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Georeferenced genbank sequence accession numbers from GBIF
<blockquote> <p>Request = I am interested in only occurrence records that have both coordinates and accessions. Unfortunately, it appears that while I can specify “Including coordinates” in Advance search, there is no “Including accessions”.</p> </blockquote> <p>GBIF: Custom HiveSQL query on the GBIF occurrence store.</p> <pre><code class="language-sql">SELECT o.associatedSequences, o.gbifID, o.decimalLatitude, o.decimalLongitude, o.kingdom, o.phylum, o.class, o.order_, o.family, o.genus, o.species, o.infraspecificEpithet, o.basisOfRecord, o.v_geodeticdatum, o.coordinateuncertaintyinmeters, o.issue FROM prod_h.occurrence_hdfs o WHERE o.associatedSequences IS NOT NULL AND o.decimalLatitude IS NOT NULL AND o.hasgeospatialissues = false</code></pre> <p>98 GBIF datasets contributed to this data export.</p> <p>Total records = 9,181,930</p>
Fig. 28. Aspidelaps lubricus cowlesi, 70 in When roads appear jaguars decline: Increased access to an Amazonian wilderness area reduces potential for jaguar conservation
Fig. 28. Aspidelaps lubricus cowlesi, 70 km N Namibe, Namibe.
Fig. 21 in When roads appear jaguars decline: Increased access to an Amazonian wilderness area reduces potential for jaguar conservation
Fig. 21. Psammophis ansorgii, Tundavala, Huila (Photo: Ninda Baptista).
Fig. 15 in When roads appear jaguars decline: Increased access to an Amazonian wilderness area reduces potential for jaguar conservation
Fig. 15. Atractaspis congica, Soyo (Photo: Warren Klein).
Fig. 13 in When roads appear jaguars decline: Increased access to an Amazonian wilderness area reduces potential for jaguar conservation
Fig. 13. Grayia ornata, Lagoa Carumba, Lunde Norte.
Fig. 7 in When roads appear jaguars decline: Increased access to an Amazonian wilderness area reduces potential for jaguar conservation
Fig. 7. Philothamnus dorsalis, Soyo (Photo: Warren Klein).
Fig. 18 in When roads appear jaguars decline: Increased access to an Amazonian wilderness area reduces potential for jaguar conservation
Fig. 18. Limaformosa savorgani, Soyo (Photo: Warren Klein).
Effective capacity analysis of full-duplex-cooperative non-orthogonal multiple access systems
Open the record for dataset details and reuse information.
Data from: Discovery of potential urine-accessible metabolite biomarkers associated with muscle disease and corticosteroid response in the mdx mouse model for Duchenne
Urine is increasingly being considered as a source of biomarker development in Duchenne Muscular Dystrophy (DMD), a severe, life-limiting disorder that affects approximately 1 in 4500 boys. In this study, we considered the mdx mice—a murine model of DMD—to discover biomarkers of disease, as well as pharmacodynamic biomarkers responsive to prednisolone, a corticosteroid commonly used to treat DMD. Longitudinal urine samples were analyzed from male age-matched mdx and wild-type mice randomized to prednisolone or vehicle control via liquid chromatography tandem mass spectrometry. A large number of metabolites (869 out of 6,334) were found to be significantly different between mdx and wild-type mice at baseline (Bonferroni-adjusted p-value < 0.05), thus being associated with disease status. These included a metabolite with m/z = 357 and creatine, which were also reported in a previous human study looking at serum. Novel observations in this study included peaks identified as biliverdin and hypusine. These four metabolites were significantly higher at baseline in the urine of mdx mice compared to wild-type, and significantly changed their levels over time after baseline. Creatine and biliverdin levels were also different between treated and control groups, but for creatine this may have been driven by an imbalance at baseline. In conclusion, our study reports a number of biomarkers, both known and novel, which may be related to either the mechanisms of muscle injury in DMD or prednisolone treatment.
Figure 2 from: Schmidt S, Broad G, Stoev P, Mietchen D, Penev L (2013) The move to open access and growth: experience from Journal of Hymenoptera Research. Journal of Hymenoptera Research 30: 1-6. https://doi.org/10.3897/jhr.30.4733
Figure 2 - JHR Statcounter statistics, showing the number of visits to the website.
Figure 2 from: Kress W, Knapp S, Stoev P, Penev L (2012) On the front line of modern data-management and Open Access publishing: Two years of PhytoKeys – the fastest growing journal in plant systematics. PhytoKeys 19: 1-8. https://doi.org/10.3897/phytokeys.19.4501
Figure 2 - Taxonomic distribution by family of the published nomenclatural novelties in PhytoKeys.
Figure 1 from: Koon-Bong Cheung D, Brunke A, Akkari N, Souza C, Pape T (2013) Rotational Scanning Electron Micrographs (rSEM): A novel and accessible tool to visualize and communicate complex morphology. ZooKeys 328: 47-57. https://doi.org/10.3897/zookeys.328.5768
Figure 1 - Specimens directly (A) and secondarily (B) mounted on an aluminum SEM stub.
