Optical Coherence Tomography: Modeling and Applications

Abstract An analytical model is presented that is able to describe the performance of OCT systems in both the single and multiple scattering regimes simultaneously. This model inherently includes the shower curtain effect, well-known for light propagation through the atmosphere. This effect has been omitted in previous theoretical models of OCT systems. It is demonstrated that the shower curtain effect is of utmost importance in the theoretical description of an OCT system. The analytical model, together with proper noise analysis of the OCT system, enables calculation of the SNR, where the optical properties of the tissue are taken into account. Furthermore, by using the model, it is possible to determine the lateral resolution of OCT systems at arbitrary depths in the scattering tissue. During the Ph.D. thesis project, an OCT system has been constructed, and the theoretical model is verified experimentally using this system. A demonstration of the imaging capabilities of the OCT system is given. Moreover, a novel truereflection OCT imaging algorithm, based on the new OCT model presented in this thesis, is demonstrated. Finally, a theoretical analysis of the Wigner phase-spac

DHA Improves Cognition and Prevents Dysfunction of Entorhinal Cortex Neurons in 3xTg-AD Mice

Defects in neuronal activity of the entorhinal cortex (EC) are suspected to underlie the symptoms of Alzheimer's disease (AD). Whereas neuroprotective effects of docosahexaenoic acid (DHA) have been described, the effects of DHA on the physiology of EC neurons remain unexplored in animal models of AD. Here, we show that DHA consumption improved object recognition (↑12%), preventing deficits observed in old 3xTg-AD mice (↓12%). Moreover, 3xTg-AD mice displayed seizure-like akinetic episodes, not detected in NonTg littermates and partly prevented by DHA (↓50%). Patch-clamp recording revealed that 3xTg-AD EC neurons displayed (i) loss of cell capacitance (CC), suggesting reduced membrane surface area; (ii) increase of firing rate versus injected current (F-I) curve associated with modified action potentials, and (iii) overactivation of glutamatergic synapses, without changes in synaptophysin levels. DHA consumption increased CC (↑12%) and decreased F-I slopes (↓21%), thereby preventing the opposite alterations observed in 3xTg-AD mice. Our results indicate that cognitive performance and basic physiology of EC neurons depend on DHA intake in a mouse model of AD

Application of WGS data for O-specific antigen analysis and <i>in silico </i>serotyping of <i>Pseudomonas aeruginosa </i>isolates

Accurate typing methods are required for efficient infection control. The emergence of whole-genome sequencing (WGS) technologies has enabled the development of genome-based methods applicable for routine typing and surveillance of bacterial pathogens. In this study, we developed the Pseudomonas aeruginosa serotyper (PAst) program, which enabled in silico serotyping of P. aeruginosa isolates using WGS data. PAst has been made publically available as a web service and aptly facilitates high-throughput serotyping analysis. The program overcomes critical issues such as the loss of in vitro typeability often associated with P. aeruginosa isolates from chronic infections and quickly determines the serogroup of an isolate based on the sequence of the O-specific antigen (OSA) gene cluster. Here, PAst analysis of 1,649 genomes resulted in successful serogroup assignments in 99.27% of the cases. This frequency is rarely achievable by conventional serotyping methods. The limited number of nontypeable isolates found using PAst was the result of either a complete absence of OSA genes in the genomes or the artifact of genomic misassembly. With PAst, P. aeruginosa serotype data can be obtained from WGS information alone. PAst is a highly efficient alternative to conventional serotyping methods in relation to outbreak surveillance of serotype O12 and other high-risk clones, while maintaining backward compatibility to historical serotype data

Rotationally acquired four-dimensional optical coherence tomography of embryonic chick hearts using retrospective gating on the common central A-scan

We introduce a new method of rotational image acquisition for four-dimensional (4D) optical coherence tomography (OCT) of beating embryonic chick hearts. The rotational axis and the central A-scan of the OCT are identical. An out-of-phase image sequence covering multiple heartbeats is acquired at every angle of an incremental rotation of the deflection mirrors of the OCT system. Image acquisition is accomplished after a rotation of 180°. Comparison of a displayed live M-mode of the central A-scan with a reference M-mode allows instant detection of translational movements of the embryo. For calculation of 4D data sets, we apply an image-based retrospective gating algorithm using the phase information of the common central A-scan present in all acquired images. This leads to cylindrical three-dimensional data sets for every time step of the cardiac cycle that can be used for 4D visualization. We demonstrate this approach and provide a video of a beating Hamburger and Hamilton stage 16 embryonic chick heart generated from a 4D OCT data set using rotational image acquisition