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ascii xyz files for all pure fullerene isomers from C20 to C80, and stable structures for C28Hn and C40Hn, n=1..5, geometrically optimised with xTB.
<p>ascii xyz files for all pure fullerene isomers from C20 to C80, and stable structures for C28Hn and C40Hn, n=1..5, geometrically optimised with xTB.</p> <p>Data refers to structures generated with the paper published in MDPI Crystals 2021 article "Methodological Investigation for Hydrogen Addition to Small Cage Carbon Fullerenes". Please cite this article if you use this data, many thanks. The article pre-print can be found here: https://www.preprints.org/manuscript/202109.0361/v1 but please cite the final published article.</p>
FASTA file containing the MYB encoding gene An2-like and Ant1 coding sequences corresponding to wild and cultivated tomato accessions
<p>The coding sequence (CDS) of the MYB encoding genes <em>Ant1</em> and <em>An2-like</em>. Sequences were retrieved from regions corresponding to the<em> Aft</em> locus from <em>Solanum galapagense </em>accession LA1141, <em>S. lycopersicum</em> variety OH8245, and 84 tomato accessions published as part of The 100 Tomato Genome Sequencing Consortium (The 100 Tomato Genome Sequencing Consortium et al., 2014). Sequences were compared to available CDS available from the Sol genomics network (SGN) and the National Center for Biotechnology Information. The CDS was retrieved from <em>S. lycopersicum</em> variety Indigo Rose [MN433087 (Yan et al., 2020)], <em>S. lycopersicum</em> accession LA1996 [MN242011.1, EF433417.1( Sapir et al., 2008; Colanero et al., 2020)], and <em>S. chilense </em>accession LA1930 [MN242012.1 (Colanero et al., 2020)], The orthologous CDS corresponding to the <em>Aft </em>MYB encoding genes from <em>Solanum tuberosum</em> L. Group Phureja clone DM1-3 genome (PGSC DM v4.03 Pseudomolecules) was retrieved from the Potato Genome Sequence Consortium (PGSC: Potato Genome Sequencing Consortium et al., 2011), and the Capsicum annum cv. CM334 genome was retrieved from <em>Capsicum annuum </em>cv CM334 genome chromosome release 1.55 (Hulse-Kemp et al. 2018). These CDS were obtained using the Basic Local Alignment Search Tool (BLAST) tool available from the Sol Genomics Network (SGN) (available at https://solgenomics.net/tools/blast/). Comparison of syntenic chromosomal regions using known positions of tomato, potato, and pepper markers with comparative map viewer from SGN: (available at https://solgenomics.net/cview) on chromosome 10, was used as a quality check for S.<em> tuberosom</em> and <em>C. annuum.</em> Orthologous CDS corresponding to <em>Salvia miltiorrhiza, Arabidopsis thaliana</em>, [NM_105308.2, NM_105310.4 (Teng et al., 2005, Cominelli et al., 2008; Beradini et al., 2015)] were chosen based on tomato <em>Aft</em> sequence homology and gene annotations of positive R2R3 MYB regulation of anthocyanin. The CDS corresponding to the <em>Aft</em> genes were retrieved from the CDS reference genomes available from the Sol Genomics Network SGN: Tomato Genome CDS (ITAG release 4.0), Potato PGSC DM v3.4 CDS sequences, <em>Capsicum annuum </em>cv CM334 Genome CDS (release 1.55), or from the National Center for Biotechnology Information (NCBI: https://www.ncbi.nlm.nih.gov) reference sequences (RefSeq) section of the Genbank records. When accessed from Genank records, the CDS sequence was extracted from the “features” section and exported as a FASTA file.</p>
Orthophotos, DSMs and interpretation files of the remote sensing assessment of archaeological damage and destruction at Nineveh, Iraq, during the ISIS occupation
<p>Archaeological heritage has long been threatened by damage or destruction during armed conflicts. Recently, however, deliberate destruction has increasingly become a major part of daily threats in some areas. In that context these datasets describe the results of a programme of remote sensing of damage at Nineveh, within a wider research initiative involving six years of monitoring in northern Iraq. Analysis of satellite imagery, low-and level airphotography observation were combined in a comprehensive assessment of the damage. These datasets present an updated topographic map of Nineveh and its city walls, with a summary of the damage encountered.</p>
