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Dataset results
3,505 results for “completive”
The complete chloroplast genome of Mimusops elengi (Sapotaceae)
<p><span>The first complete chloroplast genome sequences of <i><span>Mimusops elengi</span></i> (Sapotaceae) were reported in this study. The cpDNA of <i><span>M</span></i><i><span>.</span></i><i><span> elengi</span></i> is 159,719 bp in length, contains a large single-copy region (LSC) of 88,935 bp and a small single-copy region (SSC) of 18,606 bp, which were separated by a pair of inverted repeat (IR) regions of 26,089 bp. The genome contains 132 genes, including 87 protein-coding genes, 8 ribosomal RNA genes, and 37 transfer RNA genes. The overall GC content of the whole genome is 36.8%. Phylogenetic analysis of 12 chloroplast genomes within the family Sapotaceae suggests that the sister relationship of <i><span>Autranella</span></i> and <i><span>Tieghemella</span></i><span> is strongly supported. </span><i><span>Minusops</span></i> genus is close to <i><span>Autranella</span></i> and <i><span>Tieghemella</span></i>, although the support value is still low.</span></p>
Complete mitochondrial genome sequence of the Atlantic Mudskipper (Periophthalmus barbarus) (Linnaeus, 1766) (Perciformes: Gobiidae)
<p>The complete mitochondrial genome of the Atlantic mudskipper (<em>Periophthalmus barbarus</em>) was determined in this study. The specimen was collected from Abonnema, Nigeria (4.73075, 6.77565). The complete mitogenome sequence of <em>P. barbarus</em> would be useful for further studies on molecular phylogenetic relationship and population genetics of the subfamily Oxudercinae.</p>
Reproduction package for the paper "Completing the X-ray view of the recently discovered supernova remnant G54.41+0.03"
<p>This is a basic reproduction package for the paper "Completing the X-ray view of the recently discovered supernova remnant G54.41+0.03" by V. Domček et al. (2021). It provides raw, intermediate and final data sets, including figures and scripts to allow the reproduction of the work performed in this paper. It also lists software used and data archives containing the public observational data. </p> <p>An open access version of the paper can be found at https://arxiv.org/abs/</p>
HiFi Metagenomic Sequencing Enables Assembly of Accurate and Complete Genomes from Human Gut Microbiota.
<p>We reported 102 complete metagenome assembled genomes (cMAGs) from five human fecal HiFi sequencing samples.</p> <p>102_cMAGs_fna.tar.gz: Fasta sequence files of 102 cMAGs.</p> <p>gc_skew_figures.tar.gz: GC-skew pattern figures of 102 cMAGs. (SVG format)</p> <p>coverage_plots.tar.gz: Genome coverage plot of 102 cMAGs.</p>
A complete list of filtered variants and gene lists of frequently and recurrently mutated genes in DLBCL, MCL, T-NHL, and BL, as well as pre-assembled CNV gene list
<p>A complete list of variants which passed filtering described in supplemental methods, that were found in both PDX model sample and patient’s sample from which it was derived (S1A) and variants which were gained (S1B) or lost (S1C) during PDX model derivation. Gene lists for filtration of variants in genes of special interest are included in the table (S1D). Gene list for filtration of CNV changes in genes of special interest is included in the table (S1E). Chr - Chromosome, REF - Reference allele, ALT - Alternative allele, AA change - Amino acid change, Patient AF - Allele frequency in the patient’s sample, Patient Depth – Read depth in patient’s sample, PDX AF- Allele frequency in PDX model sample, PDX Depth - Read depth in PDX sample, DLBCL - Diffuse Large B-cell lymphoma, MCL - Mantle Cell Lymphoma, TCL - T-cell lymphoma, BL – Burkitt Lymphoma, and CNV - Copy Number Variation.</p>
Complete dataset
<p>Complete dataset regarding the Impact of the timing and use of an insecticide on arthropods in cover crop-corn systems manuscript </p>
Arabidopsis thaliana Col-CEN complete Chromosome 2 numt sequences and alignments
<p>Data associated with the assembly of complete chromosome 2 nuclear insertion of mitochondrial DNA (numt) from the <em>Arabidopsis thaliana</em> accession Columbia (Col-CEN). A full report of this project can be obtained in a manuscript titled "<strong>Complete sequence of a 641-kb insertion of mitochondrial DNA in the <em>Arabidopsis thaliana </em>nuclear genome</strong>".</p>
Submitted Completed pointings to the Gravitational Wave Treasure Map for event TEST_EVENT
Attached in a .json file is the completed pointing information for 1 observation(s) for the EM counterpart search associated with the gravitational wave event TEST_EVENT. These observations were taken on the DLT40 instrument.
