr2423) we report the raw data (.fastq) obtained from the sequencing of the fecal samples from C57BL/6J mice raised in EE or in ST from birth and collected at different time points during their lives.</p> <p>To analyze the composition of the microbiota of ST and EE mice at different ages, fresh faeces were collected longitudinally in the same subject at postnatal day (P)20 (n=6), P25 (n=6) and P90 (n=6). </p> <p>In the second dataset (Dataset2, files called zr2747) we report the raw data (.fastq) obtained from the sequencing of the fecal samples from C57BL/6J: adult donor mice living in EE (EE, n=8), adult recipient mice living in ST condition before the fecal transplantation (preFT, n=8) and 4 weeks after the fecal transplantation (postFT, n=8).</p> <p>For further details about the sample names see the “Explanation Table”.</p> <p>Bacterial DNA was extracted using a specific kit (QIAamp Powerfecal DNA kit, Qiagen) following the manufacturer's protocol. The 16S rRNA sequencing and analysis was performed by a service offered by Zymo Research (Irvine, CA, USA). </p> <p><em>Targeted Library Preparation</em>: The DNA samples were prepared for targeted sequencing with the Quick-16S™ NGS Library Prep Kit (Zymo Research). The primer sets used were Quick-16S™ Primer Set V3-V4 (Zymo Research). The sequencing library was prepared using an innovative library preparation process in which PCR reactions were performed in real-time PCR machines to control cycles and therefore limit PCR chimera formation. The final PCR products were quantified with qPCR fluorescence readings and pooled together based on equal molarity. The final pooled library was cleaned up with the Select-a-Size DNA Clean & Concentrator™, then quantified with TapeStation® (Agilent Technologies, Santa Clara, CA) and Qubit® (Thermo Fisher Scientific, Waltham, WA). </p> <p><em>Sequencing:</em> The final library was sequenced on Illumina® MiSeq™ with a v3 reagent kit (600 cycles). The sequencing was performed with >10% PhiX spike-in.</p> <p> </p>
Dataset for Stimulus-specific plasticity in human visual gamma-band activity and functional connectivity
<p>Per-trial dataset accompanying the publication Stauch, Peter, Schuler, and Fries (2020): Stimulus-specific plasticity in human visual gamma-band activity and functional connectivity.<br> Additionaly, preprocessing code is provided as Codebase.zip.</p>
Raw data for: "CalDAG-GEFI mediates striatal cholinergic modulation of dendritic excitability, synaptic plasticity and psychomotor behaviors"
<p>Figure 2. CDGI mediates the M1R modulation of dendritic excitability but not the M1R</p> <p>modulation of somatic excitability.</p> <p>(A and B) Sagittal sections through the brains of CDGI knockout mice in which the direct</p> <p>pathway was visualized (red) in D1-tdTomato mice (A) and the indirect pathway was visualized</p> <p>(green) in D2-GFP mice.</p> <p>(C) Sample somatic voltage changes evoked by 120pA current injections in iSPNs from WT</p> <p>(black) and CDGI-KO (red) before and after bath application of oxo-M (10 µM).</p> <p>(C-D) Current-response curves of iSPNs from WT (B, n=5 cells) and CDGI-KO mice (C, n=7</p> <p>cells). Somatic excitability of iSPNs was similarly enhanced by oxo-M in WT and CDGI-KO.</p> <p>(E) Sample somatic recordings in response to 140pA current injections in dSPNs from WT</p> <p>(black) and CDGI KO (red) before and after bath application of oxo-M (10 µM).</p> <p>(F-H) Current-response curves of dSPNs from WT (E) and CDGI-KO (F) mice (n=4-6).</p> <p>(I) Trains of five EPSPs were evoked by stimulation of glutamatergic afferent fibers at 40 Hz.</p> <p>Oxo-M (10 µM) increased EPSP summation in iSPNs of WT, but not in CDGI-KO or when</p> <p>M1Rs were blocked by M1R antagonist VU0255035 in WT (5 M).