Abstract
We propose and apply two methods to estimate pupil plane phase discontinuities for two realistic scenarios on the very large telescope (VLT) and Keck. The methods use both phase diversity and a form of image sharpening. For the case of VLT, we simulate the "low wind effect" (LWE) that is responsible for focal plane errors in the spectro-polarimetric high contrast exoplanet research (SPHERE) system in low wind and good seeing conditions. We successfully estimate the simulated LWE using both methods and show that they are complimentary to one another. We also demonstrate that single image phase diversity (also known as phase retrieval with diversity) is also capable of estimating the simulated LWE when using the natural defocus on the SPHERE/differential tip tilt sensor (DTTS) imager. We demonstrate that phase diversity can estimate the LWE to within 30-nm root mean square wavefront error (RMS WFE), which is within the allowable tolerances to achieve a target SPHERE contrast of 10-6. Finally, we simulate 153-nm RMS of piston errors on the mirror segments of Keck and produce NIRC2 images subject to these effects. We show that a single, diverse image with 1.5 waves (peak-to-valley) of focus can be used to estimate this error to within 29-nm RMS WFE, and a perfect correction of our estimation would increase the Strehl ratio of an NIRC2 image by 12%.

Abstract
We build on a long-standing tradition in astronomical adaptive optics (AO) of specifying performance metrics and error budgets using linear systems modeling in the spatial-frequency domain. Our goal is to provide a comprehensive tool for the calculation of error budgets in terms of residual temporally filtered phase power spectral densities and variances. In addition, the fast simulation of AO-corrected point spread functions (PSFs) provided by this method can be used as inputs for simulations of science observations with next-generation instruments and telescopes, in particular to predict post-coronagraphic contrast improvements for planet finder systems. We extend the previous results presented in Correia and Teixeira [J. Opt. Soc. Am. A 31, 2763 (2014)] to the closed-loop case with predictive controllers and generalize the analytical modeling of Rigaut et al. [Proc. SPIE 3353, 1038 (1998)], Flicker [Technical Report (W. M. Keck Observatory, 2007)], and Jolissaint [J. Eur. Opt. Soc. 5, 10055 (2010)]. We follow closely the developments of Ellerbroek [J. Opt. Soc. Am. A 22, 310 (2005)] and propose the synthesis of a distributed Kalman filter to mitigate both aniso-servo-lag and aliasing errors while minimizing the overall residual variance. We discuss applications to (i) analytic AO-corrected PSF modeling in the spatial-frequency domain, (ii) post-coronagraphic contrast enhancement, (iii) filter optimization for real-time wavefront reconstruction, and (iv) PSF reconstruction from system telemetry. Under perfect knowledge of wind velocities, we show that ~60 nm rms error reduction can be achieved with the distributed Kalman filter embodying antialiasing reconstructors on 10 m class high-order AO systems, leading to contrast improvement factors of up to three orders of magnitude at few ?/D separations (~1 - 5?/D) for a 0 magnitude star and reaching close to one order of magnitude for a 12 magnitude star.

Abstract
Optical properties of biological tissues are unique and may be used for tissue identification, tissue discrimination or even to identify pathologies. Early stage colorectal cancer evolves from adenomatous polyps that arise in the inner layer of the colorectal tube - the mucosa. The identification of different optical properties between healthy and pathological colorectal tissues might be used to identify different tissue components and to develop an early stage diagnosis method using optical technologies. Since most of the biomedical optics techniques use light within the visible and near infrared wavelength ranges, we used the inverse adding-doubling method to make a fast estimation of the optical properties of colorectal mucosa and early stage adenocarcinoma between 400 and 1000 nm. The estimated wavelength dependencies have provided information about higher lipid content in healthy mucosa and higher blood content in pathological tissue. Such data has also indicated that the wavelength dependence of the scattering coefficient for healthy mucosa is dominated by Rayleigh scattering and for pathological mucosa it is dominated by Mie scattering. Such difference indicates smaller scatterer size in healthy mucosa tissue. Such information can now be used to develop new diagnosis or treatment methods for early cancer detection or removal. One possibility is to use optical clearing technique to improve tissue transparency and create localized and temporary tissue dehydration for image contrast improvement during diagnosis or polyp laser removal. Such techniques can now be developed based on the different results that we have found for healthy and pathological colorectal mucosa.