Submitted Completed pointings to the Gravitational Wave Treasure Map for event TEST_EVENT
Attached in a .json file is the completed pointing information for 1 observation(s) for the EM counterpart search associated with the gravitational wave event TEST_EVENT. These observations were taken on the DLT40 instrument.
Submitted Completed pointings to the Gravitational Wave Treasure Map for event TEST_EVENT
Attached in a .json file is the completed pointing information for 2 observation(s) for the EM counterpart search associated with the gravitational wave event TEST_EVENT. These observations were taken on the DLT40 instrument.
Raw Data for the article: Complete intra-laboratory validation of a LAL assay for bacterial endotoxin determination in EBV-specific cytotoxic T lymphocytes
<p>Endotoxin content is a critical factor that affects the safety of biological pharmaceutical products. International pharmacopoeias describe several reference methods to determine endotoxin levels in advanced therapy medicinal product (ATMP) preparations. Administration of ATMPs must be done as rapidly as possible to ensure complete viability and potency of the cellular product. To evaluate the endotoxin content in the shortest time possible, we chose to validate an alternative method based on the use of the Charles River Portable Testing System (PTS) and FDA-approved cartridges, compliant with the requirements of the European Pharmacopoeia and providing results in <20 min. Here, we describe a unique and complete validation approach for instrument, personnel, and analytical method for assessment of endotoxins in ATMP matrices. The PTS system provides high sensitivity and fast quantitative results and uses less raw material and accessories compared with compendial methods. It is also less time consuming and less prone to operator variability. Our validation approach is suitable for a validated laboratory with trained personnel capable of conducting the ATMP release tests, and with very low intra-laboratory variability, and meets the criteria required for an alternative approach to endotoxin detection for in-process and product-release testing of ATMPs.</p>
Pseudo-atomic model of a complete gas vesicle
<p>This pseudo-atomic model is shown in our preprint:</p> <p>Huber, S. T., Terwiel, D., Evers, W. H., Maresca, D. & Jakobi, A. J. Cryo-EM structure of gas vesicles for buoyancy-controlled motility.<em> BioRxiv (2022)</em></p> <p>(Update 26.04.2023), Now in:</p> <p>Huber, S. T., Terwiel, D., Evers, W. H., Maresca, D. & Jakobi, A. J. Cryo-EM structure of gas vesicles for buoyancy-controlled motility. <em>Cell </em>186, 975–986 (2023)</p> <p> </p> <p>We use the atomic model from our determined 3.2 Å cryo-EM structure of the <em>B.megaterium</em> gas vesicle (GV) wall and copy+place it on a helical path that narrows at the tips of the GVs. Placement at the seam in the GV center is informed by high-resolution 2D class averages. The helical arrangement is informed by the determined helical symmetry of this particular helical polymorph (92.93 units per helical turn) and the tip by measurement of the cone semi-angle.</p> <p>The pseudo-atomic model consists only of copies of the wall protein GvpA2. This is likely a simplification, and the homologous proteins GvpJ and GvpS might be involved in small parts of the assembly, such as the ends of the cones. The arrangement at the contact point of the two GV halves is informed only by high-resolution 2D data, therefore the 3D arrangement of these features is hypothetical.</p> <p>For display in ChimeraX I recommend this style:</p> <blockquote> <p>car style protein modeh default arrows f xsect oval width 3 thick 3 divisions 2 barSides 4</p> </blockquote> <p>The rainbow color scheme highlighting the main chain can be displayed:</p> <blockquote> <p>select :2-13; color sel #2c2a70; select :14-23; color sel #45639a; select :24-34; color sel #98b45a; select :35-39; color sel #abb24e; select :40-50; color sel #dddb20; select :51-61; color sel #e15a3d; select :62-66; color sel #ec1e24; ~sel;</p> </blockquote> <p>The color scheme for physico-chemical properties:</p> <blockquote> <p>select :Met,Ile,Leu,Ala,Val; color sel #e1b13e; select :Ser,Thr,Gln,Asn; color sel #49c2c6; select :Glu,Asp; color sel #cb2026; select :Lys,Arg,His; color sel #3e58a8; select :Phe,Trp,Tyr; color sel #715321; select :Gly,Pro; color sel #7b7b7b; ~sel;</p> </blockquote> <p>Python dictionary with color scheme:</p> <blockquote> <p>colorscheme = {'#e1b13e':'MILAV', '#49c2c6':'STNQ', '#cb2026':'DE', '#3e58a8':'KRH', '#715321':'FYW', '#7b7b7b':'GPC'}</p> </blockquote> <p>To highlight both halves in different colors in the full model:</p> <blockquote> <p>color #1.1-865 gray; color #1.866-1730 steel blue</p> </blockquote> <p>ChimeraX command to impose helical symmetry on a single GvpA monomer:</p> <blockquote> <p>sym #1 h,0.5257,-3.87399,500,-250 coordinateSystem #1 copies True</p> </blockquote> <p> </p>