</p> <p>(J) Box plot showing the effect of oxoM on synaptic summation. The EPSP5/EPSP1 ratio was</p> <p>increased by oxoM in iSPNs of WT (p = 0.002, Wilcoxon test; n = 10), but not in iSPNs of 27</p> <p>CDGI-KO mice (p = 0.25, n = 9) or in iSPNs of WT mice in the presence of VU0255035 (p =</p> <p>0.69, n = 6).</p> <p>(K) Box plot showing the effect of oxoM on the kinetics of synaptic response. The decay time</p> <p>constant of EPSP5 was significantly increased by oxoM in iSPNs of WT (p = 0.002); but not</p> <p>when CDGI was genetically deleted (p = 0.65) or when M1R was pharmacologically blocked (p</p> <p>= 0.84).</p>
Buoyancy and Brownian motion of plastics in aqueous media: Predictions and implications for density separation and aerosol internal mixing state (Data Underlying Figures)
<p>Data underlying figures in A. Bain 'Buoyancy and Brownian motion of plastics in aqueous media: Predictions and implications for density separation and aerosol internal mixing state' RSC Environmental Science: Nano, 2022. </p> <p>CA = citric acid<br> NaCl = sodium chloride<br> AS = ammonium sulfate</p> <p>rho = difference in density (g/cm^3)<br> Rh = % relative humidity<br> radius is in micrometers<br> Pe0 are the calculated dimensionless Peclet numbers<br> </p>
Movement of plastic balls in a long-vibrating cylinder: from disorder to structure formation with examples of its instability
<p>Many plastic balls, made from PolyOxyMethylene (POM) and of three different diameters 2, 3 and 4 mm, were used to observe the formation and stability of the structure in ball beds when, after pouring into a plexiglass cylinder, they were subjected to long-term vertical vibrations with frequency 100 Hz. The vibration table Vibrax (Renfert GmbH, Germany), used in the experiment and shown in Fig. 1, can function in two modes: sinusoidal (s) and nonsinusoidal (ns). The vibration table can act at four power levels of the vibrations, selected by an operator using the right knob of the table (see Fig. 1). In the presented series of 43 vibration experiments, always the highest power level was used. </p> <p>Locations of surface balls on all sides of a vibrated cylindrical bed were simultaneously recorded on one video frame thanks to the use of two perpendicular mirrors (see Fig. 1), which enables observation of four images: one of the real cylinder and three of its mirror reflections. An explanation of the scene, as seen by the recording camera, is given in the scheme in Fig. 2. Video names were given in a standard form to inform the user about the most important parameters (more in README.txt).</p> <p> </p>
Assemblies, synapse clustering and network topology interact with plasticity to explain structure-function relationships of the cortical connectome
<p>Dataset linked to the article with the same title</p> <p>The model itself is very similar to its non-plastic counterpart under the following DOI: <a href="../record/7930275">10.5281/zenodo.7930275</a>, i.e. a 1.5 mm diameter cortical tissue comprising 211,712 neurons and their connectivity in the front limb and jaw subregions and the dysgranular zone of the Paxinos & Watson rat brain atlas. It's formatted in the open <a href="https://github.com/AllenInstitute/sonata">SONATA</a> standard and contains neuron locations and their properties (such as morphological types, cortical layer, etc.), their detailed morphologies, and synaptic connectivity (with all their anatomical and physiological parameters). The main difference from the non-plastic version is the addition of plasticity related parameters to <em>O1/S1nonbarrel_neurons__S1nonbarrel_neurons__chemical/edges.h5. </em>Extrinsic synaptic connections from the thalamus are included in this release, but for inputs from neurons in the remainder of non-barrel somatosensory cortex please see the non-plastic version of the circuit.