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opencc-by-4.0Aug 2024View details →

Processed CODEX Datasets from - Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens

This entry provides access to processed CODEX data files of three studies analyzed in the article "Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens". Details of datasets can be found in the Methods section of the article. For each dataset: <ul> <li>A comma-separated values (CSV) file containing metadata of regions is included</li> <li>A zip file containing multiple CSV files is included: <ul> <li>`{region_id}.cell_data.csv`, a table containing three columns: "CELL_ID", "X", and "Y". This table provides centroid locations for all cells segmented in this region.</li> <li>`{region_id}.expression.csv`, a table containing multiple columns: "CELL_ID", "DAPI", "CD45", etc. This table provides detailed protein biomarker expression quantified and normalized for all cells in this region.</li> <li>`{region_id}.cell_types.csv`, a table containing two columns: "CELL_ID" and "CELL_TYPE". This table provides cell type annotations for all cells in this region.</li> <li>`{region_id}.cell_features.csv`, a table containing two columns: "CELL_ID" and "SIZE". This table provides morphology descriptors (only containing cell size for these studies) for all cells in this region.</li> </ul> </li> </ul> These data files are also available through the Enable Medicine Public Study page: <a href="https://app.enablemedicine.com/portal/atlas-library/studies/92394a9f-6b48-4897-87de-999614952d94?sid=1168">https://app.enablemedicine.com/portal/atlas-library/studies/92394a9f-6b48-4897-87de-999614952d94?sid=1168</a>. Raw multiplexed immunofluorescence images will be accessible through the visualizer app of Enable Medicine Portal. Codes for this study are stored in <a href="https://gitlab.com/enable-medicine-public/space-gm">https://gitlab.com/enable-medicine-public/space-gm</a>. Please direct all further questions and/or issues to the gitlab repository or lead contact (A.E.T.).

opencc-by-4.0Apr 2023View details →

Fig. 2. Typical Spirurina type X in Molecular characterization of the parasitic nematode genus Crassicauda; larvae parasitic on the firefly squid and adults on beaked whales off the coast of Japan

Fig. 2. Typical Spirurina type X larva. (A) whole body, (B) head, and (C) tail.

opencc-by-4.0Aug 2023View details →

Fig. 2 in Molecular detection and characterization of a novel Theileria genotype in Dama Gazelle (Nanger dama)

Fig. 2. The clade credibility values of phylogram generated from bayesian analysis.

opencc-by-4.0Jul 2024View details →

Characterization of extended defects in 2D materials using aperture-based dark-field STEM in SEM

This is the raw data for the manuscript: Characterization of extended defects in 2D materials using aperture-based dark-field STEM in SEM   A readme file containing all descriptions can be found in the main folder.    Abstract: Quantitative diffraction contrast analysis with defined diffraction vectors is a wellestablished method in TEM for studying defects in crystalline materials. A comparable transmission techniques is however not available in the more widely used SEM platforms. In this work, we transfer the aperture-based dark-field imaging method from the TEM to the SEM, thus enabling quantitative diffraction contrast studies at lower voltages in SEM. This is achieved in STEM mode by inserting a custom-made aperture between the sample and the STEM detector and centering the hole on a desired reflection. To select individual reflections for dark-field imaging, we use our Low Energy Nanodiffraction (LEND) setup [Schweizer et al., Ultramicroscopy 213, 112956 (2020)], which captures transmission diffraction patterns from a fluorescent screen positioned below the sample. The aperture-based dark-field STEM method is particularly useful for studying extended defects in 2D materials, where (i) stronger diffraction at the lower voltages used in SEM is advantageous, but at the same time (ii) two-beam conditions cannot be established, making quantitative diffraction contrast analysis with standard bright-field and annular dark-field detectors impossible. We demonstrate the method by studying basal plane dislocations in bilayer graphene, which have attracted considerable research interest due to their exceptional structural and electronic properties. Direct comparison of results obtained on identical dislocations by the established TEM method and by the new aperture-based dark-field STEM method in SEM shows that a reliable Burgers vector analysis is possible by  applying the wellknown g·b=0 invisibility criterion. We further use the LEND setup to acquire 4D-STEM data and show that the virtual dark-field images match well with those in aperturebased dark-field STEM images for reliable Burgers vector analysis.

opencc-by-4.0Sep 2022View details →

Figure 1 in Isolation and characterization of Klebsiella oxytoca from the rhizosphere of Lotus corniculatus and its biostimulating features

Figure 1. Pure colonies of the LCK121 strain from the rhizosphere of L. corniculatus.