Supplementary Materials from the article Characterization and molecular evolution analysis of Periploca forrestii inferred from its complete chloroplast genome sequence
<p>Table S1. Base composition of chloroplast genome in <em>P. forrestii</em>, Table S2. The lengths of introns and exons for the splitting genes, Table S3. The GC content of the codons from <em>P. forrestii </em>chloroplast genome, Table S4. Preferred codons in chloroplast genome of <em>P. forrestii</em>, Table S5. Long repeat sequences in the <em>P. forrestii </em>chloroplast genome, Figure S1. Codon bias analysis of P. forrestii chloroplast genome. (A) Neutrality plot analysis; (B) Analysis of PR2 bias plot; (C) Analysis on ENC and GC3 relationship.</p>
Beyond single host, single parasite interactions: quantifying competence for complete multi-host, multi-parasite communities
<p>Understanding parasite transmission in communities requires knowledge of each species' capacity to support transmission. This property, "competence", is a critical currency for modeling transmission under community change and for testing diversity-disease theory. Despite the central role of competence in disease ecology, we lack a clear understanding of the factors that generate competence and drive its variation.</p> <p>We developed novel conceptual and quantitative approaches to systematically quantify competence for a multi-host, multi-parasite community. We applied our framework to an extensive dataset: five amphibian host species exposed to four parasitic trematode species across five ecologically realistic exposure doses. Together, this experimental design captured twenty host-parasite interactions while integrating important information on variation in parasite exposure. Using experimental infection assays, we measured multiple components of the infection process and combined them to produce competence estimates for each interaction.</p> <p>With directly estimated competence values, we asked which components of the infection process best explained variation in competence: barrier resistance (the initial fraction of administered parasites blocked from infecting a host), internal clearance (the fraction of established parasites lost over time) or pre-transmission mortality (the probability of host death prior to transmission). We found that variation in competence among the twenty interactions was best explained by differences in barrier resistance and pre-transmission mortality, underscoring the importance of host resistance and parasite pathogenicity in shaping competence.</p> <p>We also produced dose-integrated estimates of competence that incorporated natural variation in exposure to address questions on the basis and extent of variation in competence. We found strong signals that host species identity shaped competence variation (as opposed to parasite species identity). While variation in infection outcomes across hosts, parasites, individuals, and doses was considerable, individual heterogeneity was limited compared to among-species differences. This finding highlights the robustness of our competence estimates and suggests that species-level values may be strong predictors for community-level transmission in natural systems.</p> <p>Competence emerges from distinct underlying processes and can have strong species-level characteristics; thus, this property has great potential for linking mechanisms of infection to epidemiological patterns.</p>
Data from: Skeletal and soft tissue completeness of the acanthodian fossil record
<p>Acanthodians are a poorly understood paraphyletic grade of extinct Palaeozoic fishes. They play an increasingly prominent role in our understanding of vertebrate evolution as part of the chondrichthyan stem-group even though their evolutionary history is scarce. The limited preservation of their mostly cartilaginous skeleton largely results in a bias towards isolated remains such as fin spines and scales. Here, we quantify the quality of the acanthodian fossil record by using a variation of the Skeletal Completeness Metric (SCM), an approach that calculates how complete the skeletons of individuals are compared to their theoretical complete skeleton. A novel Soft Tissue Completeness Metric (STCM) is introduced to estimate the percentage of soft body tissue preserved as an alternate measurement of completeness. Completeness scores for >1600 specimens comprising >300 taxa obtained from museum collection visits and literature surveys were assembled into a database. Acanthodian completeness peaks in the Lochkovian, Givetian, Bashkirian-Moscovian, and the Asselian, with lowest scores in the Llandovery. There is no correlation between acanthodian taxonomic richness and completeness. Acanthodians show a significantly lower completeness distribution than many tetrapod groups, but a similarly low distribution to bats. Skeletons deposited in freshwater are significantly more complete than in marine environments where sea level significantly negatively correlates with observed completeness. Our assessment of completeness reveals only weak spatial biases influencing the acanthodian fossil record while environmental biases are much higher. Variation in completeness will have an impact on the utility of characters for assessing the phylogenetic relationships and inclusion of the various acanthodian groups.</p>