</p> <p><strong>Analyzing the model</strong></p> <p>The model can be analyzed in terms of its anatomy, physiology and connectivity using the packages <a href="https://neurom.readthedocs.io/en/stable/">NeuroM</a>, <a href="https://bluebrainsnap.readthedocs.io/en/stable/">BlueBrain SNAP</a> and <a href="https://github.com/BlueBrain/ConnectomeUtilities">ConnectomeUtilities</a>. (see first Jupyter notebook)</p> <p><strong>Simulating the model</strong></p> <p>To simulate the model we'd recommend using out using our open-source simulator <a href="https://github.com/BlueBrain/neurodamus">Neurodamus</a>. The reference version is the branch <em>nbS1-2023</em>, which is archived under the following DOI: <a href="http://doi.org/10.5281/zenodo.8075202">10.5281/zenodo.8075202</a>. Instructions on how to use the simulator are provided on the GitHub page linked above. Briefly, you'll first have to <a href="https://github.com/BlueBrain/neurodamus#install-neurodamus">install Neurodamus</a>. Next, build a <em>"special"</em> executable that include compiled versions of ion channel and synapse models. To do that, follow <a href="https://github.com/BlueBrain/neurodamus#build-special-with-mod-files">these instructions</a>, where <em>mod-files-from-released-circuit </em>is replaced by the location of <em>O1/mods</em> on your system. Finally, <a href="https://github.com/BlueBrain/neurodamus#examples">run a simulation</a>. The specific simulation conditions and stimuli are specified in simulation configuration files. An exemplary simulation configuration is included in this release (<em>simulation_config.zip</em>).</p> <p><strong>Analyzing simulation results</strong></p> <p>Simulation results can be analyzed with <a href="https://bluebrainsnap.readthedocs.io/en/stable/">BlueBrain SNAP</a>, <a href="https://github.com/BlueBrain/ConnectomeUtilities">ConnectomeUtilities</a>, and <a href="https://github.com/BlueBrain/assemblyfire">assemblyfire</a>. Notebooks 2-5 go though these analysis and recreate some of the panels from our article. In most cases the notebooks can be run with the shared HDF5 files and don't require running any simulations.</p> <p><strong>Version 2</strong></p> <p>Bug fix in simulation_config.json and therefore new version of results (and corresponding notebooks). The underlying circuit model (O1.xz) did not change from v1.</p> <p>--</p> <p><em>The development of this dataset was supported by funding to the Blue Brain Project, a research center of the École polytechnique fédérale de Lausanne (EPFL), from the Swiss government’s ETH Board of the Swiss Federal Institutes of Technology.</em></p>
Diffusion coefficients on amorphous polystyrene and modelling of migration levels from plastic packaging
<p>This dataset is actually supplementary data of the scientific article:</p> <p>Martinez-Lopez, Brais; Gontard, Natalie and Peyron, Stephane "Worst case prediction of additives migration from polystyrene for food safety purposes: a model update" in Food Additives and Contaminants Part A, doi:10.1080/19440049.2017.1402129.</p> <p>If you use it, please cite it using the reference file we have provided.</p> <p>This description is the same as in the file "readme.txt", included in the upload.</p> <p>List of files:</p> <ul> <li>The file database_D contains the experimental diffusivity data for amorphous polystyrene used for the figure 1b. It is a spreadsheet file with two tabs. In the first tab, the diffusion coefficients can be found by choosing molecule family (and the publication were they were found) and temperature in celsius degrees. The second tab contains the same diffusivity data, but they are ranged by increasing molecular weight and temperature. This file is available in open document (.ods) and microsoft excel (.xlsx) formats.