Figure 1 in Spectral characterization and biological evaluation of biomolecules from the peels of three orange fruits: a comparative study

Figure 1. Schematic representation of experimental protocol.

Figure 9 in Spectral characterization and biological evaluation of biomolecules from the peels of three orange fruits: a comparative study

Figure 9. FT-IR spectroscopy of RM of African Navel orange peel.

Figure 10 in Spectral characterization and biological evaluation of biomolecules from the peels of three orange fruits: a comparative study

Figure 10. The dose-response curve of RM of orange peels against MCF-7 cells.

Figure 7 in Spectral characterization and biological evaluation of biomolecules from the peels of three orange fruits: a comparative study

Figure 7. FT-IR spectroscopy of RM of Valencia orange peel.

opencc-by-4.0Jul 2024View details →

Flow Cytometry Data from "Bacterial cell surface characterization by phage display coupled to high-throughput sequencing"

This record contains the flow cytometry data from the manuscript "Bacterial cell surface characterization by phage display coupled to high-throughput sequencing." Files are in <a href="https://docs.flowjo.com/flowjo/advanced-features/fj-acs/">Archive Cytometry Standard (ACS) format</a> . Each <code>.acs</code> file is a zip container which holds both the raw <code>.fcs</code> files and a FlowJo workspace (<code>.wsp</code>) file. Keywords in the workspace file identify which primary antibody (<code>primary</code>) was used and which cell genotype (<code>strain</code>) was used for each sample. The workspace also encodes the gating scheme and compensation matrix applied to each sample. Plots in the manuscript are exported from Layout views in the workspace.

opencc-by-4.0Sep 2024View details →

Particle displacement characterization during gas replacement of hydrate-bearing sediment

Text S1 is uploaded with name “Polymerization analysis.txt”. Detailed method information includes polymerization analysis. (Figure 5). Movie S1 is uploaded with name “Movie S1.gif”. Detailed information includes longitudinal cross-sectional X-ray CT images of the HBS.

opencc-by-4.0Sep 2024View details →

Characterization of metal-removing Mn oxides at a coal mine drainage treatment site in Glasgow, PA

Dataset for: Characterization of metal-removing Mn oxides at a coal mine drainage treatment site in Glasgow, PA Includes the following: XRD, XAFS, FTIR, Raman, ICP-OES, EDS

opencc-by-4.0Sep 2024View details →

Characterization of Patient Activation Among Childhood Cancer Survivors in the St. Jude Lifetime Cohort (SJLIFE)

This dataset corresponds to a manuscript titled "Characterization of Patient Activation Among Childhood Cancer Survivors in the St. Jude Lifetime Cohort (SJLIFE) which can be found in the journal Cancers.

Table 2 in Obtainment and characterization of digestive aspartic proteases from the fish Caranx hippos (Linnaeus, 1766)

Table 2. Effect of enzyme inhibitors and metal ions on the proteolytic activity of EE.<table><tbody><tr><th>Chemical Agent</th><th>Residual Activity (%)</th><th>Inhibition (%)</th></tr></tbody><tbody><tr><th>Control</th><td>100 ± 4.19a*</td><td>0</td></tr><tr><th>DTT</th><td>104 ± 3.25b</td><td>0</td></tr><tr><th>Pepstatin A</th><td>0c</td><td>100</td></tr><tr><th>Pb2+</th><td>85 ± 0.10d</td><td>15</td></tr><tr><th>Mg2+</th><td>87 ± 3.35e</td><td>13</td></tr><tr><th>Al3+</th><td>89 ± 1.20f</td><td>11</td></tr><tr><th>Mn2+</th><td>90 ± 2.05g</td><td>10</td></tr><tr><th>K+</th><td>91 ± 2.55h</td><td>9</td></tr><tr><th>Hg2+</th><td>94 ± 0.72i</td><td>6</td></tr><tr><th>Cd2+</th><td>97 ± 2.16j</td><td>3</td></tr><tr><th>Cu2+</th><td>98 ± 5.51k</td><td>2</td></tr><tr><th>Ca2+</th><td>101 ± 1.08l</td><td>0</td></tr></tbody></table>

