Journal: RSC Advances

Article Title: Synthetic non-classical luminescence generation by enhanced silica nanophotonics based on nano-bio-FRET

doi: 10.1039/d0ra02939d

Figure Lengend Snippet: Laser fluorescence microscopy of individual small cyanobacteria aggregates: (a) red-green LUT; (b) fire LUT applied; (c) zoomed fire LUT image; and (d) 3D fluorescent surfaces of bacterial tetramers. Laser excitation at 488.0 nm.

Article Snippet: From these nano-biosurfaces, strong luminescent intensities were generated that permitted faster detection and counting with 3D fluorescence plots ( ).

Techniques: Fluorescence, Microscopy

Journal: Biomicrofluidics

Article Title: Solution pH change in non-uniform alternating current electric fields at frequencies above the electrode charging frequency

doi: 10.1063/1.4904059

Figure Lengend Snippet: Field and medium comparison experiments at 5 kHz and 5.5 Vpp. Columns are organized by methanol and water in uniform and nonuniform DEP electric field configurations. Rows are organized by time with t = 0, 8, and 120 s and intensity difference obtained by MATLAB image analysis. Fluorescein intensity changes are apparent in water in both uniform and non-uniform DEP electric field configurations as emphasized in (n) and (o) while negligible changes were observed in methanol in (m) and (p).

Article Snippet: The respective rows from top to bottom are: first row shows 2-D gray scale image averaged pixel by pixel from 5 experimental repeats (a)–(d), the second row is a 3-D mesh image where the z height corresponds to the intensity magnitude (e)–(h), and the third row is a 3-D mesh of the pixel by pixel standard deviation calculated from the 5 experiments (i)–(l). fig ft0 fig mode=article f1 fig/graphic|fig/alternatives/graphic mode="anchored" m1 Open in a separate window FIG. 4. caption a7 (a)–(d) Gray-scale 2-D dye intensity plot at t = 0, 8, 80, and 120 s under 5.5 V pp and 5 kHz. (e)–(h) 3-D MATLAB plot of the same data at the same time points. (i)–(l) Calculated standard deviations of 5 repeats of the data in the first two rows. (m) Diagram illustrating regions examined for intensity analysis. (n) Time dependencies of the regions in (m).

Techniques: Comparison

Journal: Biomicrofluidics

Article Title: Solution pH change in non-uniform alternating current electric fields at frequencies above the electrode charging frequency

doi: 10.1063/1.4904059

Figure Lengend Snippet: (a)–(d) Gray-scale 2-D dye intensity plot at t = 0, 8, 80, and 120 s under 5.5 Vpp and 5 kHz. (e)–(h) 3-D MATLAB plot of the same data at the same time points. (i)–(l) Calculated standard deviations of 5 repeats of the data in the first two rows. (m) Diagram illustrating regions examined for intensity analysis. (n) Time dependencies of the regions in (m). Line intensity (solid green) was utilized for all subsequent analysis.

Article Snippet: The respective rows from top to bottom are: first row shows 2-D gray scale image averaged pixel by pixel from 5 experimental repeats (a)–(d), the second row is a 3-D mesh image where the z height corresponds to the intensity magnitude (e)–(h), and the third row is a 3-D mesh of the pixel by pixel standard deviation calculated from the 5 experiments (i)–(l). fig ft0 fig mode=article f1 fig/graphic|fig/alternatives/graphic mode="anchored" m1 Open in a separate window FIG. 4. caption a7 (a)–(d) Gray-scale 2-D dye intensity plot at t = 0, 8, 80, and 120 s under 5.5 V pp and 5 kHz. (e)–(h) 3-D MATLAB plot of the same data at the same time points. (i)–(l) Calculated standard deviations of 5 repeats of the data in the first two rows. (m) Diagram illustrating regions examined for intensity analysis. (n) Time dependencies of the regions in (m).