Actinidia chinensis Red5 genome assembly (version 2) and annotation files
<p>We present version 2 of the genome assembly for <em>Actinidia chinensis</em> var. <em>chinensis</em> genotype Red5. The Red5 genome was originally assembled using short read Illumina data (Pilkington et al, 2018; <a href="https://doi.org/10.1186/s12864-018-4656-3">https://doi.org/10.1186/s12864-018-4656-3</a>). In version 2 we employed Pacific BioSciences Sequel Single Molecule Real Time (SMRT) sequencing technology in place of Illumina paired end read sequencing for the main assembly but leveraged that short read data (Pilkington et al, 2018) for post assembly base correction of long read assembly contigs. Additionally the Illumina long insert libraries from Pilkington et al (2018) were used for post assembly scaffolding of contigs. Scaffold assignment to linkage groups leveraged the genetic map described in Pilkington et al (2018) as well as consensus evidence from DNA synteny comparisons to existing whole genome sequences from <em>Actinidia</em>.</p> <p>To meet the file size restrictions some dataset components have been split into multiple parts.</p> <p><strong>Assembly</strong></p> <p>The assembly work flow used the FALCON/FALCON-unzip assembly suite is described in Red5_version_2_genome_assembly.md. The assembly yielded both primary and haplotig contig data sets, the metrics for which are documented in this file. The CDS and predicted peptide fasta and GFF3 gene annotation for the primary and haplotig sets are provided in separate files.</p> <p><strong>File Descriptions</strong></p> <ul> <li>Files named chr1.fasta to chr29.fasta represent the primary assembly linkage group level assembly units</li> <li>Files named haplotig_part_1.fasta to haplotig_part_10.fasta represent the haplotig contig sets split into 10 parts to meet upload file size restrictions</li> <li>Files named primary_assembly.primary.gff3 and haplotig.gff3 contain the gene model annotations for the primary and haplotig assembly datasets respectively</li> <li>primary_assembly.cds.fasta and primary_assembly.pep.fasta contain the CDS and peptide sequences for the annotations on the primary contigs</li> <li>haplotig.cds.fasta and haplotig.pep.fasta contain the CDS and peptide sequences for the annotations on the haplotig contigs</li> <li>haplotigs.placements.tsv and haplotigs.reassignments.tsv describe the placement of haplotigs relative to the primary contigs as derived from purge_haplotigs</li> <li>The file Red5_version_2_genome_assembly.md describes the assembly work flow and code steps used as well as assembly metrics</li> <li>Files HYV3_1.v.R5V2_1.png to HYV3_29.v.R5V2_29.png depict Circos plots of DNA:DNA synteny based on 1coords alignment filter of nucmer alignments using dnadiff</li> </ul> <p>See Red5_version_2_genome_assembly.md for description of assembly methods and assembly metrics.</p> <p><strong>Funding</strong></p> <p>This work was funded by Kiwifruit Royalty Investment Program by The New Zealand Institute for Plant & Food Research Ltd. with support from Zespri, and the CORE grant Endeavour Smart Idea Fund (UOOX1801) from the New Zealand Ministry of Business, Innovation and Employment (MBIE). The funding bodies had no role in the design of the study, the collection, analysis, or interpretation of data or writing this manuscript.</p>
Pre-parsed reaction rule files from RetroRules (rr02-rp2-hs)