</li> <li>The file migration modelling is also a spreadsheet file, and contains several tabs. The first tab (diffusion coefficient) is an implementation of equation 1, the predictive model for overestimated diffusion coefficients. The given Ap and tau parameter sets are the ones specified in Table 2 for amorphous polystyrene. The second tab (migration levels) is an implementation of equation 3, the solution to Fick's second law that is used to predict migration levels in food, for pre-selected values of alpha (equation 5). The tabs labeled alpha =... contain the sums used in the equation, whereas the tab "roots" contains the first 200 roots of trascendental equation 4, needed to calculate the sum or terms. This file is also available in open document (.ods) and microsoft excel (.xlsx) formats.</li> <li>The file "table.pdf" sums the main characteristics of the molecule families, together with the references where they were found (in the second page).</li> <li>The file reference.bib contains the reference that should be cited if you use this dataset for your own work.</li> <li>Finally, the file readme.txt contains this very same description.</li> </ul> <p>These files have undergone thorough check, so there should not be any mistakes. In the rare event that you find one, please report it to the author so it can get fixed.</p> <p>bramar@food.dtu.dk</p> <p>Brais Martínez López, PhD<br> Assistant professor<br> DTU Fødevareinstituttet<br> Danmarks Tekniske Universitet<br> Søltofts Plads<br> Bygning 227<br> 2800 Kgs. Lyngby</p> <p> </p> <p> </p> <p> </p>
Supplementary data and scripts for Willemsen et al., 2019 "Genome plasticity in Papillomaviruses and de novo emergence of E5 oncogenes"
<p>Supplementary data for Willemsen et al., 2019 "Genome plasticity in Papillomaviruses and <em>de novo</em> emergence of E5 oncogenes". The data set consists of three folders: “Alignments”, “Bali-Phy” and “RandomPermutationTests”. The “Alignments” folder contains the different alignments used for phylogenetic tree construction and comparison. The “Bali-Phy” folder contains the final results and convergence diagnostics of the Common Ancestry tests obtained by using the Bali-Phy software. The “RandomPermutationTests” folder contains all the data and scripts to repeat the random permutation tests described in the manuscript. Please see the corresponding README files for more information.</p>
The terrestrial carnivorous plant Utricularia reniformis sheds light on environmental and life-form genome plasticity: Annotation, Gene Ontology and raw data
<p><strong>Description:</strong> In this work, we deeply sequenced (genome and transcriptome of different organs), assembled, and analyzed the 311-Mbp genome of the terrestrial carnivorous plant <em>U. reniformis</em> (Lentibulariaceae). This project presents great importance to the understanding of genomic, evolutive and functional aspects of<em> U. reniformis</em>, which may, with the next-generation sequencing and computational biology approaches shed light to a better understanding not only for the biology and evolution of <em>Utricularia</em> genus, but also for other genera and lineages of the Lentibulariaceae family. Here we present all the raw data generated, including annotation and gene ontology files.</p> <p><strong>External Information</strong></p> <p><a href="https://genomevolution.org/coge/GenomeInfo.pl?gid=54799">Genome Browser</a> avaliable at CoGe Portal (https://genomevolution.org/coge/GenomeInfo.pl?gid=54799)</p> <p><a href="http://https://www.ncbi.nlm.nih.gov/bioproject/290588">GenBank </a><a href="http://https://www.ncbi.nlm.nih.gov/bioproject/290588">Bioproject</a> (https://www.ncbi.nlm.nih.gov/bioproject/290588) for raw genomic and transcriptomic reads</p> <p><a href="https://bv.fapesp.br/en/auxilios/84264/genomics-and-transcriptomics-of-utricularia-reniformis-lentibulariaceae-an-evolutive-and-function/">FAPESP grant website</a> contaning the project abstract and other information.