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Fig. 3 in Sensory Structures On The Antenniform Legs Of Whip Spider Phrynichus Phipsoni (Arachnida, Amblypygi) From The Indian State Of Goa: Scanning Electron Microscopic Elucidation
Fig. 3. Sensory assembly on the whip (Antenniform leg) of Phrynichus phipsoni from Goa, India: 8 — rod sensilla within groove, 9 — plate organ, 10 — slit sensilla, 11 — trichobothria, 12 — sockets of trichobothria
Fig. 1 in Sensory Structures On The Antenniform Legs Of Whip Spider Phrynichus Phipsoni (Arachnida, Amblypygi) From The Indian State Of Goa: Scanning Electron Microscopic Elucidation
Fig. 1. Resting captive specimen of whip spider Phrynichus phipsoni (Pocock, 1894). Note the whip like configuration, position, and length of the antenniform first pair of non-ambulatory leg. The various segments have been marked for reference: 1 — vertically raised femur; 2 — femur-patella-tibia joint; 3 — tibia; 4 — tibio-tarsal articulation; 5 — tarsus; 6 — distal tarsal tip.
Fig. 2 in Sensory Structures On The Antenniform Legs Of Whip Spider Phrynichus Phipsoni (Arachnida, Amblypygi) From The Indian State Of Goa: Scanning Electron Microscopic Elucidation
Fig. 2. Sensory assembly on the whip (Antenniform leg) of Phrynichus phipsoni from Goa, India: 1 — terminal tarsal claw; 2 — bristles; 3 — leaf like sensilla; 4 — pore sensilla; 5 — club sensilla; 6 — tarsal organ; 7 — pit organ.
Figure 14 in Mastiglanis durantoni from French Guyana, a second species in the genus (Siluriformes: Heptapteridae), with a CT scan survey of phylogenetically-relevant characters
Figure 14. – Schematic illustrations of the occipital process and part of posterior cranial fontanel in species of Mastiglanis. A: Mastiglanis durantoni, MZUSP 118119, paratype; B-G: M. asopos, B: MZUSP 93307 (Rio Negro basin), C: MZUSP 81411 (Rio Negro basin), D: MZUSP 86958 (Rio Preto da Eva basin), E-G: MZUSP 97150 (Rio Xingu basin). Scale bars = 1 mm.
Figure 13 in Mastiglanis durantoni from French Guyana, a second species in the genus (Siluriformes: Heptapteridae), with a CT scan survey of phylogenetically-relevant characters
Figure 13. – CT scan image of posterior portion of skull and anterior part of vertebral column of Mastiglanis durantoni, MZUSP 118118, paratype, ventral view. Anterior to top. Abbreviations: bo, basioccipital; ex, exoccipital; fr, frontal; pa, parasphenoid; par, parapophysis; plr, pleural rib; pro, prootic; pt, pterotic; ptr, pterosphenoid; pts, posttemporo-supracleithrum; sph, sphenotic; tp4a, anterior ramus of transverse process of vertebra 4; tp4p, posterior ramus of transverse process of vertebra 4; tp5, transverse process of vertebra 5; tr, tripus; trs, transscapular process; vc5-7, vertebral centra 5 to 7.
Figure 12 in Mastiglanis durantoni from French Guyana, a second species in the genus (Siluriformes: Heptapteridae), with a CT scan survey of phylogenetically-relevant characters
Figure 12. – CT scan image of suspensorium of Mastiglanis durantoni, MZUSP 118118, paratype, lateral view. Anterior to left. Abbreviations: ent, entopterygoid; hy, hyomandibula; io, interopercle; mt, metapterygoid; op, opercle; po, preopercle; qu, quadrate; sbpo, subpreopercle; spo, suprapreopercle.
Figure 9 in Mastiglanis durantoni from French Guyana, a second species in the genus (Siluriformes: Heptapteridae), with a CT scan survey of phylogenetically-relevant characters
Figure 9. – Live specimen of Mastiglanis durantoni n. sp, lateral view, French Guiana (photo by P.Y. Le Bail). Specimen not preserved.
Figure 6 in Mastiglanis durantoni from French Guyana, a second species in the genus (Siluriformes: Heptapteridae), with a CT scan survey of phylogenetically-relevant characters
Figure 6. – CT scan image of premaxilla of Mastiglanis durantoni, MZUSP 118118, paratype. A: Dorsal view; B: Ventral view. Anterior to top.