<p>RetroRules (https://retrorules.org/) is a database of reaction rules for metabolic pathway discovery and metabolic engineering. Reaction rules are generic descriptions of reactions to be used in retrosynthesis workflows in order to enumerate possible biosynthetic routes connecting target molecules to precursors. The use of such rules is becoming more and more important in the context of synthetic biology applied to de novo pathway discovery and in systems biology to discover underground metabolism due to enzyme promiscuity.</p> <p>Pre-parsed reaction rule files are ready-to-use files that provide all the non-stereo reaction rules for diameter 2 to 16. The present dataset have the following specifications:</p> <ul> <li>release: rr02</li> <li>diameters: 2 to 16</li> <li>Hs handling: explicit</li> <li>Compatibility: RetroPath2.0 ready</li> </ul> <p>How to cite: Duigou T, du Lac M, Carbonell P, Faulon JL. RetroRules: a database of reaction rules for engineering biology. <em>Nucleic Acids Research</em>, 2019. | doi: <a href="https://doi.org/10.1093/nar/gky940">10.1093/nar/gky940</a> | PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/30321422">30321422</a></p> <p> </p>
Pre-parsed reaction rule files from RetroRules (rr01-rp2-hs)
<p>RetroRules (https://retrorules.org/) is a database of reaction rules for metabolic pathway discovery and metabolic engineering. Reaction rules are generic descriptions of reactions to be used in retrosynthesis workflows in order to enumerate possible biosynthetic routes connecting target molecules to precursors. The use of such rules is becoming more and more important in the context of synthetic biology applied to de novo pathway discovery and in systems biology to discover underground metabolism due to enzyme promiscuity.</p> <p>Pre-parsed reaction rule files are ready-to-use files that provide all the non-stereo reaction rules for diameter 2 to 16. The present dataset have the following specifications:</p> <ul> <li>release: rr01</li> <li>diameters: 2 to 16</li> <li>Hs handling: explicit</li> <li>Compatibility: RetroPath2.0 ready</li> </ul> <p>How to cite: Duigou T, du Lac M, Carbonell P, Faulon JL. RetroRules: a database of reaction rules for engineering biology. <em>Nucleic Acids Research</em>, 2019. | doi: <a href="https://doi.org/10.1093/nar/gky940">10.1093/nar/gky940</a> | PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/30321422">30321422</a></p> <p> </p>
Pre-parsed reaction rule files from RetroRules (rr02-rp3-nohs)
<p>RetroRules (https://retrorules.org) is a database of reaction rules for metabolic pathway discovery and metabolic engineering. Reaction rules are generic descriptions of reactions to be used in retrosynthesis workflows in order to enumerate possible biosynthetic routes connecting target molecules to precursors. The use of such rules is becoming more and more important in the context of synthetic biology applied to de novo pathway discovery and in systems biology to discover underground metabolism due to enzyme promiscuity.</p> <p>Pre-parsed reaction rule files are ready-to-use files that provide all the non-stereo reaction rules for diameter 2 to 16. The present dataset have the following specifications:</p> <ul> <li>release: rr02</li> <li>diameters: 2 to 16</li> <li>Hs handling: implicit</li> <li>Compatibility: RetroPath RL ready</li> </ul> <p>How to cite: Duigou T, du Lac M, Carbonell P, Faulon JL. RetroRules: a database of reaction rules for engineering biology. <em>Nucleic Acids Research</em>, 2019. | doi: <a href="https://doi.org/10.1093/nar/gky940">10.1093/nar/gky940</a> | PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/30321422">30321422</a></p> <p> </p>
3D-Scere static files and result table
<p>Static files, result table and graphical representations associated with the 3D-Scere project (dashboard and publication).</p> <p> </p> <p>3D_distances.parquet.gzip: three-column parquet file with 3D distances between <em>Saccharomyces cerevisiae </em>chromosomal features.</p> <p>SCERE.db: SQLite database of <em>Saccharomyces cerevisiae </em>features build from the <a href="https://www.yeastgenome.org/">SGD</a>.</p> <p>Table1.tsv: tab-separated values file with Kolmogorov Smirnov test results for <em>Saccharomyces cerevisiae </em>transcription factors.</p> <p>supplementary-data-file-S4.zip: ZIP file with graphical representations associated to each transcriptional module.</p>
Alkali-silica reaction. A multi-disciplinary approach. Supplementary Materials: Movie file.
