Journal: Investigative Ophthalmology & Visual Science

Article Title: The Relationship Between Visual Sensitivity and Eccentricity, Cone Density and Outer Segment Length in the Human Foveola

doi: 10.1167/iovs.62.9.31

Figure Lengend Snippet: ISETBio model testing the impact of cone density and OS length. ( A ) The ISETBio model evaluated the threshold photons to elicit a certain number of isomerizations, fitted for 0.01 D, 0.03 D, and 0.05 D residual defocus. The simulation revealed only a small influence of cone density and therefore spacing on sensitivity thresholds (m = –0.010 and ρ = –0.90 with 0.03 D), too small to explain the observations. ( B ) To test the influence of OS length and therefore optical density on sensitivity, we fed the observed range of OS lengths (25–40 µm) in our ISETBio model, which predicted a strong impact of different OS lengths on thresholds ( m = –0.008 and ρ = –0.99 with 0.03 D). ( C ) The pooled data of the rescaled thresholds, from which the OS length and density influence was removed (see Methods), against the distance from the participant's PRL ( Fig. 4 ). The dotted line in A and B represent the linear regression introduced in .

Article Snippet: To independently model the impact of the biophysical properties of the cones, such as cone diameter, OS length, and cone class, on sensitivity thresholds, the Image Systems Engineering Toolbox for Biology (ISETBio) for MATLAB , was used.

Techniques:

Journal: Investigative Ophthalmology & Visual Science

Article Title: The Relationship Between Visual Sensitivity and Eccentricity, Cone Density and Outer Segment Length in the Human Foveola

doi: 10.1167/iovs.62.9.31

Figure Lengend Snippet: Possible sources of threshold variability. ( A ) We used the cone maps to model the light catch for each cone at the target site. The left two panels show two different test sites of P2, with a similar light catch situation. The observed thresholds for these test sites differed significantly ( P = 0.03, Mann–Whitney U test; n = 4). The right two panels show two different test sites of P4, with different light catch situations. In the first condition, three cones are supposed to catch the same number of photons, whereas in the second condition the major portion of stimulus photons are being caught by a single cone. The observed thresholds for these test sites differ insignificantly ( P = 0.49, Mann–Whitney U test; n = 4). ( B ) The data pooled across all participants. Small light catch numbers indicate a three-cone position, and high numbers a single-cone center position. Example datasets shown in A are highlighted with filled symbol s . There was no significant correlation between observed thresholds and stimulus delivery condition. ( C ) This observation was confirmed by an ISETBio model testing the influence of stimulus position on the number of isomerizations. The model showed a maximal change of 0.1 log10 isomerizations for different stimulus positions. ( D ) The ISETBio model tested the influence of different cone class compositions at the test site. This model does not contain any inter-cone class inhibition and therefore shows that only a slight increase of isomerizations if solely L-cones were activated. The error bars in C and D indicate the ISETBio simulated retinal noise.

Article Snippet: To independently model the impact of the biophysical properties of the cones, such as cone diameter, OS length, and cone class, on sensitivity thresholds, the Image Systems Engineering Toolbox for Biology (ISETBio) for MATLAB , was used.

Techniques: MANN-WHITNEY, Inhibition

Journal: Microorganisms

Article Title: State-of the-Art Constraint-Based Modeling of Microbial Metabolism: From Basics to Context-Specific Models with a Focus on Methanotrophs

doi: 10.3390/microorganisms11122987

Figure Lengend Snippet: GSM models constructed to investigate metabolism of C1-utilizing bacteria. Models in the table are given in chronological order.

Article Snippet: Methylomicrobium album BG8 , iJV806 , 803 , 1358 , 1367 , KBase COBRA Toolbox Cobrapy KEGG CycleFreeFlux [ ] , [ ] , 27% , 53.52%.

Techniques: Construct, Bacteria, Microscopy, Combined Bisulfite Restriction Analysis Assay