</p> <p><strong>Papers published related to <em>Utricularia reniformis</em> genome</strong></p> <pre><strong>[1]</strong> Silva SR, Diaz YC, Penha HA, Pinheiro DG, Fernandes CC, Miranda VF, MichaelTP, Varani AM. <strong>The Chloroplast Genome of Utricularia reniformis Sheds Light on the Evolution of the ndh Gene Complex of Terrestrial Carnivorous Plants from the Lentibulariaceae Family</strong>. PLoS One. 2016 Oct 20;11(10):e0165176. doi:<strong><a href="https://www.ncbi.nlm.nih.gov/pubmed/27764252">10.1371/journal.pone.0165176</a></strong>. </pre> <pre><strong>[2] </strong>Silva SR, Alvarenga DO, Aranguren Y, Penha HA, Fernandes CC, Pinheiro DG, Oliveira MT, Michael TP, Miranda VFO, Varani AM. <strong>The mitochondrial genome of the terrestrial carnivorous plant Utricularia reniformis (Lentibulariaceae): Structure, comparative analysis and evolutionary landmarks.</strong> PLoS One. 2017 Jul19;12(7):e0180484. doi: <strong><a href="https://www.ncbi.nlm.nih.gov/pubmed/28723946">10.1371/journal.pone.0180484</a></strong>.</pre> <pre><strong>[3] </strong>Silva SR, Moraes AP, Penha HA, Julião MHM, Domingues DS, Michael TP, Miranda VFO, Varani AM. <strong>The Terrestrial Carnivorous Plant Utricularia reniformis Sheds Light on Environmental and Life-Form Genome Plasticity.</strong> Int J Mol Sci. 2019 Dec 18;21(1). pii: E3. doi: <strong><a href="https://www.ncbi.nlm.nih.gov/pubmed/31861318">10.3390/ijms21010003</a></strong>.</pre> <p><strong>Acknowledgements</strong></p> <p>This work was supported by Sao Paulo Research Foundation FAPESP, Grant ID: [1325164-6]</p> <p> </p> <p><strong>---------------------------------------------------------</strong><br> <strong>FILES DESCRIPTION</strong><br> <strong>---------------------------------------------------------</strong><br> <br> ----------------<br> <strong>ANNOT-vFinal.sql: </strong>MySQL database containing all integrated annotation information of Urenif and Ugibba<br> ----------------<br> <strong>TABLE fields description</strong><br> gene_name gene name generated by EVidence Modeler + PASA<br> length gene lenght<br> status duplicate_gene_classifier status (0:singleton, 1:dispersed, 2:proximal, 3: tandem, 4:WGD)<br> product gene product <br> GOterms Blast2GO/OmicsBox GOterms<br> GO_mapping Blast2GO/OmicsBox GOterms derived from direct mapping (UniProt)<br> GO_annotation Blast2GO/OmicsBox annotated GOterms<br> GO_interpro Blast2GO/OmicsBox derived from InterProScan<br> EC Blast2GO/OmicsBox EC number<br> EC_name Blast2GO/OmicsBox enzyme name<br> NOG_annot EggNOG annotation description<br> NOG_EC EggNOG EC number<br> NOG_GO EggNOG GOterms<br> NOG_class EggNOG COG/KOG classfication<br> KEGG_Pathway EggNOG KEGG pathyways<br> KEGG_ko EggNOG KEGG ko<br> CAZy EggNOG CAZy enzymes<br> TAIR_gene Closest A. thaliana gene name (homologous) TAIR database lasted version<br> TAIR_annot Closest A. thaliana gene product (homologous) TAIR database lasted version <br> ortho MCL clustering among Vvinifera, Athaliana, and Slycopersicum (S:singleton, C: clustered, Y: shared)<br> ortho_two MCL clustering among Urenif and Ugibba (S:singleton, C: clustered, Y: shared)<br> -<br> -<br> ----------------<br> <strong>CEGs.zip </strong> 336 shared and concatenated CEGs from Urenif, U. gibba, Genlisea nigrocaulis, G. hispidula, G. aurea, G. pygmaea, and G. repens.