<p>Movie file being part of the Supplementary Materials document of the manuscript with the same title and submitted to the <a href="https://letters.rilem.net/index.php/rilem">RILEM Technical Letters</a>.</p>
Visual-Evoked Potential (VEP) Event-Related Files from the General Anesthesia and Brain Activity (GABA) Study and Infant Sibling Project (ISP)
<p>HAPPE+ER software was optimized for developmental data using a subset of EEG files from 4-month and 10-month old infants in the General Anesthesia and Brain Activity (GABA) Study. While medically necessary, 1-2 million infants each year undergo general anesthesia – a process that sedates brain activity and impacts early sensory experiences during a time typically characterized by rapid neurocognitive development. The GABA study examines sensory and socioemotional neurodevelopment longitudinally from infancy through childhood in individuals who have and who have never undergone general anesthesia during different windows in the first year of life. The GABA study was carried out in accordance with the recommendations of the Institutional Review Board at Boston Children’s Hospital. All caregivers provided assent for their child’s participation in the GABA study and for the release of the deidentified data. </p> <p>To facilitate the use and understanding of HAPPE+ER software, we have provided a subset of the validation files from the GABA study to serve as a tutorial dataset for how to run event-related potential (ERP) data through this automated processing pipeline. Five files (a.raw - e.raw) are from four 4-month and one 10-month old infants during a pattern reversal visual-evoked potential (VEP) paradigm. Pattern reversal occurred every 500 milliseconds. The pattern stimulus onset is indicated in each file by the code: vep+. Data was collected using a 128-channel EGI HydroCel Geodesic Sensor Net and EGI Net Amps 400, sampled at 1000Hz with an online reference to channel CZ. </p> <p>We have also included a subset of files from the Infant Sibling Project (ISP), an investigation examining infants at high versus low familial risk for autism spectrum disorder over the first 3 years of life. Baseline EEG data was collected while a young child sat in a parent’s lap watching a research assistant blow bubbles or show toys for several minutes. The Infant Sibling Project was carried out in accordance with the recommendations of the Institutional Review Board at Boston University and Boston Children’s Hospital (#X06-08-0374), with written informed consent from all caregivers prior to their child’s participation in the study. All files here have been deidentified, including alteration of exact acquisition dates. Acquisition times have not been altered. For additional information about data collection paradigms, and sample studies published on the larger ISP data set, please see the following references:</p> <ol> <li>Levin, A. R., Varcin, K. J., O’Leary, H. M., Tager-Flusberg, H., and Nelson, C. A. (2017). EEG power at 3 months in infants at high familial risk for autism. J. Neurodev. Disord. 9, 1–13.</li> <li>Gabard-Durnam, L.J., Wilkinson, C., Kapur, K. et al. Longitudinal EEG power in the first postnatal year differentiates autism outcomes. Nat Commun 10, 4188 (2019). <a href="https://doi.org/10.1038/s41467-019-12202-9">https://doi.org/10.1038/s41467-019-12202-9</a></li> </ol> <p>Here we provide a subset of the full dataset with a simulated VEP signal added into the data, as example files for HAPPE+ER. To create these files, we selected a subset of 39 spatially-distributed channels in the baseline EEG files and created sixteen 30-second files using continuous segments of relatively artifact-free (clean) baseline data from the full-length files. Next, from 30-second sections of the same individuals’ EEG that were artifact-laden, we ran ICA and extracted artifact independent components (identified by an expert and labeled artifact by both ICLabel and MARA automated algorithms). We inserted the artifact ICs into that individual’s clean 30-second data segment to create an additional 16 artifact-added files. We then selected a channel from a simulated VEP dataset (included here as simulated_full.set) with a stereotyped and prominent simulated VEP waveform, in this case Oz, and added its timeseries (included here as simulated_singleChan.set) to each channel of the clean and artifact-added files to create two VEP datasets with a known ERP morphology (sim-artifact_a-p and sim-clean_a-p). For additional information about the creation of this simulated data and VEP data with a known ERP morphology, please refer to Monachino et al., in revision; DOI: https://doi.org/10.1101/2021.07.02.450946.