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◂Fig. 5 Cells of phylogenetically related strains (light microscopy). a Thecate cell in dorsal view. b Thecate cell in ventral view, note the sulcus extending onto the epitheca (arrow). c Putatively necrotic, thecate cell. d Thecate cell with one bulge on the epitheca (arrow), note that this was the only such cell among thousands of inspected cells. e, f Coccoid cells, apparently without thecae. g Two thecate cells enclosed in the parental theca. h Two connected, immotile cells enclosed in the parental thecae. j Lid of epitheca in dorsal-apical view (mirrored), composed of plates 2′‒4′, all intercalary plates and plates 2′′‒6′′. l‒m Same opened theca in ventral view (l) and dorsal view (m), note the sulcus extending onto the epitheca (arrow), the dorsal opening and all apical and all intercalary plates and plates 3′′‒5′′ remaining with the hypotheca. n Chloroplasts (as inferred from autofluorescence), note the space occupied by the nucleus. Plate labelling follows the Kofoidean notation, n′: apical plate; n′′: precingular plate; n′′′: postcingular plate; na: anterior intercalary plate. Scale= 10 µm in Bumps on the back: An unusual morphology in phylogenetically distinct Peridinium aff. cinctum (= Peridinium tuberosum; Peridiniales, Dinophyceae)
◂Fig. 5 Cells of phylogenetically related strains (light microscopy). a Thecate cell in dorsal view. b Thecate cell in ventral view, note the sulcus extending onto the epitheca (arrow). c Putatively necrotic, thecate cell. d Thecate cell with one bulge on the epitheca (arrow), note that this was the only such cell among thousands of inspected cells. e, f Coccoid cells, apparently without thecae. g Two thecate cells enclosed in the parental theca. h Two connected, immotile cells enclosed in the parental thecae. j Lid of epitheca in dorsal-apical view (mirrored), composed of plates 2′‒4′, all intercalary plates and plates 2′′‒6′′. l‒m Same opened theca in ventral view (l) and dorsal view (m), note the sulcus extending onto the epitheca (arrow), the dorsal opening and all apical and all intercalary plates and plates 3′′‒5′′ remaining with the hypotheca. n Chloroplasts (as inferred from autofluorescence), note the space occupied by the nucleus. Plate labelling follows the Kofoidean notation, n′: apical plate; n′′: precingular plate; n′′′: postcingular plate; na: anterior intercalary plate. Scale= 10 µm
Label-Free Differentiation of Living versus Dead Single Yeast Cells using Broadband Electrical Impedance Spectroscopy
<p>Data to support manuscript.</p>
W-RAG sampled data and weak labels
Open the record for dataset details and reuse information.
Fig. 1. Type specimens and label data. A in Cafius semiaereus (Cameron), a New Synonym of Cafius cupreipennis (Cameron) (Coleoptera: Staphylinidae: Staphylininae)
Fig. 1. Type specimens and label data. A) Cafius cupreipennis, B) C. semiaereus.
Fig. 1. Type specimens and label data. A in Cafius zealandicus Cameron, a New Synonym of Cafius maritimus (Broun) (Coleoptera: Staphylinidae: Staphylininae)
Fig. 1. Type specimens and label data. A) Cafius maritimus, B) C. zealandicus.
Fig. 1. Type specimens and label data. A in Cafius velutinus Fauvel, a New Synonym of Cafius catenatus Fauvel (Coleoptera: Staphylinidae: Staphylininae)
Fig. 1. Type specimens and label data. A) Cafius catenatus, holotype, B) C. velutinus, lectotype.
Linked collectors and determiners for: Insect collection, UiT, University Museum (TSZ). Insect labeling project and PhD-duty-work.
Natural history specimen data linked to collectors and determiners held within, "Insect collection, UiT, University Museum (TSZ). Insect labeling project and PhD-duty-work". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/b581fcfa-9f31-431a-8431-1800ef8a554b">https://bionomia.net/dataset/b581fcfa-9f31-431a-8431-1800ef8a554b</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/b581fcfa-9f31-431a-8431-1800ef8a554b">https://gbif.org/dataset/b581fcfa-9f31-431a-8431-1800ef8a554b</a>. Formatted as a Frictionless Data package.