Dataset: The availability and completeness of open funder metadata - Case study for publications funded by the Dutch Research Council
<p>Data and code belonging to the manuscript: <strong>The availability and completeness of open funder metadata - Case study for publications funded by the Dutch Research Council </strong></p> <p><strong>Abstract:</strong><br> Research funders spend considerable efforts collecting information on outcomes of the research they fund. To help funders track publication output associated with their funding, Crossref initiated FundRef in 2013, enabling publishers to register funding information using persistent identifiers. However, it is hard to assess the coverage of funder metadata because it is unknown how many articles are the result of funded research and therefore should include funder metadata. </p> <p>In this paper we looked at 5,004 publications reported by researchers to be the result of funding by a specific funding agency: the Dutch Research Council NWO. Only 67% of these articles contain funding information in Crossref, with a subset acknowledging NWO as funder name and/or Funder IDs linked to NWO (53% and 45%, respectively). </p> <p>Web of Science (WoS), Scopus and Dimensions are all able to infer additional funding information from funding statements in the full text of the articles. Funding information in Lens largely corresponds to that in Crossref, with some additional funding information likely taken from PubMed. </p> <p>We observe interesting differences between publishers in the coverage and completeness of funding metadata in Crossref compared to proprietary databases, highlighting potential to increase the quality of open metadata on funding. </p> <p><strong>This dataset contains the following files:</strong></p> <ul> <li><strong>DOIs_unique_CR_Lens_Wos_Scopus_Dim.csv</strong><em> - </em>Dataset of unique DOIs (n= 5,004) with collected information from Crossref and presence/absence of funder information in Lens, Web of Science, Scopus and Dimensions </li> <li><strong>NWO_funder_names_Crossref.txt</strong><em> </em>- List of funder name variants for NWO found in Crossref</li> <li><strong>Google_Apps_Script.js</strong> - Google Apps Script for retrieving information from Crossref and processing Dimensions results </li> <li><strong>DOI_cleaning.R</strong><em> - </em>R script for cleaning DOIs</li> </ul>
Wikipedia Complete Citation Corpus
<p><strong>Wikipedia Complete Citation Corpus</strong> (<strong>WCCC</strong>) is a corpus of citations, references and sources mined from the English Wikipedia. WCCC was created as a knowledge base used in a machine-learning model for recommending reliable sources to support (or refute) a given textual claim, but can be used for many other purposes.</p> <p>The solution was described in the paper <em>"Countering Disinformation by Finding Reliable Sources: a Citation-Based Approach"</em>, presented at the 2022 International Joint Conference on Neural Networks (IJCNN 2022). Please refer to the article (in <a href="https://doi.org/10.1109/IJCNN55064.2022.9891941">conference proceedings</a> or <a href="https://home.ipipan.waw.pl/p.przybyla/bib/Learning_to_Cite_3_CR.pdf">authors' version</a>) for more information on the process of mining the corpus, comparisons with similar resources and the role it plays in recommending sources. The research was done within the <a href="https://homados.ipipan.waw.pl/">HOMADOS</a> project at the <a href="https://ipipan.waw.pl/">Institute of Computer Science</a>, Polish Academy of Sciences.</p> <p>WCCC contains 4.8 million documents with 50.8 million citations of 24.3 million sources. The dataset is divided into 10 parts (WCCC-part0.zip to WCCC-part9.zip) with approximately the same size. Each of the parts contains batch archives (e.g. batch130.zip), each covering up to 1000 Wikipedia articles. An article is identified by its ID number and described by the following files:</p> <ul> <li><ID>_text.txt: the textual content of the article,</li> <li><ID>_citations.txt: the citations occurring in this article, saved as tab-separated values of (1) character offset in the textual content and (2) reference ID,</li> <li><ID>_references.txt: the references cited in the article, saved as tab-separated values of (1) reference ID and (one or many) pairs of (2) source ID and (3) location in the source (e.g. page number),</li> <li><ID>_sources.txt: the sources referenced in the article, saved as tab-separated values of (1) source ID and (2) source description (in wikicode).