Table 3 in Phytochemical characterization, and antioxidant and antibacterial activities of the hydroethanolic extract of Anadenanthera peregrina stem bark

Table 3. Diameter of the inhibitory zone of the hydroethanolic extract of Anadenanthera peregrina stem bark against Staphylococcus aureus (ATCC 25923) and Escherichia coli (ATCC 25922).<table><tbody><tr><th></th><th>A. peregrina extract concentration</th><th></th><th></th></tr></tbody><tbody><tr><th>Strain</th><td></td><td></td><td></td><td>C +</td><td>C -</td></tr><tr><th></th><td>50 µL</td><td>100 µL</td><td>200 µL</td><td></td><td></td></tr><tr><th>E. coli</th><td>-</td><td>-</td><td>-</td><td>29 mm</td><td>-</td></tr><tr><th>S. aureus</th><td>10 mm</td><td>16 mm</td><td>20 mm</td><td>35 mm</td><td>-</td></tr></tbody></table>

Table 2 in Phytochemical characterization, and antioxidant and antibacterial activities of the hydroethanolic extract of Anadenanthera peregrina stem bark

Table 2. Physicochemical properties,antioxidant activity,and total phenolic content of the hydroethanolic extract of A.peregrina stem bark.<table><tbody><tr><th>Sample</th><th>pH</th><th>Density (g cm 3)</th><th>DPPH (IC 50)</th><th>Total Phenolics (g GAE 100 g- 1)</th></tr></tbody><tbody><tr><th>A. peregrina extract</th><td>5.21 ± 0.01</td><td>0.956</td><td>44.13 mg mL-1</td><td>6.40 ± 0.08</td></tr></tbody></table>

Table 1 in Phytochemical characterization, and antioxidant and antibacterial activities of the hydroethanolic extract of Anadenanthera peregrina stem bark

Table 1. Phytochemical prospecting of the main secondary metabolite groups of the hydroethanolic extract of A. peregrina stem bark.<table><tbody><tr><th>Secondary metabolite</th><th>Hydroethanolic extract of A. peregrina</th></tr><tr><th>Cardiac glycosides</th></tr></tbody><tbody><tr><th>Kedd reagent test</th><td>++</td></tr><tr><th>Keller–Kiliani reagent test</th><td>++</td></tr><tr><th>Baljet reagent test</th><td>-</td></tr><tr><th>Raymond–Marthoud reagent test</th><td>+++</td></tr><tr><th>Alkaloids</th></tr><tr><th>Libermann–Bouchardat reagent test</th><td>-</td></tr><tr><th>Wagner reagent test</th><td>-</td></tr><tr><th>Mayer’s reagent test</th><td>-</td></tr><tr><th>Organic acids</th></tr><tr><th>Pascová reagent test</th><td>++</td></tr><tr><th>Reducing sugars</th></tr><tr><th>Fehling reagent test</th><td>++</td></tr><tr><th>Non-reducing sugars</th></tr><tr><th>Fehling + HCl test</th><td>-</td></tr><tr><th>Coumarins</th></tr><tr><th>UV light 254 and 365 nm</th><td>+</td></tr><tr><th>Saponins</th></tr><tr><th>Foamy</th><td>-</td></tr><tr><th>Haemolytic</th><td>+++</td></tr><tr><th>Polysaccharides</th></tr><tr><th>Reactive lugol</th><td>-</td></tr><tr><th>Phenols</th></tr><tr><th>FeCl 3 Tannins</th><td>+++</td></tr><tr><th>FeCl3 Flavonoids</th><td>Gr</td></tr><tr><th>Pb(C2 H 3O2)2</th><td>++</td></tr><tr><th>Purines</th><td>-</td></tr><tr><th>Catechins</th><td>+++</td></tr><tr><th>Benzoquinone derivatives</th><td>+++</td></tr><tr><th>Depsids and depsidones</th><td>+++</td></tr><tr><th>Steroids and triterpenoids</th><td>-</td></tr><tr><th>Sesquiterpenolactones</th><td>-</td></tr></tbody></table>