Abstract
Colorectal carcinoma is a major health concern worldwide and its high incidence and mortality require accurate screening methods. Following endoscopic examination, polyps must be removed for histopathological characterization. Aiming to contribute to the improvement of current endoscopy methods of colorectal carcinoma screening or even for future development of laser treatment procedures, we studied the diffusion properties of glucose and water in colorectal healthy and pathological mucosa. These parameters characterize the tissue dehydration and the refractive index matching mechanisms of optical clearing (OC). We used ex vivo tissues to measure the collimated transmittance spectra and thickness during treatments with OC solutions containing glucose in different concentrations. These time dependencies allowed for estimating the diffusion time and diffusion coefficient values of glucose and water in both types of tissues. The measured diffusion times for glucose in healthy and pathological mucosa samples were 299.2 +/- 4.7 s and 320.6 +/- 10.6 s for 40% and 35% glucose concentrations, respectively. Such a difference indicates a slower glucose diffusion in cancer tissues, which originate from their ability to trap far more glucose than healthy tissues. We have also found a higher free water content in cancerous tissue that is estimated as 64.4% instead of 59.4% for healthy mucosa. (C) 2017 Society of Photo-Optical Instrumentation Engineers (SPIE)

Abstract
The optical dispersion and water content of human liver were experimentally studied to estimate the optical dispersions of tissue scatterers and dry matter. Using temporal measurements of collimated transmittance [T-c(t)] of liver samples under treatment at different glycerol concentrations, free water and diffusion coefficient (D-gl) of glycerol in liver were found as 60.0% and 8.2 x 10(-7) cm(2)/s, respectively. Bound water was calculated as the difference between the reported total water of 74.5% and found free water. The optical dispersion of liver was calculated from the measurements of refractive index (Rl) of tissue samples made for different wavelengths between 400 and 1000 nm. Using liver and water optical dispersions at 20 degrees C and the free and total water, the dispersions for liver scatterers and dry matter were calculated. The estimated dispersions present a decreasing behavior with wavelength. The dry matter dispersion shows higher Rl values than liver scatterers, as expected. Considering 600 nm, dry matter has an Rl of 1.508, whereas scatterers have an Rl of 1.444. These dispersions are useful to characterize the Rl matching mechanism in optical clearing treatments, provided that [T-c(t)] and thickness measurements are performed during treatment. The knowledge of D-gl is also important for living tissue cryoprotection applications. (C) 2017 Society of Photo-Optical Instrumentation Engineers (SPIE)

Abstract
In obstructive sleep apnea, respiratory effort is maintained but ventilation decreases/disappears because of the partial/total occlusion in the upper airway. It affects about 4% of men and 2% of women in the world population. The aim was to define an auxiliary diagnostic method that can support the decision to perform polysomnography (standard test), based on risk and diagnostic factors. Our sample performed polysomnography between January and May 2015. Two Bayesian classifiers were used to build the models: Naive Bayes (NB) and Tree augmented Naive Bayes (TAN), using all 39 variables or just a selection of 13. Area under the ROC curve, sensitivity, specificity, predictive values were evaluated using cross-validation. From a collected total of 241 patients, only 194 fulfill the inclusion criteria. 123 (63%) were male, with a mean age of 58 years old. 66 (34%) patients had a normal result and 128 (66%) a diagnostic of obstructive sleep apnea. The AUCs for each model were: NB39 - 72%; TAN39 - 79%; NB13 - 75% and TAN13 - 75%. The high (34%) proportion of normal results confirm the need for a pre-evaluation prior to polysomnography. The constant seeking of a validated model to screen patients with suspicion of obstructive sleep apnea is essential, especially at the level of primary care.