Figure 7 in Mastiglanis durantoni from French Guyana, a second species in the genus (Siluriformes: Heptapteridae), with a CT scan survey of phylogenetically-relevant characters
Figure 7. – CT scan image of lower jaw of Mastiglanis durantoni, MZUSP 118118, paratype, lateral view, left side, anterior to left. Abbreviations: aa, anguloarticular; den, dentary; lsp, opening for latero-sensory pore; tr, trabeculae.
Figure 5 in Mastiglanis durantoni from French Guyana, a second species in the genus (Siluriformes: Heptapteridae), with a CT scan survey of phylogenetically-relevant characters
Figure 5. – CT scan image of anterior portion of neurocranium of Mastiglanis durantoni, MZUSP 118118, paratype, dorsal view. Abbreviations: fr, frontal; le, lateral ethmoid; me, mesethmoid.
Figure 3 in Mastiglanis durantoni from French Guyana, a second species in the genus (Siluriformes: Heptapteridae), with a CT scan survey of phylogenetically-relevant characters
Figure 3. – Heads in ventral view, showing difference in upper-jaw lengths. A: Mastiglanis durantoni, n. sp., paratype, MZUSP 118118, 46.9 mm SL; B: Mastiglanis asopos, paratype, MZUSP 7446, 43.9 mm SL.
Figure 2 in Mastiglanis durantoni from French Guyana, a second species in the genus (Siluriformes: Heptapteridae), with a CT scan survey of phylogenetically-relevant characters
Figure 2. – Mastiglanis durantoni, n. sp., holotype, MNHN 2015- 244, 63.7 mm SL. (A) Dorsal and (B) ventral views of head.
Figure 1 in Mastiglanis durantoni from French Guyana, a second species in the genus (Siluriformes: Heptapteridae), with a CT scan survey of phylogenetically-relevant characters
Figure 1. – Mastiglanis durantoni, n. sp., holotype, MNHN 2015- 244, male, 63.7 mm SL, Tampok River, tributary to Maroni stream, French Guiana. Lateral view.
Metadata for Confocal Laser Scanning Microscopy Images of Monoculture and Mixed-Species Biofilms Formed by Bacterial Isolates of Dairy Origin
<p>In a project conducted by ILVO (Belgium), a wide variety of bacterial species were recovered from the surface of a dairy pasteurizer after cleaning and disinfection (C&D). The biofilm-forming ability of these bacteria was determined in both single-species and various mixed-culture combinations. Some work related to this study has been published in Frontiers: "Synergistic interactions in multispecies biofilm combinations of bacterial isolates recovered from diverse food processing industries". Bacterial species were mixed in different combinations to assess the community biofilm mass and growth dynamics of individual species. ILVO and the University of Copenhagen conducted experiments aimed at revealing the structural characteristics and spatial organization of bacterial species within different mixed-species biofilms. In our research, we employed oligonucleotide FISH probes, each conjugated with a unique fluorescent dye: Cy5 for <em>Stenotrophomonas rhizophila</em> (B68), Cy3 for <em>Bacillus licheniformis</em> (B65), and FAM for <em>Microbacterium lacticum</em> (B30). C1 combination refers to a combination containing B68 and B30. </p> <p><span>Images of the biofilms formed on the coupons were captured using a confocal laser scanning microscope (LSM 800, Zeiss) with a Plan-Apochromat 63x/1.4 oil-immersion objective. Z-stacks were recorded to obtain three-dimensional (3D) images. Standard images were made with an image size of 1024 × 1024 pixels, corresponding to physical dimensions of 101.4 × 101.4 μm for each image. For each image, two separate channels were applied to detect any dual-species combination using a flexible detector (GaAsP-PMT) in the LSM 800 system. Representative 3D views of images were generated using the 3D model function in the ZEN system 3.7.</span></p> <p>Biofilms were grown in BHI for 24 h on plastic coupons. The samples were imaged at different time points: 6h, 12h, 18h and 24h. Each samples had three replicates and for each replicate imaging was performed from 3-6 different positions. </p> <p>Details of the oligonucleotide probes are given below:</p> <table> <tbody> <tr> <td> <p><strong><span>Name of the species</span></strong></p> </td> <td> <p><strong><span>Sequences</span></strong></p> </td> <td> <p><strong><span>Max. excitation</span></strong></p> </td> <td> <p><strong><span>Max. emission</span></strong></p> </td> <td> <p><strong><span>Fluorophores</span></strong></p> </td> </tr> <tr> <td> <p><em><span>S. rhizophila</span></em><span> B68<span> </span></span></p> </td> <td> <p><span>GGGCCTTTACCCCGCCA</span></p> </td> <td> <p><span>649 nm</span></p> </td> <td> <p><span>670 nm</span></p> </td> <td> <p><span>Cy5</span></p> </td> </tr> <tr> <td> <p><em><span>B. licheniformis</span></em><span> B65</span></p> </td> <td> <p><span>ACCGCCTGCGCGCGCTT</span></p> </td> <td> <p><span>550 nm</span></p> </td> <td> <p><span>570 nm</span></p> </td> <td> <p><span>Cy3</span></p> </td> </tr> <tr> <td> <p><em><span>M. lacticum</span></em><span> B30</span></p> </td> <td> <p><span>CCCCACCCTTTCGCTCC</span></p> </td> <td> <p><span>495 nm</span></p> </td> <td> <p><span>520 nm</span></p> </td> <td> <p><span>FAM</span></p> </td> </tr> </tbody> </table>