<br> ----------------</p> <p><strong>ProcessRepeats_mod</strong> Modified version of RepeatMasker, ProcessRepeats script for detection of plant evolutionary lineages<br> ----------------</p> <p><strong>----------------------------------------------------------------------------------------------------------------------------------------------<br> <em>Utricularia gibba</em> files<br> ----------------------------------------------------------------------------------------------------------------------------------------------</strong><br> <strong>Ugibba</strong><strong>-no-masked.fa </strong> Ugibba genome excluding organellar genomes (provided by Lan et al., 2017)<br> <strong>Ugibba-softmasked.fa</strong> Ugibba genome RepeatMasker softmasked and excluding organellar genomes (provided by Lan et al., 2017)<br> <strong>Ug.collinearity </strong> MCScanX collinearity file<br> <strong>Ug-duplicates.txt</strong> MCScanX duplicate_gene_classifier short report<br> <strong>Ug.gene_type </strong> MCScanX duplicate_gene_classifier full report<br> <strong>Ug.tandem </strong> Ugibba tandem genes generated by MCScanX tool<br> <strong>Ugibba_annot.annot </strong> Blast2GO/OmicsBox annotation file (eudicotyledons filtered and Viridiplantae GOSlim) <strong>Ugibba_annot-</strong><strong>noclean</strong><strong>.</strong><strong>annot</strong><strong> </strong> Blast2GO/OmicsBox annotation file (not filtered)<br> <strong>Ugibba</strong><strong>.cDNA</strong> Ugibba cDNAs fasta file<br> <strong>Ugibba</strong><strong>.CDS </strong> Ugibba CDSs fasta file<br> <strong>Ugibba</strong><strong>-EVM.all-no-TEs-PASA-ANNOTATED.gff3</strong> Ugibba GFF3 file fully annotated (including gene products and GO terms)</p> <p><strong>Ugibba</strong><strong>-EVM.all-no-TEs-PASA.gff3</strong> Ugibba GFF3 file fully annotated (genes only)<br> <strong>Ugibba_export.txt</strong> Blast2GO/OmicsBox full exported table<br> <strong>Ugibba_fasta.fasta</strong> Blast2GO/OmicsBox Ugibba fasta proteins containg annotation (product and GO terms)<br> <strong>ugibba_frozen_cleaned-validated.box</strong> Full Blast2GO/OmicsBox file</p> <p><strong>ugibba_frozen.box</strong> Full Blast2GO/OmicsBox file (containing TEs genes annotation)</p> <p><strong>ugibba_nogs_emapper_annotations.box</strong> Full Blast2GO/OmicsBox EggNOG file (containing TEs genes annotation)</p> <p><strong>Ugibba_GAF.txt</strong> GAF file<br> <strong>Ugibba</strong><strong>.gene</strong> Ugibba gene fasta file<br> <strong>Ugibba_GOstat.txt </strong> GOstat file<br> <strong>Ugibba</strong><strong>-PASA-assemblies.fasta </strong> Ugibba PASA assemblies<br> <strong>Ugibba</strong><strong>-PASA.stats </strong> Ugibba annotation STATS<br> <strong>Ugibba</strong><strong>.</strong><strong>prot</strong><strong> </strong> Ugibba protein fasta file<br> <strong>Ugibba</strong><strong>-RepeatMasker.gff </strong> Ugibba RepeatMasker gff file<br> <strong>Ugibba</strong><strong>-RepeatMasker.gff3 </strong> Ugibba RepeatMasker gff3 file<br> <strong>Ugibba</strong><strong>-RepeatMasker.tbl </strong> Ugibba RepeatMasker results<br> <strong>Ugibba</strong><strong>-RepeatMasker-v2.gff3</strong> Ugibba RepeatMasker gff3 second version file<br> <strong>Ugibba</strong><strong>-RNAseq-assembled.fasta </strong> Ugibba RNAseq assembled transcriptome (Trinity)<br> <strong>Ugibba_TEs_DANTE_2019.fa </strong> Ugibba TEs library, detected by REPET and annotated by PASTEC and DANTE<br> <strong>Ugibba_WEGO.txt </strong> WEGO file</p> <p><strong>----------------------------------------------------------------------------------------------------------------------------------------------<br> <em>Utricularia reniformis</em> files<br> ----------------------------------------------------------------------------------------------------------------------------------------------</strong><br> <strong>Urenif</strong><strong>-no-masked.fa </strong> Urenif genome excluding organellar genomes<br> <strong>Urenif</strong><strong>-</strong><strong>softmasked</strong><strong>.fa</strong> Urenif genome RepeatMasker softmasked and excluding organellar genomes<br> <strong>Ur.collinearity </strong> MCScanX collinearity file<br> <strong>Ur-duplicates.txt </strong> MCScanX duplicate_gene_classifier short report<br> <strong>Ur.gene_type</strong> MCScanX duplicate_gene_classifier full report<br> <strong>Ur.tandem</strong> Urenif tandem genes generated by MCScanX tool<br> <strong>Urenif_annot.annot</strong> Blast2GO/OmicsBox annotation file (eudicotyledons filtered and Viridiplantae GOSlim)<br> <strong>Urenif_annot-</strong><strong>noclean</strong><strong>.</strong><strong>annot</strong> Blast2GO/OmicsBox annotation file (not filtered)<br> <strong>Urenif</strong><strong>.cDNA</strong> Urenif cDNAs fasta file<br> <strong>Urenif</strong><strong>.CDS </strong> Urenif cDNAs fasta file<br> <strong>Urenif</strong><strong>-EVM.all-no-TEs-PASA-ANNOTATED.gff3</strong> Urenif GFF3 file fully annotated (including gene products and GO terms)</p> <p><strong>Urenif</strong><strong>-EVM.all-no-TEs-PASA.gff3</strong> Urenif GFF3 file fully annotated (genes only)<br> <strong>Urenif_export.txt</strong> Blast2GO/OmicsBox full exported table<br> <strong>Urenif_fasta.fasta</strong> Blast2GO/OmicsBox Urenif fasta proteins containg annotation (product and GO terms)<br> <strong>urenif_frozen_cleaned-validated.box</strong> Full Blast2GO/OmicsBox file</p> <p><strong>urenif_frozen.box</strong> Full Blast2GO/OmicsBox file (containing TEs genes annotation)</p> <p><strong>urenif_nogs_emapper_annotations.box</strong> Full Blast2GO/OmicsBox EggNOG file (containing TEs genes annotation)<br> <strong>Urenif_GAF.txt </strong> GAF file<br> <strong>Urenif</strong><strong>.gene</strong> Urenif gene fasta file<br> <strong>Urenif_GOStat.txt </strong> GOstat file<br> <strong>Urenif</strong><strong>-PASA-assemblies.fasta</strong> Urenif PASA assemblies<br> <strong>Urenif</strong><strong>-PASA.stats </strong> Urenif annotation STATS<br> <strong>Urenif</strong><strong>.</strong><strong>prot</strong><strong> </strong> Urenif protein fasta file<br> <strong>Urenif</strong><strong>-RepeatMasker.gff </strong> Urenif RepeatMasker gff file<br> <strong>Urenif</strong><strong>-RepeatMasker.gff3 </strong> Urenif RepeatMasker gff3 file<br> <strong>Urenif</strong><strong>-RepeatMasker.tbl </strong> Urenif RepeatMasker results<br> <strong>Urenif</strong><strong>-RepeatMasker-v2.gff3 </strong> Urenif RepeatMasker gff3 second version file<br> <strong>Urenif</strong><strong>-RNAseq-assembled.fasta </strong> Urenif RNAseq assembled transcriptome (Trinity)<br> <strong>Urenif_TEs_DANTE_2019.fa </strong> Urenif TEs library, detected by REPET and annotated by PASTEC and DANTE<br> <strong>Urenif_WEGO.txt </strong> WEGO file<br> <strong>----------------------------------------------------------------------------------------------------------------------------------------------<br> ----------------------------------------------------------------------------------------------------------------------------------------------</strong></p>
Stress-Strain Analysis of Polycrystalline Copper with Goss Texture Using Crystal Plasticity FEM
<pre>Stress-strain analysis of single-phase polycrystalline copper with a Goss texture using a cubic representative volume element (RVE) and periodic boundary conditions, performed with Abaqus through the crystal plasticity finite element method.</pre>
Plasmid Maps for a Nuclear Transformation Vector in Chlamydomonas reinhardtii for the Expression and Secretion of the Plastic-Degrading Enzyme (PHL7)
