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5,061 results for “access”
Data from: IKey+: a new single-access key generation web service
Single-access keys are a major tool for biologists who need to identify specimens. The construction process of these keys is particularly complex (especially if the input dataset is large) so having an automatic single-access key generation tool is essential. As part of the European project ViBRANT, our aim was to develop such a tool as a web service, thus allowing end-users to integrate it directly into their workflow. IKey+generates single-access keys on demand, for single users or research institutions. It receives user input data (using the standard SDD format), accepts several key-generation parameters (affecting the key topology and representation), and supports several output formats. IKey+ is freely available (sources and binary packages) at www.identificationkey.fr. Furthermore, it is deployed on our server and can be queried (for testing purposes) via a simple web client also available at www.identificationkey.fr. Finally a client plugin will be integrated to the Scratchpads biodiversity networking tool (scratchpads.eu).
Data from: Don't put all your eggs in one basket: a cost-effective and powerful method to optimize primer choice for rRNA environmental community analyses using the Fluidigm Access Array
With the increasing democratization of high-throughout sequencing (HTS) technologies, along with the concomitant increase in sequence yield per dollar, many researchers are exploring HTS for microbial community ecology. Many elements of experimental design can drastically affect the final observed community structure, notably the choice of primers for amplification prior to sequencing. Some targeted microbes can fail to amplify due to primer-targeted sequence divergence and be omitted from obtained sequences, leading to differences among primer pairs in the sequenced organisms even when targeting the same community. This potential source of taxonomic bias in HTS makes it prudent to investigate how primer choice will affect the sequenced community prior to investing in a costly community-wide sequencing effort. Here we use Fluidigm's micro-fluidic Access Arrays (IFC) followed by Illumina® MiSeq Nano sequencing on a culture-derived local mock community to demonstrate how this approach allows for a low-cost combinatorial investigation of primer pairs and experimental samples (up to 48 primer pairs and 48 samples) to determine the most effective primers that maximize obtained communities whilst minimizing taxonomic biases.
Data from: Primary care management of headaches and how direct-access MRI fits: a qualitative study of UK general practitioners' views
Objectives To develop a better understanding of General Practitioners' (GPs) views and experiences of the management of patients with headaches and use of direct access magnetic resonance imaging (MRI) scans, and observe outcomes of an educational session offered by a GP with a Special Interest (GPwSI) to GPs. Design A qualitative study using semi-structured interviews, analysed using thematic analysis. A GPwSI in headaches visited practices delivering a talk on headache medication, diagnosis, and management. Setting Sixteen (16) primary care family practices in South London, United Kingdom. Participants Twenty (20) General Practitioners. Results Not all GPs were aware of the availability of direct access MRI, but all acknowledged having used referral or direct-scans to manage patients' concern about their headaches. A normal scan result helped resolve uncertainty for patient and GP, and helped management towards discussion of preventative treatment. However, patients with psychological and/or severe headache symptoms could not necessarily be reassured. GPs reported difficulty interpreting radiology reports, particularly incidental abnormalities. Those who received the educational talk gained knowledge in diagnosis and medication, improving their confidence in management. Conclusions Increased access to imaging, training in headache management, addressing physical and psychological symptoms, and standardized reporting of scans, may improve GP use of direct access MRI in future.
Data from: In an age of open access to research policies: physician and public health NGO staff research use and policy awareness
Introduction: Through funding agency and publisher policies, an increasing proportion of the health sciences literature is being made open access. Such an increase in access raises questions about the awareness and potential utilization of this literature by those working in health fields. Methods: A sample of physicians (N=336) and public health non-governmental organization (NGO) staff (N=92) were provided with relatively complete access to the research literature indexed in PubMed, as well as access to the point-of-care service UpToDate, for up to one year, with their usage monitored through the tracking of web-log data. The physicians also participated in a one-month trial of relatively complete or limited access. Results: The study found that participants' research interests were not satisfied by article abstracts alone nor, in the case of the physicians, by a clinical summary service such as UpToDate. On average, a third of the physicians viewed research a little more frequently than once a week, while two-thirds of the public health NGO staff viewed more than three articles a week. Those articles were published since the 2008 adoption of the NIH Public Access Policy, as well as prior to 2008 and during the maximum 12-month embargo period. A portion of the articles in each period was already open access, but complete access encouraged a viewing of more research articles. Conclusion: Those working in health fields will utilize more research in the course of their work as a result of (a) increasing open access to research, (b) improving awareness of and preparation for this access, and (c) adjusting public and open access policies to maximize the extent of potential access, through reduction in embargo periods and access to pre-policy literature.