Data and code for figures: Design, fabrication and characterization of kinetic-inductive force sensors for scanning probe applications
<p>This directory contains the datasets, code (if applicable) for measurement libraries, data processing and figure generation for the research article "Design, fabrication and characterization of kinetic-inductive force sensors for scanning probe applications", Beilstein J. Nanotechnol. 2024, 15, 242-255.</p>
Quick scan 'Locations for highest-potential greenhouse development in the world'
<p><br>Forecast studies show an increasing demand for greenhouses worldwide, as governments encourage local, safe and sustainable food production. Climate change, scarcity of water and other key resources are adding to the trend towards greenhouses.</p> <p>This project shows a world map of the highest suitability for greenhouses, broken down by mid-tech and high-tech greenhouses. This is done by performing a quick scan, which means synthesis and application of existing knowledge and data. Of the countries with the highest potential, more detailed maps are shown.</p> <p>This paper is commissioned by the Netherlands Enterprise Agency (Rijksdienst voor Ondernemend Nederland (RVO)) and funded by the European Community. Dutch Green Delta (DGD) and some of their partners contributed with their expertise and experiential knowledge.</p> <p>The total area of covered crops is very difficult to indicate because there are no clear definitions and hence no uniform data. This study estimates approximately 700,000 hectares of protected horticulture worldwide, of which approximately 53,000 hectares are high-tech greenhouses. This is in line with other literature sources. China provides the greatest uncertainty in data. </p> <p>Based on the analysis of area suitability, USA is the country with the highest relative score for high-tech, followed by France, Germany, UK and Ukraine. For mid-tech, the USA and France are also the countries with the highest relative score, followed by India, Libya, and Brazil.<br>Based on the highest market opportunities for greenhouses explored for the production and sales of tomato, the top 5 countries are Germany, the Netherlands, France, the USA, and Spain.<br>Based on the presence of existing greenhouses, Mexico is the country with the highest surface for high-tech, followed by the Netherlands, Turkey, Belgium and Germany. For mid-tech surfaces the top 5 countries are China, Turkey, Spain, Republic of Korea, and Egypt.</p> <p>Based on the combination of the 3 analyses above, the top 10 countries with the strongest expected growth in high-tech greenhouses are: the USA, France, Spain, Germany, Poland, the Netherlands, Italy, Japan, Turkey, and China. When we differentiate these countries in 3 categories we identify:<br>• Emerging countries: the USA, Poland, Italy, Saudi Arabia, and the UK.<br>• Conversion countries from mid-tech to high-tech greenhouses: Spain, France, China, Japan, India, and South Korea.<br>• Countries that already have areas of high-tech greenhouses: Germany, the Netherlands, Turkey, Belgium, and Mexico.</p> <p>The whitepaper, PowerPoint, all maps, and PowerBI datafiles generated by this project can be downloaded below. </p>
Data from: Deep mutational scanning of HBV reveals a mechanism for cis preferential reverse transcription
<p>Hepatitis B virus (HBV) is a small double-stranded DNA virus that chronically infects 296 million people. Over half of its compact genome encodes protein in two overlapping reading frames, and during evolution, multiple selective pressures can act on shared nucleotides. This study combines an RNA-based HBV cell culture system with deep mutational scanning to uncouple <em>cis-</em> and <em>trans</em>-acting sequence requirements in the HBV genome. The results support a leaky ribosome scanning model for polymerase translation, provide a fitness map of the HBV polymerase at single nucleotide resolution, and identify conserved prolines adjacent to the HBV polymerase termination codon that stall ribosomes. Further experiments indicated that stalled ribosomes tether the nascent polymerase to its template RNA, ensuring <em>cis</em>-preferential RNA packaging and reverse transcription of the HBV genome.</p>
Supplementary material for: Calibrating coordinate system alignment in a scanning transmission electron microscope using a digital twin.