Jind-Multi: An extended framework to leverage multiple labeled datasets for the automatic annotation of single-cell RNA and ATAC data
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FIG. 1 in High-quality herbarium-label transcription by citizen scientists improves taxonomic and spatial representation of the tropical plant family Annonaceae
FIG. 1. — Label of specimen P02032119, illustrating some challenges of deciphering specimen labels. Collected by Pobéguin in 1895. No s.n., Isolona calycina Pierre, nomen nudum in herb. (never validly published). "Le calice y est 2 fois plus longue et plus large que chez les autres espèces" [The calyx here is two times longer and wider than in the other species]. "Hab. Côte de l'Ivoire. Cult in H[ortus] B[otanicus] M[usei] Par[isiensis] 4/1905. Floret [blossoms]" (referring to the sampling of the specimen in 1905).
FIG. 3 in High-quality herbarium-label transcription by citizen scientists improves taxonomic and spatial representation of the tropical plant family Annonaceae
FIG. 3. — Spatial distribution and density of Annonaceae records transcribed by the 'Herbonautes' citizen science project, grouped by specimens (A, an individual specimen being defined as a single barcoded sheet), by species (B) and by botanical collectors (C), log scaled, grid resolution 1 × 1° (c. 110 × 110 km at the equator), equirectangular (EPSG 4326) projection.
FIG. 2 in High-quality herbarium-label transcription by citizen scientists improves taxonomic and spatial representation of the tropical plant family Annonaceae
FIG. 2. — Cumulative percentage of specimens representing percentage of species, by dataset. The dashed line with grey boxes represents the Herbonautes dataset, continuous line with white boxes represent the GBIF dataset.
Data from: Stable isotope labeled n-alkanes to assess digesta passage kinetics through the digestive tract of ruminants
We describe the use of carbon stable isotope (13C) labeled n-alkanes as a potential internal tracer to assess passage kinetics of ingested nutrients in ruminants. Plant cuticular n-alkanes originating from intrinsically 13C labeled ryegrass plants were pulse dosed intraruminally in four rumen-cannulated lactating dairy cows receiving four contrasting ryegrass silage treatments that differed in nitrogen fertilization level (45 or 90 kg nitrogen ha−1) and maturity (early or late). Passage kinetics through the gastrointestinal tract were derived from the δ13C (i.e. the ratio 13C:12C) in apparently undigested fecal material. Isotopic enrichment was observed in a wide range of long-chain n-alkanes (C27–C36) and passage kinetics were determined for the most abundant C29, C31 and C33 n-alkanes, for which a sufficiently high response signal was detected by combustion isotope ratio mass spectrometry. Basal diet treatment and carbon chain length of n-alkanes did not affect fractional passage rates from the rumen (K1) among individual n-alkanes (3.71–3.95%/h). Peak concentration time and transit time showed a quantitatively small, significant (p≤0.002) increase with carbon chain length. K1 estimates were comparable to those of the 13C labeled digestible dry matter fraction (3.38%/h; r = 0.61 to 0.71; p≤0.012). A literature review has shown that n-alkanes are not fermented by microorganisms in the rumen and affirms no preferential depletion of 13C versus 12C. Our results suggest that 13C labeled n-alkanes can be used as nutrient passage tracers and support the reliability of the δ13C signature of digestible feed nutrients as a tool to measure nutrient-specific passage kinetics.
Data from: Immunotherapy-related adverse events (irAEs): extraction from FDA drug labels and comparative analysis
Objectives: Immune checkpoint inhibitors (ICIs) have dramatically improved outcomes in cancer patients. However, ICIs are associated with significant immune-related adverse events (irAEs) and the underlying biological mechanisms are not well-understood. To ensure safe cancer treatment, research efforts are needed to comprehensively detect and understand irAEs. Materials and Methods: We manually extracted and standardized irAEs from FDA drug labels for six FDA-approved ICIs. We compared irAE profile similarities among ICIs and 1,507 FDA-approved non-ICI drugs. We investigated how irAEs have differential effects on human organs by classifying irAEs based on their targeted organ systems. Finally, we identified broad-spectrum (non-target specific) and narrow-spectrum (target-specific) irAEs. Results: A total of 893 irAEs were extracted. 31.4% irAEs were shared among ICIs as compared to the 8.0% between ICIs and non-ICI drugs. irAEs were resulted from both on- and off-target effects: irAE profiles were more similar for ICIs with same target than different targets, demonstrating the on-target effects; irAE profile similarity for ICIs with the same target is less than 50%, demonstrating unknown off-target effects. ICIs significantly target many organ systems, including endocrine system (3.4-fold enrichment), metabolism (3.7-fold enrichment), immune system (3.6-fold enrichment) and autoimmune system (4.8-fold enrichment). We identified 21 broad-spectrum irAEs shared among all ICIs, 20 irAEs specific for PD-L1/PD-1 inhibition, and 28 irAEs specific for CTLA-4 inhibition. Discussion and Conclusion: Our study presents the first effort toward building a standardized database of irAEs. The extracted irAEs can serve as a goldstandard for automatic irAE extractions from other data resources and set a foundation to understand biological mechanisms of irAEs.