<p><strong>pJP32PHL7 Vector:</strong></p> <ul> <li> <p><strong>Size:</strong> 5692 bp</p> </li> <li> <p><strong>Key Features:</strong></p> <ul> <li><strong>HSP70 Promoter:</strong> A heat shock protein promoter fused with the <em>rbcS2</em> promoter to drive expression of downstream genes.</li> <li><strong>Ble Resistance Gene:</strong> Confers resistance to bleomycin, useful for selection in <em>Chlamydomonas reinhardtii</em>.</li> <li><strong>PHL7 Gene:</strong> Encodes the plastic-degrading enzyme PHL7, inserted downstream of the <em>F2A</em> site for expression in the host.</li> <li><strong>Intron Sequences:</strong> Contains multiple <em>rbcS2</em> introns for enhancing expression in <em>Chlamydomonas</em>.</li> <li><strong>Selectable Marker (AmpR):</strong> Confers ampicillin resistance for selection in <em>E. coli</em>.</li> <li><strong>Replication Origin:</strong> Includes <em>ori</em> and <em>F1 ori</em> for replication in <em>E. coli</em>.</li> </ul> <p> </p> </li> <li> <p><strong>Applications:</strong> This vector is designed for nuclear transformation in <em>Chlamydomonas reinhardtii</em>, enabling the expression and secretion of the plastic-degrading enzyme (PHL7) under the control of a hybrid <em>HSP70</em>rbcS2 promoter.</p> </li> </ul> <p><strong>pJP32PHL7dg Vector:</strong></p> <ul> <li> <p><strong>Size:</strong> 5692 bp</p> </li> <li> <p><strong>Key Features:</strong></p> <ul> <li><strong>HSP70 Promoter:</strong> Retains the HSP70 and <em>rbcS2</em> fusion promoter for gene expression.</li> <li><strong>LacZ Alpha Fragment:</strong> Includes a LacZ alpha fragment for blue/white screening.</li> <li><strong>PHL7 Gene:</strong> Encodes the plastic-degrading enzyme PHL7, linked downstream of the <em>F2A</em> site, allowing for expression in the host.</li> <li><strong>Ble Resistance Gene:</strong> Also confers bleomycin resistance for selection in <em>Chlamydomonas</em>.</li> <li><strong>Selectable Marker (AmpR):</strong> Confers ampicillin resistance for selection in <em>E. coli</em>.</li> <li><strong>Intron Sequences:</strong> Contains <em>rbcS2</em> introns for optimizing gene expression in the host organism.</li> </ul> <p> </p> </li> <li> <p><strong>Applications:</strong> The pJP32PHL7dg vector is similarly designed for nuclear transformation in <em>Chlamydomonas reinhardtii.</em> It also facilitates the expression and secretion of the plastic-degrading enzyme PHL7, driven by the hybrid <em>HSP70</em>rbcS2 promoter, but without glycosilation sites.</p> </li> </ul>
Morphological and physical chemical characterization of main agricultural plastics articles used for protected cultivation systems during ageing in fields, and collection practices
<p>This dataset includes data generated upon the implementation of the ST 1.2.1 "Analysis of degradation and fragmentation of AP and transfer of MNP to soil". The activities dealt with the study of degradation and fragmentation from weathering and agricultural practices of conventional and biodegradable AP relevant for transfer of MNP to soil (during both use and end of life). In particular, the experimental data refer to characterization of biodegradable mulch films, pristine (coded M-BIO0) or subjected to photo-oxidative weathering (M-BIO192), as well as the same samples buried in soil for varying time periods, up to 353 days. The folders included contain gel permeation chromatography (GPC) and Matrix-assisted Laser Desorption Ionization (MALDI-TOF) data, which account for the change in film molecular weight upon soil burial. Furthermore, Differential Scanning Calorimetry (DSC) data and Scanning Electron Microscopy (SEM) and Water Contact Angle (WCA) images of some selected samples are also provided. The folder named MS RAW FILES.zip includes all the mass spectrometry raw data.</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.