<h1>Calibrating coordinate system alignment in a scanning transmission electron microscope using a digital twin.</h1> <h2>Supplementary material</h2> <p>This deposition contains supplementary material for a paper on coordinate system calibration in 4D STEM. A preprint of the paper is available at <a href="https://arxiv.org/abs/2403.08538">https://arxiv.org/abs/2403.08538</a>.</p> <h2>Contents</h2> <div> <div><code>20221025_154811.zip</code>: Overfocused 4D STEM test dataset</div> <div> </div> <div><code>overfocus.sif</code>: Apptainer image with complete software stack. <code>apptainer run --writable overfocus.sif</code> to execute. It starts a Jupyterlab instance with two notebooks, one to genreate test data and the other to perform the interactive adjustment. This documents the software version that was used for the figures in the paper.</div> <div> </div> <div><code>requirements.txt</code>: Python package versions of dependencies in <code>overfocus.sif</code>. </div> <div> </div> <div><code>COM - Jupyter Notebook - Google Chrome 2023-01-25 12-40-07_processed.mp4</code>: Screen capture video with explanation of the first live calibration with an early prototype.</div> <div> </div> <div><code>video description.docx</code>: Explanation of the plots and adjustment process in the screen capture video.</div> <div> </div> <div><code>Microscope-Calibration.tar.gz</code>: Repository archive of the software and examples for calibration in the version used in the paper.</div> <div> </div> <div><code>TemGym.tar.gz</code>: Repository archive of TemGym Basic in the version used in the paper.</div> </div>
Figs 16–21 in Redescription of Strombidium coronatum (Leegaard, 1915) Kahl, 1932 (Ciliophora, Spirotricha) based on live observation, protargol impregnation, and scanning electron microscopy
Figs 16–21. Strombidium coronatum, Irish Sea specimens (16–18, scanning electron micrographs; 19–21, protargol impregnation, micrographs of several focal planes were stacked, using the computer program CombineZP from Alan Hadley). 16 – ventrolateral view; 17 – left lateral view showing uniquely shaped peristome, which is roughly triangular in outline and almost flat, extending in the sagittal plane. The extrusomes insert in short oblique rows anteriorly to the girdle kinety; note that some of them are just ejected (arrowhead); 18 – posterior cell portion showing the sharp, longitudinal ridges that have already been illustrated in the original description by Leegaard (1915); 19 – left lateral view of an early divider; 20 – dorsolateral view of an early divider; 21 – ventrolateral view. AP – apical protrusion, BM – buccal membranelles, CM – collar membranelles, DC – distended cell surface, EX – extrusome attachment sites, GK – girdle kinety, MA – macronucleus, OP – oral primordium, VK – ventral kinety. Scale bars: 40 µm (16), 20 µm (17, 19–21), and 10 µm (18).
Fig.ç4.Ec hinoderes ohtsukai sp. nov., paratype, female (ZIHU 3983), scanning electron micrographs. A, Mouth cone, lateral view; B, introvert, lateral view. Abbreviations: oo, outer oral styles; sc, scalids; sp, spinoscalids; tr, trichoscalids. Digits a er the labels refer to introvert ring numbers. in A New Brackish-water Species of Echinoderes (Kinorhyncha: Cyclorhagida) from the Seto Inland Sea, Japan
Fig.ç4.Ec hinoderes ohtsukai sp. nov., paratype, female (ZIHU 3983), scanning electron micrographs. A, Mouth cone, lateral view; B, introvert, lateral view. Abbreviations: oo, outer oral styles; sc, scalids; sp, spinoscalids; tr, trichoscalids. Digits a er the labels refer to introvert ring numbers.
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.