Data from: Can recombinant human thrombomodulin increase survival among patients with severe septic-induced disseminated intravascular coagulation: a single-centre, open-label, randomised controlled trial
Objective: To determine whether treatment with recombinant human thrombomodulin (rhTM) increases survival among severe septic patients with sepsis-induced disseminated intravascular coagulation (DIC) Design: Single-center, open-label, randomized controlled trial Setting: Single tertiary hospital Participant: 92 severe septic patients with sepsis-induced DIC Interventions: Patients with DIC scores ≥4, as defined by the Japanese Association of Acute Medicine, were diagnosed with DIC. Randomization was performed by the envelope method. The treatment group (rhTM group, n = 47) was intravenously treated with rhTM within 24 h of admission (day 0), and the control group (n = 45) did not receive any anti-coagulants, except in cases of deep venous thrombosis and pulmonary embolism. Primary and secondary measurements: Data were collected on days 0 (admission), 1, 2, 3, 5, 7, and 10. The primary outcome was survival at 28 and 90 days. The secondary endpoints comprised changes in DIC scores, platelet counts, D-dimer, antithrombin III (ATIII), and C-reactive protein (CRP) levels, and Sequential Organ Failure Assessment (SOFA) scores. All analyses were conducted on an intent-to-treat basis. Main Results: The 28-day survival rates were 84 and 83% in the control and rhTM groups, respectively (p = 0.745, log rank test). The 90-day survival rates were 73% and 72% in the control and rhTM groups, respectively (p = 0.94, log rank test). Meanwhile, the rates of recovery from DIC (<4) were significantly higher in the rhTM group than in the control group (p = 0.001, log rank test). Relative change from baseline of D-dimer levels were significantly lower in the rhTM group than in the control group, on day 3 and 5. Conclusion: rhTM treatment decreased D-dimer levels and facilitated DIC recovery in severe septic patients with sepsis-induced DIC. However, the treatment did not improve survival in this cohort.
Labels file - Wikidata dump of Dec 7, 2020
<p>File with all labels of nodes used in the analysis in KGTK format</p>
Data from: Cannabis labelling is associated with genetic variation in terpene synthase genes
<p>Genetic data consisting of >100,000 single nucleotide polymorphisms (SNPs) collected using genotype-by-sequencing, from 137 drug-type Cannabis samples from the Netherlands. This genetic data along with terpene and cannabinoid content data collected with GC-FID, was used to analyze Cannabis labelling and to perfom a genome-wide association study.</p>
The bradykinin-2 receptor antagonist, icatibant, improves lung function in patients with SARS-CoV2 associated ARDS - First results of a prospective off-label use patient-related observational study.