Techniques:

Journal: Haematologica

Article Title: Impact of Sox11 over-expression in Ba/F3 cells

doi: 10.3324/haematol.2018.197467

Figure Lengend Snippet: Phenotypical, proliferative and transcriptional changes in Ba/F3 cells upon 72 h of induced Sox11 expression. (A) Western Blot of SOX11 protein expression in Sox11-ON (doxycycline supplemented medium) and Sox11-OFF (control medium) cells at 72 h, detected with the rabbit polyclonal anti-SOX11 antibody HPA000536, Sigma-Aldrich. B) Bright field microscopy images of cell aggregates following 72 h of continuous Sox11 expression (10x), imaged by Nikon Ti-E microscope. C) Sox11-ON cells incorporates less 3H-Thymidine at 72 h of Sox11 induction following a 4 h pulse, as compared to Sox11-OFF cells, measured in counts per minute, error bars represent the standard deviation (P=0.0086, n=3). D) Mean relative absorption measured by XTT (n=3). Metabolic activity is significantly reduced (P=0.0124) in Sox11-ON cells as compared to Sox11-OFF cells. E) Volcano plot representation of transcript level differences by Affymetrix MTA-1 mouse arrays (Microarray data has been made available through the GEO database with accession number GSE108419). Names are shown for the genes with the largest transcript level fold change (log2FC ≥1.3 or ≤−1.3). Blue and red: genes with significantly altered transcript levels in Sox11-ON cells and a fold change below -2 (blue) (FDR q-value ≤0.05 and log2FC ≥−1) or above 2 (red) (FDR q-value ≤0.05 and log2FC ≥1); gray: genes significantly changed at the transcript level (FDR q-value ≤0.05); black: genes with non-significant transcript level changes. F) Expression levels after Sox11 induction in genes specifically expressed at different stages of B-cell development. Only the pro-B restricted genes Id1 and Tal1 had significantly altered transcript levels in Sox11-ON cells (FDR q-value: 0.006 and 0.016, respectively). None of the other investigated pro-B and pre-B cell associated genes were altered at the transcript level. Genes associated with later B-cell developmental stages are shown for comparison. Transcript levels are presented as a gene-wise standardized expression (Z-score). FC: fold change.

Article Snippet: E) Volcano plot representation of transcript level differences by Affymetrix MTA-1 mouse arrays (Microarray data has been made available through the GEO database with accession number GSE108419).

Techniques: Expressing, Western Blot, Microscopy, Standard Deviation, Activity Assay, Microarray

Journal: Journal of Veterinary Internal Medicine

Article Title: Utility of the combined use of 3 serologic markers in the diagnosis and monitoring of chronic enteropathies in dogs

doi: 10.1111/jvim.16132

Figure Lengend Snippet: 3D scatter graphs representations of the seropositivity titers to OmpC (ACA), calprotectin (ACNA), and gliadin‐derived peptides (AGA) obtained from serum samples collected from the different cohorts of dogs enrolled for the field study. Each dot represents the combined marker titer set obtained from the serum sample analysis from each dog enrolled in this analysis. Cohorts are defined by the color of the dots as outlined in the Figure. Black (n = 33) are normal; red (n = 24) non‐IBD; green (n = 157) CE/IBD. The 3‐axes plot can separate graphically each cohort. The algorithm developed can place a given sample into each of the different cohorts based on the 3 input values. CE, chronic enteropathies; IBD, inflammatory bowel disease

Article Snippet: 3D scatter plots were performed with Python Open Source (Plotly Express) built on javascript.

Techniques: Derivative Assay, Marker

Journal: Scientific Reports

Article Title: Small RNA sequencing evaluation of renal microRNA biomarkers in dogs with X-linked hereditary nephropathy

doi: 10.1038/s41598-021-96870-y

Figure Lengend Snippet: 3D principal component analysis (PCA) plots for all canine kidney tissue samples (n = 23), comparing 3–5 affected (XLHN) dogs and 4 controls at each clinical time point (T1, T2, and T3). The x, y, and z axes represent principal components (PC) 1, PC2, and PC3, respectively. The results of CPSS 2.0 were used. (Red: control group; Green: affected group).

Article Snippet: The 3D PCA plots were made using Plotly ( https://plotly.com/r/ ).

Techniques: Control