Data from: De novo transcriptome assemblies of four accessions of the metal hyperaccumulator plant Noccaea caerulescens
Noccaea caerulescens of the Brassicaceae family has become the key model plant among the metal hyperaccumulator plants. Populations/accessions of N. caerulescens from geographic locations with different soil metal concentrations differ in their ability to hyperaccumulate and hypertolerate metals. Comparison of transcriptomes in several accessions provides candidates for detailed exploration of the mechanisms of metal accumulation and tolerance and local adaptation. This can have implications in the development of plants for phytoremediation and improved mineral nutrition. Transcriptomes from root and shoot tissues of four N. caerulescens accessions with contrasting Zn, Cd and Ni hyperaccumulation and tolerance traits were sequenced with Illumina Hiseq2000. Transcriptomes were assembled using the Trinity de novo assembler and were annotated and the protein sequences predicted. The comparison against the BUSCO plant early release dataset indicated high-quality assemblies.The predicted protein sequences have been clustered into ortholog groups with closely related species. The data serve as important reference sequences in whole transcriptome studies, in analyses of genetic differences between the accessions and other species, and for primer design.
Data from: One-shot dilation versus serial dilation technique for access in percutaneous nephrolithotomy: a systematic review and meta-analysis
Objective: The purpose of this study was to systematically review the outcomes of the use of one-shot dilation (OSD) and serial tract dilation for percutaneous nephrolithotomy (PCNL). Methods: A systematic review and meta-analysis was conducted. The randomized controlled trials (RCTs) included in the study were identified from EMBASE, MEDLINE, and the Cochrane Central Register of Controlled Trials. The last search was performed on April 30, 2018. Summary effects were calculated as risk ratios (RRs) with 95% confidence intervals (CIs) or mean differences (MDs) with 95% CIs. The endpoints included access time, fluoroscopy time, successful dilation rate, stone-free rate, postoperative decrease in hemoglobin levels, transfusion rate, complication rate, and length of postoperative hospital stay. Results: A total of 7 RCTs were included in the study, with clinical data reported for 697 patients. The overall access time was approximately 110 seconds shorter in the OSD group than in the serial dilation group (MD, -110.14; 95% CI, -161.99 to -58.30; P<0.0001). The fluoroscopy time was shorter with OSD in all RCTs. In addition, the decrease in postoperative hemoglobin levels was approximately 0.23 g/dl less in patients in the OSD group than in those in the serial dilation group (MD, -0.23; 95% CI, -0.39 to -0.07; P=0.004). No relationship was found between the successful dilation rate, stone-free rate, transfusion rate, or complication rate and the method of tract dilation. Conclusion: OSD is a safe and efficacious tract dilation technique that can reduce the access time, fluoroscopy time, and postoperative decrease in hemoglobin level. No difference was found in the successful dilation rate, stone-free rate, transfusion rate, or rate of complications between the OSD and serial dilation groups. The difference in the length of postoperative hospital stay was uncertain. OSD may be a better method of tract creation for PCNL.
Data from: Population genomics of pearl millet (Pennisetum glaucum (L.) R. Br.): comparative analysis of global accessions and Senegalese landraces
Background: Pearl millet is a staple food for people in arid and semi-arid regions of Africa and South Asia due to its high drought tolerance and nutritional qualities. A better understanding of the genomic diversity and population structure of pearl millet germplasm is needed to support germplasm conservation and genetic improvement of this crop. Here we characterized two pearl millet diversity panels, (i) a set of global accessions from Africa, Asia, and the America, and (ii) a collection of landraces from multiple agro-ecological zones in Senegal. Results: We identified 83,875 single nucleotide polymorphisms (SNPs) in 500 pearl millet accessions, comprised of 252 global accessions and 248 Senegalese landraces, using genotyping by sequencing (GBS) of PstI-MspI reduced representation libraries. We used these SNPs to characterize genomic diversity and population structure among the accessions. The Senegalese landraces had the highest levels of genetic diversity (π), while accessions from southern Africa and Asia showed lower diversity levels. Principal component analyses and ancestry estimation indicated clear population structure between the Senegalese landraces and the global accessions, and among countries in the global accessions. In contrast, little population structure was observed across in the Senegalese landraces collections. We ordered SNPs on the pearl millet genetic map and observed much faster linkage disequilibrium (LD) decay in Senegalese landraces compared to global accessions. A comparison of pearl millet GBS linkage map with the foxtail millet (Setaria italica) and sorghum (Sorghum bicolor) genomes indicated extensive regions of synteny, as well as some large-scale rearrangements in the pearl millet lineage. Conclusions: We identified 83,875 SNPs as a genomic resource for pearl millet improvement. The high genetic diversity in Senegal relative to other regions of Africa and Asia supports a West African origin of this crop, followed by wide diffusion. The rapid LD decay and lack of confounding population structure along agro-ecological zones in Senegalese pearl millet will facilitate future association mapping studies. Comparative population genomics will provide insights into panicoid crop evolution and support improvement of these climate-resilient crops.
Journal based analysis of the Open Access Europe PMC articles.