</p> <p>Additional files included below are the HAPPE+ER data and pipeline quality metric output spreadsheets for the five GABA study data files for an example run, the output spreadsheet containing the ERP timeseries from the generateERPs script, the .mat file containing the parameter settings for HAPPE+ER for that run, an Excel file with the bad channels for each file, and a tutorial document illustrating the results of this example run. </p>
Avizo files for Oriensmilus liupanensis left skull base
<p>A new genus and species of sabretooth, Oriensmilus liupanensis (Barbourofelinae, Nimravidae, Carnivora), from the middle Miocene of China suggests barbourofelines are nimravids, not felids</p> <p>Since the early 2000s, a revival of a felid relationship for barbourofeline sabretooths has become popular due to recent discoveries of fragmentary fossils from Africa. According to this view, barbourofelines trace their common ancestor with felids through shared similarities in dental morphology going back to the early Miocene of Africa and Europe. However, whether or not such an idea is represented in the basicranial morphology, a conservative area of high importance in family-level relationships, is yet to be tested. A nearly complete skull of Oriensmilus liupanensis gen. and sp. nov. from the middle Miocene Tongxin Basin of northern China represents the most primitive known barbourofeline with an intact basicranial region, affording an opportunity to re-examine the relationship of felids and nimravines. We also present an update on East Asian records of barbourofelines. The new skull of Oriensmilus possesses a suite of characters shared with nimravines, such as the lack of an ossified (entotympanic) bullar floor, absence of an intrabullar septum, lack of a ventral promontorial process of the petrosal, presence of a small rostral entotympanic on the dorsal side of the caudal entotympanic, and a distinct caudal entry of the internal carotid artery and nerve that pierces the caudal entotympanic at the junction of the ossified and unossified caudal entotympanics. The absence of an ossified bullar floor in O. liupanensis and its presence in those from the middle Miocene of Sansan, France thus help to bracket the transition of this character, which must have happened in the early part of the middle Miocene. Spatial relationships between bullar construction and the middle ear configuration of the carotid artery in Oriensmilus strongly resemble those in nimravines but are distinctly different from felids and other basal feliforms. Despite the attractive notion that early barbourofelines arose from a Miocene ancestor that also gave rise to felids, the basicranial evidence argues against this view.</p>
Documentation and digital files in support of "Aftershock regions of Aleutian–Alaska megathrust earthquakes, 1938–2021" by Carl Tape and Anthony Lomax: Parts B, C, and D
<p>These files support a manuscript to be submitted entitled "Aftershock regions of Aleutian–Alaska megathrust earthquakes, 1938-2021," by Carl Tape and Anthony Lomax. This collection contains Parts B, C, and D. A separate collection contains Part A. This research was supported by the U.S. Geological Survey (USGS), Department of the Interior, under USGS award number G19AP00050.</p>
Habitat Protection Indexes - new monitoring measures for the conservation of threatened marine habitats - Datasets and supporting files
<p>The supporting datasets, scripts, and supplementary information for the manuscript, "Habitat Protection Indexes - new monitoring measures for the conservation of threatened marine habitats," are available within this repository.</p> <p>We conduct an analysis on the coverage of protected areas that cover six threatened marine and coastal and developed two indexes, the Local Proportion of Habitat Protected Index and the Global Proportion of Habitat Protected Index, describing the protection of these habitats locally and globally. The habitats considered are the following: cold corals, warm water corals, knolls and seamounts, mangroves, saltmarshes, and seagrasses.