Genome Sequences of 14 Siphophages That Infect Serratia marcescens.

We announce the complete genome sequences of 14 bacteriophages isolated from wastewater treatment plants. These phages define two previously undescribed types which we call the Carrot-like phage cluster (phages Carrot, BigDog, LittleDog, Niamh, Opt-148, Opt-169, PhooPhighters, Rovert, Serratianator, Stoker, Swain, and Ulliraptor) and Tlacuache-like phage cluster (Tlacuache and Opt-155).

Complete Genome Sequences of Five SO-1-Like Bacteriophages That Infect .

The order is composed of Gram-negative bacteria that range from harmless symbionts to well-studied pathogens. We announce complete genome sequences of five related SO-1-like bacteriophages (also known as the genus) isolated from wastewater that infect Escherichia coli (Opt-212, Over9000, Pubbukkers, and Teewinot) or Shigella boydii (StarDew).

Multiscale optimization of the geometric wavefront sensor.

Since wavefront distortions cannot be directly measured from an image, a wavefront sensor (WFS) can use intensity variations from a point source to estimate slope or curvature of a wavefront. However, processing of measured aberration data from WFSs is computationally intensive, and this is a challenge for real-time image restoration or correction. A multi-resolutional method, known as the ridgelet transform, is explored to estimate wavefront distortions from astronomical images of natural source beacons (stars).

A Low Redundancy Wavelet Entropy Edge Detection Algorithm.

Fast edge detection of images can be useful for many real-world applications. Edge detection is not an end application but often the first step of a computer vision application. Therefore, fast and simple edge detection techniques are important for efficient image processing.

Subjective measurement of the Stiles-Crawford effect with different field sizes.

The Stiles-Crawford effect of the first kind (SCE) is the phenomenon in which light entering the eye near the center of the pupil appears brighter than light entering near the edge. Previous investigations have found an increase in the directionality (steepness) of the effect as the testing location moves from the center of the visual field to parafoveal positions, but the effect of central field size has not been considered. The influence of field size on the SCE was investigated using a uniaxial Maxwellian system in which stimulus presentation was controlled by an active-matrix liquid crystal display.

Subjective measurement of the Stiles-Crawford effect of the first kind with variation in accommodation.

Purpose: To measure the Stiles-Crawford effect of the first kind (SCE-I), corresponding to central vision, with innovative technology to evaluate changes in the directionality and photoreceptor alignment with accommodation.

Methods: A uniaxial Maxwellian system (spot size in pupil 0.5 mm diameter) was employed, incorporating a spatial light modulator to flicker at 2 Hz between two 2.

Appraisal of Low-Cost Pushbroom Hyper-Spectral Sensor Systems for Material Classification in Reflectance.

Near infrared (NIR) remote sensing has applications in vegetation analysis as well as geological investigations. For extra-terrestrial applications, this is particularly relevant to Moon, Mars and asteroid exploration, where minerals exhibiting spectral phenomenology between 600 and 800 nm have been identified. Recent progress in the availability of processors and sensors has created the possibility of development of low-cost instruments able to return useful scientific results.

Digital holographic microscope for human eye retinal structures recording in vivo.

We introduce the digital holographic microscope for recording in vivo human eye retinal structures. Current eye imaging technologies cannot provide images with resolutions better than 1 µm within depths of a few hundred micrometers. This can be improved with digital holography, in which a hologram of the eye captured with digital camera contains information about structures over the full depth of the eye.

Shack-Hartmann wavefront sensing using spatial-temporal data from an event-based image sensor.

An event-based image sensor works dramatically differently from the conventional frame-based image sensors in a way that it only responds to local brightness changes whereas its counterparts' output is a linear representation of the illumination over a fixed exposure time. The output of an event-based image sensor therefore is an asynchronous stream of spatial-temporal events data tagged with the location, timestamp and polarity of the triggered events. Compared to traditional frame-based image sensors, event-based image sensors have advantages of high temporal resolution, low latency, high dynamic range and low power consumption.

Evaluating the vertical HIV transmission risks among South African female sex workers; have we forgotten PMTCT in their HIV programming?

Background: Female sex workers (FSW) have a greater HIV burden compared to other reproductive-aged women and experience high incidence of pregnancies. However, there are limited data on mother-to-child transmission of HIV in the context of sex work. This study assessed the uptake of prevention of mother-to-child transmission (PMTCT) services to understand the vertical HIV transmission risks among FSW in South Africa.

Fixation Stability with Bessel Beams.

Significance: Ophthalmic imaging instruments that require stable fixation can benefit by using Bessel beams in the form of monitor-based Bessel images.

Purpose: The purpose of this study was to investigate fixation stability using laser Bessel and Gaussian beams and monitor-based images of these targets.

Methods: The right eyes of 16 participants were presented with seven fixation targets: monitor-based images of a bull's eye/cross hair, a Gaussian beam, a Bessel beam with four rings and a Bessel beam with three rings; laser Gaussian beam, laser Bessel beam with four rings, and laser Bessel beam with three rings.

Characterizing the Patterns of HIV Disclosure to Clients Among South African Female Sex Workers in Port Elizabeth.

Female sex workers (FSW) in South Africa are disproportionately affected by HIV, yet little is known about their HIV-status disclosure with clients. Among 410 FSW participating in a cross-sectional study, 213 were HIV positive and aware of their status prior to enrollment. Among FSW aware of their HIV-status, 35% (74/213) reported disclosing their HIV-status to paying clients, whereas 75% (118/158) of those with regular, non-paying partners disclosed to them.