Table 1 in Obtainment and characterization of digestive aspartic proteases from the fish Caranx hippos (Linnaeus, 1766)

Table 1. Purification of acidic digestive proteases from the stomach of C. hippos fish.<table><tbody><tr><th>Process step</th><th>* Total Activity (U)</th><th>Total Protein (mg)</th><th>Specific activity (mU. mg- 1)</th><th>Purification (fold)</th><th>Yield (%)</th></tr></tbody><tbody><tr><th>Crude Extract</th><td>1,546 ± 50</td><td>3,523± 102</td><td>439</td><td>1</td><td>100</td></tr><tr><th>EE</th><td>764 ± 36</td><td>1,103 ± 75</td><td>693</td><td>1.6</td><td>49.4</td></tr></tbody></table>

opencc-by-4.0Oct 2020View details →

Table 2 in Molecular characterization of the re-emerging West Nile virus in avian species and equids in Israel, 2018, and pathological description of the disease

Table 2 Pathological findings and calculated viral genome copies of WNV-positive avian species<table><thead><tr><th>Bird no.</th><th>Species</th><th>Common name</th><th>Sequencing</th><th>Isolation</th><th>Tissues tested and calculated target copies per reaction</th></tr></thead><tbody><tr><th>AV148</th><td>Larus michahellis</td><td>Yellow legged seagull</td><td>Yes</td><td>Yes</td><td>Cloacal swab: 5.8×10 6; brain: 2.8×10 6; kidney: 1.2×10 7</td></tr><tr><th>AV152</th><td>Anser anser</td><td>Domesticated goose</td><td>Yes</td><td>Yes</td><td>Cloacal swab:9.7×10 5; brain 3.3× 10 5; kidney: 4700; eye swab: 1.3× 10 6</td></tr><tr><th>AV153</th><td>Anser anser</td><td>Domesticated goose</td><td>Yes</td><td>Yes</td><td>Cloacal swab: 6.8×10 5; brain: 1.2×10 7; viscera: 6.8× 10 5</td></tr><tr><th>AV156</th><td>Asio otus</td><td>Long eared owl</td><td>Yes</td><td>No</td><td>Cloacal swab: 6.8×10 5; brain: 2.6×10 4; viscera: 4.9× 10 7</td></tr><tr><th>AV157</th><td>Asio otus</td><td>Long eared owl</td><td>Yes</td><td>No</td><td>Cloacal swab: 6.8×10 5; brain: 5800; kidney: 360; eye swab: 50</td></tr><tr><th>AV169</th><td>Corvus cornix</td><td>Hooded crow</td><td>Yes</td><td>No</td><td>Cloacal swab: 4700; blood: 1100</td></tr><tr><th>AV178</th><td>Phasianus colchicus</td><td>Common pheasant</td><td>No</td><td>No</td><td>Brain: 4700</td></tr><tr><th>1459</th><td>Corvus cornix</td><td>Hooded crow</td><td>Yes</td><td>No</td><td>Cloacal swab: 2300</td></tr><tr><th>1505</th><td>Corvus cornix</td><td>Hooded crow</td><td>Yes</td><td>No</td><td>Brain: 4700</td></tr><tr><th>1514</th><td>Corvus cornix</td><td>Hooded crow</td><td>Yes</td><td>Yes</td><td>Brain: 9.9× 10 7</td></tr></tbody></table>