</p> <p>The index scores of each jurisdiction are made available for download in the dataset: <em>habitat_protection_indexes_average.csv</em></p> <p>The habitat specific index scores for each jurisdiction are made available for download in the dataset: <em>habitat_protection_indexes.csv. </em></p> <p>Column name descriptions are available in the text file: <em>Column_name_descriptions_20220301</em></p> <p>The scripts used to run the workflow to calculate the indexes, create figures, and calculate statistics for the manuscript are also included. The script <em>01_Workflow sources</em> the first 9 scripts in the <em>scripts</em> folder to calculate the indexes which relies on the functions script within the functions folder. The rest of the scripts in the folder create the figures and calculate the statistics for the manuscript.</p> <p>A readme pdf file is included here to ease with reproducing the workflow, but we strongly suggest to please visit our github (<a href="https://github.com/jkumagai96/Marine_Habitat_protection">https://github.com/jkumagai96/Marine_Habitat_protection</a>) to reproduce the entire calculation where we provide detailed information on how to run the workflow and package management.</p>
Data Analysis files for "Dissipative Quantum Feedback in Measurements Using a Parametrically Coupled Microcavity"
<p>Data Analysis for the paper "Dissipative Quantum Feedback in Measurements Using a Parametrically Coupled Microcavity", which is published in PRX Quantum <strong>3</strong>, 020309 (2022).</p>
Publication and Maintenance of Relational Data in Enterprise Knowledge Graphs Created (Files used in the experiments)
<p>This dataset contains two files created for the experiments presented in the article: Publication and Maintenance of RDB2RDF Views Externally Materialized in Enterprise Knowledge Graphs.</p> <p><strong>mapR2RML_MusicBrainz_completo.txt</strong><strong>:</strong> We created the R2RML mapping for translating MBD data into the Music Ontology vocabulary, which is used for publishing the LMB view. The LMB view was materialized using the D2RQ tool. It took 67 minutes to materialize the view with approximately 41.1 GB of NTriples. We also provided SPARQL endpoint for querying LMB View.</p> <p><strong>TriggersAndProcedures.txt</strong>: We created the triggers, procedures, and class in java to implement the rules required to compute and publish the changesets.</p> <p><strong>relationalViewDefinition.pdf</strong>: This document gives details about the process of creating the relational views used in the experiments.</p>
RINEX files from low-cost GNSS receivers in Wrocław, Poland; January - March, 2021
<p>Daily RINEX files with multi-GNSS (GPS, GLONASS, Galileo) observations at 30 sec. interval obtained with low-cost GNSS receiver u-blox ZED-F9P and u-blox patch antennas (except BX02 - ArduSimple survey antenna). Time period (depending on stations): 27.02.2021 - 28.03.2021.</p>
Data files for: Meteorological factors in the production of Gigantic Jets by tropical thunderstorms in Colombia
<p>Data includes:</p> <ul> <li>Gigantic jet locations and times</li> <li>Vertical profiles for GJ and null cases</li> <li>CSV files with meteorological variables per GJ event and null case</li> </ul>
Perspectives on Medical Education Journal Data and Supplemental Files (2012 - 2019)
<p>This is the supplemental data, figures, and tables for <em>Joining the meta-research movement: A bibliometric case study of Perspectives on Medical Education</em>. </p> <p>For Figures 2-4 from the manuscript, to open the network maps, use both the network and map file for each figure in VoS viewer - https://www.vosviewer.com/</p>
Data file for: Three-Dimensional Electrical Imaging Across the Cona Woka Rift and Yalaxiangbo Dome in Southern Tibetan Plateau
<p>The magnetotellurics data were used to study the lithospheric electrical structure across the Cona Woka rift and Yalaxiangbo dome in the southern Tibetan plateau, conducted by Institute of Geophysical and Geochemical Exploration, Chinese Academy of Geological Sciences. The data file of CN6.dat was generated by the Matlab code EM3DVP.</p> <p>You are recommended to refer to the Kelbert et al., 2014 paper: https://doi.org/10.1016/j.cageo.2014.01.010 for a brief understanding of the data file formats.</p> <p> </p>
Data files for figures in "Characteristics of the two types of Kuroshio large meanders in the Shikoku Basin"
<p>Processed data files used to create the figures in the paper "Characteristics of the two types of Kuroshio large meanders in the Shikoku Basin".</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.