<p>SARS-CoV2-associated adult respiratory distress syndrome (COVID19-ARDS) frequently leads to fatal respiratory failure in COVID19. Currently, there is no curative treatment option for severe COVID19-ARDS other than mechanical ventilation therapy and extracorporal membrane oxygenation (ECMO). We investigated whether modification of the kallikrein-kinin system in vivo attenuates the progression of SARS-CoV2-induced ARDS. The aim of the study was to investigate the effect of blockade of the B2R on the course of COVID19-ARDS. In an observational study including 53 COVID19-ARDS patients, patients received the bradykinin-2-receptor antagonist (B2RAg) icatibant. After icatibant substitution, respiratory rate in COVID19-ARDS reduced by a maximum of 32% (24.9/min to 16.8/min) with a concomitant reduction in oxygen substitution by 59% (6.1 LO<sub>2</sub>/min to 2.5 LO<sub>2</sub>/min). The data show that the use of icatibant in the early phase of COVID19-ARDS is suitable to stabilize pulmonary gas exchange. Furthermore, early icatibant substitution seems to be able to reduce the rate of necessary invasive ventilation in COVID19-ARDS. Observational data suggest that inhibition of bradykinin signalling leads to stabilization of lung function in SARS-CoV2-associated ARDS. Further prospective placebo-controlled studies are needed to investigate the impact of the kallikrein-kinin system on the development of COVID19-ARDS in vivo.</p>
Labelled Arabidopsis dataset for testing membrane segmentation models
<p>Labels of 3D dataset of confocal imaged arabidopsis for testing segmentation models.</p>
UV-VIS Spectra Activated Droplet Sorting for Label-Free Chemical Identification and Collection in Droplets
<p>Data underlying the figures in the publication “UV-VIS Spectra Activated Droplet Sorting for Label-Free Chemical Identification and Collection in Droplets”, published in <em>Analytical Chemistry, </em><strong>2021</strong>.</p> <p>Table of contents:</p> <p><strong>1. Fig2_BSA_calibration_2000us</strong>; Excel file containing the BSA UV-VIS spectra corresponding to <em>Figure 2</em>. It demonstrates the calibration of the UV-VIS in-droplet measurement. Spectroscopy settings: 2000 us integration time and 200 nm to 800 nm wavelength range. Samples: PBS (control), 500 uM BSA, 250 uM BSA, 100 uM BSA, 50 uM BSA, and 10 uM BSA.</p> <p><strong>2. Fig3_Data</strong>; Excel file containing the UV-VIS time-lapse data for high-throughput droplet measurements used in all subfigures of <em>Figure 3</em>. <em>Fig3data.csv</em> is a semi-colon separated csv file for UV-VIS measurements collected over ~30 minutes. Saved wavelengths include 250, 280, 300, 311, 315, 400, 500, and 600 nm. An integration time for the spectrometer of 500 us was used.</p> <p><strong>3. Fig4_C_Postsorting and Fig4_C_Presorting</strong>; Overlaid bright field & fluorescent images of droplets containing E. coli expressing gfp microcolonies before and after droplet sorting.</p> <p><strong>4. Fig4ABD_Data</strong>; Zip. archive containing the experimental data for <em>Figure 4</em>. Interaction of polymersome-based melanosome mimics with HaCaT cells. (A) Cell proliferation assay showing the non-toxicity of different polymersomes encapsulating dopamine and Tyrosinase (dashed purple), L-DOPA and</p> <p><strong>5. Fig5A_Combined Data</strong>; Excel file containing the UV-VIS spectra for <em>Figure 5A</em>. Separate sheets contain spectra for the 3 conditions: empty droplet, mutant (ergothionase activity negative) droplets, and wild type (positive) droplets. UV-VIS range from 200 nm to 1000 nm.</p> <p><strong>6. Fig5B_Ergothionase assay_wild type mutant mix</strong>; Excel file containing the UV-VIS time-lapse data for high-throughput droplet measurements used in <em>Figure 5B</em>.</p> <p>“Fig5B_Ergothionase assay_wild type mutant mix.csv” is a semi-colon separated csv file. Wavelengths 280, 311, 400, and 600 nm are saved. An integration time of 2000 ms was used.</p> <p>“Fig5B_Ergothionase assay_wild type mutant mix_settings.conf” is a configuration file for the spectrophotometer used for this measurement. It describes all spectrometer settings used in the droplet sorting process.</p> <p><strong>7. Fig5C_Combined Data</strong>; Excel file containing the 311 nm absorbance data of <em>Figure 5C</em>; from droplets before and after droplet sorting. The data from both conditions are separated as sheets within the file. An integration time of 2000 ms was used for these measurements.</p> <p><strong>8. SI_Absorbance_by_Geometry</strong>; Excel file containing the data used in <em>Figure S1</em> to test different UV-VIS detection region geometries.</p>
Figure 2 from: Drinkwater R, Cubey R, Haston E (2014) The use of Optical Character Recognition (OCR) in the digitisation of herbarium specimen labels. PhytoKeys 38: 15-30. https://doi.org/10.3897/phytokeys.38.7168
Figure 2 - Box plot of Complete and Partial Protocol results. R1C – Random 1 complete; R1P – Random 1 Partial; CollC – Collector only Complete; CollP – Collector only Partial; CouC – Country only Complete; CouP – Country only Partial; CCC – Collector & Country Complete; CCP – Collector & Country Partial; OCRC – Collector & Country OCR Complete; OCRP – Collector & Country OCR Partial; R2C – Random 2 Complete; R2P – Random 2 Partial.
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.