<p>This file shows the 20 most-represented journals that tag data citations in the XML within articles in the Open Access set from Europe PMC (May 2013). Secondly, it shows the 20 most-represented journals according to number of individual articles, demonstrating that the journals that undertake tagging of data citations most frequently are not the same as those that occur most frequently.</p>
@gccaedits data - October 2015 accession
<p>@gccaedits data - October 2015 accession</p> <p>Description</p> <p>This release contains Twitter archive requests of the @gccaedits account up to October 1, 2015.</p> <p>You should be able to download the release and open an index.html, from a given accession, with your browser to view the archive.</p> <p>License</p> <p>The contents of each accession's data directory and tweets.csv are Public Domain (CC0) licensed.</p>
Publishers of journals listed in the Directory of Open Access Journals (DOAJ)
<p>The file contains all publishers of journals listed in the Directory of Open Access Journals (DOAJ).</p> <p>On August 1, 2017, 9,621 journals were listed in the Directory of Open Access Journals (DOAJ). Only 32 publishers published more than 20 of these journals and thus have a quantitatively significant influence on Open Access. PLOS can not be found among them, but still has influence, but more qualitative than quantitative.</p> <p>These 32 publishers publish 2,950 journals, which are 31% of all journals listed in the DOAJ. At this date, the DOAJ reported 7,474 publishers, thus 0.43% of all DOAJ-listed publishers produced 31% of the journals.</p> <p>Of these 2,950 journals, 1,641 (56%) are in the hand of publishers who already dominate the market in the subscription model: e.g. Elsevier, Springer Nature (including BioMed Central, Frontiers), Wiley, SAGE, De Gruyter, Taylor & Francis, OUP, Wolters Kluwer).</p> <p>The data was gathered at August 1, 2017 using the Directory of Open Access Journals web interface. The total number of journals at this point of time was 9,621.</p>
Supplementary material 4 from: Jin S, Parks KS, Janzen DH, Hallwachs W, Dyer LA, Whitfield JB (2023) The wing interference patterns (WIPs) of Parapanteles (Braconidae, Microgastrinae): demonstrating a powerful and accessible tool for species-level identification of small and clear winged insects. Journal of Hymenoptera Research 96: 967-982. https://doi.org/10.3897/jhr.96.111382
Data files and R code
Supplementary material 3 from: Jin S, Parks KS, Janzen DH, Hallwachs W, Dyer LA, Whitfield JB (2023) The wing interference patterns (WIPs) of Parapanteles (Braconidae, Microgastrinae): demonstrating a powerful and accessible tool for species-level identification of small and clear winged insects. Journal of Hymenoptera Research 96: 967-982. https://doi.org/10.3897/jhr.96.111382
Wing interference patterns
Supplementary material 2 from: Jin S, Parks KS, Janzen DH, Hallwachs W, Dyer LA, Whitfield JB (2023) The wing interference patterns (WIPs) of Parapanteles (Braconidae, Microgastrinae): demonstrating a powerful and accessible tool for species-level identification of small and clear winged insects. Journal of Hymenoptera Research 96: 967-982. https://doi.org/10.3897/jhr.96.111382
Qualitative descriptions and materials examined for Parapanteles species included in this study
Supplementary material 1 from: Jin S, Parks KS, Janzen DH, Hallwachs W, Dyer LA, Whitfield JB (2023) The wing interference patterns (WIPs) of Parapanteles (Braconidae, Microgastrinae): demonstrating a powerful and accessible tool for species-level identification of small and clear winged insects. Journal of Hymenoptera Research 96: 967-982. https://doi.org/10.3897/jhr.96.111382
Taxonomic summary of published wing interference pattern images and/or descriptions
Open Access Resources
<p>Data analysis from from DOAJ, DOAB, OpenDOAR, re3Data, CWTS Leiden Ranking (2023)</p>
BigWig and Bed Files for Chromatin Accessibility
Open the record for dataset details and reuse information.
Open-Access-Infografik: Open vs. Closed Access
<p>Die Infografik verdeutlicht, dass Open Access es der Öffentlichkeit und Wissenschaftler*innen ermöglicht, frei auf Publikationen und damit auf Forschungsergebnisse zuzugreifen. Obwohl Forschung oft durch Steuergelder finanziert wird, bleibt der Zugang bei Closed Access kostenpflichtig. Sogar Wissenschaftler*innen haben nur indirekten Zugriff über ihre Institutionen, die entsprechende Journale abonnieren müssen.</p> <p>Wir freuen uns, wenn die Infografik nachgenutzt wird, zum Beispiel als Poster, Postkarte oder als Puzzle.</p>
Redefining Urban Park Accessibility
<p>Datasets used for urban park accessibility </p>
Dataset of 'Radar Evidence of an Accessible Cave Conduit on the Moon below the Mare Tranquillitatis Pit'
Open the record for dataset details and reuse information.
N-List & Open Access Academic Resources,
<div> <table> <tbody> <tr> <td> <p>N-List & Open Access Academic Resources,</p> </td> <td> <p>Pavanatma College Murickassery,Kerala,</p> </td> <td> <p>14th,July, 2020.</p> </td> </tr> </tbody> </table> </div> <p> </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.