</li> <li><ID>.txt: human-readable text, created by enriching textual content with the article title and reference IDs.</li> </ul> <p>Additionally, article metadata are included in the meta.tsv file. Each line describes a single article through the following tab-separated fields:</p> <ul> <li>article ID,</li> <li>title of the article,</li> <li>Wikipedia ID of the article, which can be used to access the article through URL, i.e. https://en.wikipedia.org/?curid=<WIKI_ID></li> <li>length of the textual content of the article (number of characters),</li> <li>number of sources in the article,</li> <li>number of references in the article,</li> <li>number of citations in the article.</li> </ul> <p>Files metaTrain.tsv and metaTest.tsv contain the same information, but split into training and test set, as used in the work.</p> <p>Please refer to <a href="https://home.ipipan.waw.pl/p.przybyla/bib/Learning_to_Cite_3_CR.pdf">the paper</a> for an in-depth explanation of the data structure (citations, references, sources, etc.). WCCC was created using Wikipedia dump from 01.02.2021, but you can repeat the mining process using a different dump (or different procedure) by using the <a href="https://github.com/piotrmp/finding_reliable_sources">published source code</a>. If you intend to apply the corpus in a fact-checking use-case, you might also look at the <a href="https://dx.doi.org/10.5281/zenodo.6539087">evaluation datasets we publish separately</a>, one of which is based on WCCC with additional elements (e.g. source identifiers: URL/ISBN/DOI).</p>
Raw data for "Complete Alignment of a KB-Mirror System guided by Ptychography"
<p>All raw datasets for each figure presented in the article.</p>
Complete allele-specific silencing of the gain-of-function mutation of Huntington's disease
<p>Dominant gain-of-function mechanism in Huntington's disease (HD) suggests selective inactivation of mutant <em>HTT</em> produces the biggest therapeutic benefit. Here, we developed a complete allele-specific CRISPR/Cas9 strategy to permanently silence mutant <em>HTT</em> through nonsense-mediated decay (NMD), capitalizing on an exonic PAM (protospacer adjacent motif)-Altering SNP (PAS). Comprehensive sequence/haplotype analysis identified PAS-generated NGG PAM sites on exons of common <em>HTT </em>haplotypes in HD patients, revealing a single clinically meaningful PAS-based mutant-specific NMD-CRISPR/Cas9 strategy. The alternative allele of rs363099 eliminates NGG PAM site on the most frequent normal <em>HTT </em>haplotype in HD, permitting mutant <em>HTT-</em>specific CRISPR/Cas9 therapeutics in ~20% of HD patients with European ancestry. Our rs363099-based CRISPR/Cas9 showed perfect allele specificity and good targeting efficiencies in cells derived from HD patients. Dramatically reduced mutant <em>HTT </em>mRNA and complete loss of mutant HTT protein indicate that our allele-specific CRISPR/Cas9 strategy completely inactivates mutant <em>HTT </em>through NMD. RNAseq analysis also supported high levels of on-target gene specificity because no other genes except <em>HTT </em>were altered in clonal lines developed through our NMD-CRISPR/Cas9 strategy. Together, our data demonstrating significant target population, selective inactivation of mutant <em>HTT</em>, good targeting efficiency, and lack of recurrent off-targeting establish its therapeutic value of novel rs363099-based mutant <em>HTT-</em>specific NMD-CRISPR/Cas9 strategy in HD.</p>
BdSL47: A complete dataset of sign alphabet and digits of Bangla Sign Language (BdSL) using depth information via MediaPipe
<p><strong>BdSL47</strong> is the first open-access complete dataset in Bangla Sign Language that contains hand signs from both 10 sign digits (from sign ০ to sign ৯) and 37 sign alphabet (from sign অ to sign ँ).</p> <p>Dataset summary :</p> <ul> <li>100 RGB images per sign (total 47 signs) from each of 10 users</li> <li>Total input images : 100×47×10 = 47000</li> <li>Input images are processed via MediaPipe, which provided <ul> <li>an output image with hand key-points being detected</li> <li>3D coordinate values of 21 predefined key-points</li> <li>Total 63 coordinate values for each sample</li> </ul> </li> <li>The values are stored in csv files</li> <li>1 CSV file contains values from 100 samples of 1 sign from 1 user</li> <li>Total CSV files : 47×10 = 470</li> </ul> <p>The dataset has been made public for further research purposes. It is also available upon request <a href="https://drive.google.com/drive/u/8/folders/1wmJUlgWUrWNnOvzuL8Ci82Hm3zUx4wS-" rel="noopener">here</a>.</p>
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.