Supplementary Table 2. Accession numbers
<p>Table with the accession numbers of all the genomes downloaded from NCBI RefSeq for the construction of the phylogenomic tree.</p>
A verified open-access AI-based chemical microparticle image database for in-situ particle visualization and quantification in multi-phase flow
<p>This report provided a new method and idea for the detection, segmentation, classification, and quantitative analysis of four dispersed phase particles - "DPPs" (agglomeration, bubble, crystal, and droplet) in chemical multi-phase flow processes.</p>
Wu et al. Polysulfamide paper data - open access
<p>Data used in the main manuscript of "Investigating hydrogen bond-induced self-assembly of polysulfamides using molecular simulations and experiments" by Wu et al., published on Macromolecules in 2023</p>
WNVDB: an open access dataset of reported West Nile outbreaks in Italy
<p>In Italy, the epidemiological surveillance of West Nile virus (WNV) infections in humans is regulated by the <a href="https://www.statoregioni.it/media/2371/p-1-csr-rep-n-1-15gen2020.pdf">“National prevention, surveillance and response plan for arboviral diseases (PNA) 2020-2025“</a>. The document integrates veterinary (animal and entomological) surveillance of West Nile virus (WNV) - essential for risk estimation - and human cases into a single plan.</p> <p>Surveillance of imported and local human infections is carried out all year round throughout the country, and between early May and late November in Regions where an endemic area has been identified. In these areas the surveillance of human cases must be strengthened and special attention must be paid to the diagnosis of WNV disease in the population. The reporting system also collects positivities for WNV detected in donors of blood, blood derivatives and organs, tissues and cells, with a view to the application of specific preventive measures and any febrile clinical forms found in the country.</p> <p>Human surveillance is coordinated at national level by the Istituto Superiore di Sanità (ISS) and the Ministry of Health, which transmits the data to the European Commission and the ECDC. The Regions, in full autonomy, define the regulatory-programmatic documents for epidemiological and laboratory surveillance on their territory and transmit the data to the ISS and the Ministry. The Department of Infectious Diseases of the Istituto Superiore di Sanità, with the coordination of Office V of the Directorate General for Prevention of the Ministry of Health and in collaboration with the Centre for the Study of Exotic Diseases (Cesme) of the Experimental Zooprophylactic Institute of Abruzzo and Molise 'Giuseppe Caporale' (IZS Teramo), publishes the data of the surveillance system in a periodical bulletin.</p> <p>In order to inform citizens and make the collected data available, which is only useful for communication and information purposes, the following information is made available under the CC-BY-4.0 licence</p> <ul> <li>National evolution data</li> <li>Regional data</li> <li>Provincial data</li> <li>Summary bulletins</li> </ul> <p> </p> <p>The complete list of bulletins is available at the following link: <a href="https://www.epicentro.iss.it/westnile/bollettino">https://www.epicentro.iss.it/westnile/bollettino</a></p>
A Retrospective Cohort to Access the Accuracy of Agitated Saline Bubble–Enhanced Ultrasound to Visualize Appropriated Position of Hemodialysis Catheter: Does Catheter Venous Site Matter?
<p><strong>Background:</strong> The non-tunnelled hemodialysis catheter (HDC) is commonly used to start renal replacement therapy in hospitalised patients, especially in acute kidney injury. Malposition of HDC is associated with delayed therapy and inadequate dialysis. Agitated saline bubble-enhanced ultrasound (SBUS) has become a new method to visualise catheter position at the same time of insertion. Our aim is to analyse the concordance of SBUS and chest radiography (CXR) to assess HDC position, according to the site of insertion: right vs left internal jugular vein (IJV).</p> <p><strong>Methods</strong>: From December 2019 to May 2021, we evaluated 152 hospitalized patients submitted to IJV catheter insertion. We evaluated the time from puncture to CXR result, procedure-related complications, blood flow and the accuracy of SBUS when compared to CXR to detect HDC position adequacy at both sites.</p> <p><strong>Results: </strong>The median [IQR] time between catheter insertion and CXR result was 191 [93;288] minutes, no difference between puncture sites. Complications after catheter insertion were mostly arterial puncture (2% overall), similar incidence between sites. The incidence of inadequate blood flow was higher at the left IJV than at the right IJV. For HDC at the right IJV, there was high concordance between position-adequacy assessment by SBUS and CXR ( of Gwet = 0.95, CI: 0.915; 0.992), 95.6% accuracy. For HDC at the left IJV the concordance was low ( of Gwet 0.37, IC: -0.21; 0,94), as was accuracy (64.3%).</p> <p><strong>Conclusion:</strong> Compared with chest radiography, agitated saline bubble-enhanced ultrasound is a suitable method to check catheter placement when right internal jugular vein is used, but not left for internal jugular vein.</p>
Community-Based Health Coach for Access to Germline Genetic Testing Among African American Men With Prostate Cancer
ClinicalTrials.gov study NCT04763980. IPD Sharing: NO. Countries: 1. Publications: 0.
Accessing Care, Clinical Trials and Screening for Underserved Children and Adults With Type 1 Diabetes (ACCESS-T1D)
ClinicalTrials.gov study NCT06908057. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Safe Laparoscopic Access in Patients With Previous Abdominal and Pelvic Surgery
ClinicalTrials.gov study NCT05565508. IPD Sharing: UNDECIDED. Countries: 1. Publications: 0.
ScienceDex guides
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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.