Centroid estimation for a Shack-Hartmann wavefront sensor based on stream processing.

Using center of gravity to estimate the centroid of the spot in a Shack-Hartmann wavefront sensor, the measurement corrupts with photon and detector noise. Parameters, like window size, often require careful optimization to balance the noise error, dynamic range, and linearity of the response coefficient under different photon flux. It also needs to be substituted by the correlation method for extended sources.

Improvements to Phakometry Using Bessel Beams.

Significance: The main problem with phakometry is the low visibility of the third Purkinje image. We built a phakometer using Bessel beams, which have properties of being resistant to diffraction and the potential for self-reconstruction. This instrument had lenticular images three times brighter than those of a conventional phakometer.

Using a programmatic mapping approach to plan for HIV prevention and harm reduction interventions for people who inject drugs in three South African cities.

Background: Stigma, criminalisation and a lack of data on drug use contribute to the "invisibility" of people who inject drugs (PWID) and make HIV prevention and treatment service delivery challenging. We aimed to confirm locations where PWID congregate in Cape Town, eThekwini and Tshwane (South Africa) and to estimate PWID population sizes within selected electoral wards in these areas to inform South Africa's first multi-site HIV prevention project for PWID.

Methods: Field workers (including PWID peers) interviewed community informants to identify suspected injecting locations in selected electoral wards in each city and then visited these locations and interviewed PWID.

Engagement in the HIV care cascade and barriers to antiretroviral therapy uptake among female sex workers in Port Elizabeth, South Africa: findings from a respondent-driven sampling study.

Background: Female sex workers (FSWs) are disproportionately affected by HIV, even in the context of broadly generalised HIV epidemics such as South Africa. This has been observed in spite of the individual and population-level benefits of HIV treatment. We characterise the HIV care cascade among FSWs and relationships with antiretroviral therapy (ART) use.

Intelligent estimation of noise and blur variances using ANN for the restoration of ultrasound images.

Ultrasound (US) imaging is a widely used clinical diagnostic tool in medical imaging techniques. It is a comparatively safe, economical, painless, portable, and noninvasive real-time tool compared to the other imaging modalities. However, the image quality of US imaging is severely affected by the presence of speckle noise and blur during the acquisition process.

Sparsity Prior Computed Tomography Reconstruction Using a Nonstandard Simultaneous X-ray Acquisition Model.

In this article we systematically evaluate the performance of several state-of-the-art, sparsity prior computed tomography (CT) reconstruction algorithms, using a nonstandard simultaneous x-ray acquisition method. Sparsity prior is an efficient strategy in CT reconstruction, relying on iterative algorithms such as the algebraic reconstruction technique to produce a crude reconstruction, based on which sparse approximation is performed. The simultaneous x-ray acquisition model ensures rapid capture of x-rays; however, it captures a significantly fewer number of attenuation measurements, and the projections are nonuniform.

Peripheral detection and resolution with mid-/long-wavelength and short-wavelength sensitive cone systems.

This study compared neural resolution and detection limits of the human mid-/long-wavelength and short-wavelength cone systems with anatomical estimates of photoreceptor and retinal ganglion cell spacings and sizes. Detection and resolution limits were measured from central fixation out to 35° eccentricity across the horizontal visual field using a modified Lotmar interferometer. The mid-/long-wavelength cone system was studied using a green (550 nm) test stimulus to which S-cones have low sensitivity.

Speckle-reduction algorithm for ultrasound images in complex wavelet domain using genetic algorithm-based mixture model.

Compared with other medical-imaging modalities, ultrasound (US) imaging is a valuable way to examine the body's internal organs, and two-dimensional (2D) imaging is currently the most common technique used in clinical diagnoses. Conventional 2D US imaging systems are highly flexible cost-effective imaging tools that permit operators to observe and record images of a large variety of thin anatomical sections in real time. Recently, 3D US imaging has also been gaining popularity due to its considerable advantages over 2D US imaging.

Restoring atmospheric-turbulence-degraded images.

Image data experiences geometric distortions and spatial-temporal varying blur due to the strong effects of random spatial and temporal variations in the optical refractive index of the communication path. Simultaneously removing these effects from an image is a challenging task. An efficient approach is proposed in this paper to address this problem.

Pregnancy Intentions and Safer Pregnancy Knowledge Among Female Sex Workers in Port Elizabeth, South Africa.

Objective: To assess the association between human immunodeficiency virus (HIV) and pregnancy intentions and safer conception knowledge among female sex workers in Port Elizabeth, South Africa.

Methods: This cross-sectional study recruited female sex workers in Port Elizabeth using respondent-driven sampling and completed an interviewer-administered questionnaire alongside HIV testing and counseling. In this secondary analysis, robust Poisson regression was used to model prevalence ratios for positive fertility intentions in this cross-sectional study.

Relationship between retinal distance and object field angles for finite schematic eyes.

Aim: Retinal anatomical studies have used the Drasdo & Fowler three-refracting surface schematic eye to convert between retinal distances and object field angles. We compared its performance at this task with those of more sophisticated four-refracting surface schematic eyes.

Method: Raytracing was performed for Drasdo & Fowler, Lotmar, Navarro, Liou & Brennan, Kooijman and Atchison schematic eyes, and some of their variants.

Improvements to the modal holographic wavefront sensor.

The Zernike coefficients of a light wavefront can be calculated directly by intensity ratios of pairs of spots in the reconstructed image plane of a holographic wavefront sensor (HWFS). However, the response curve of the HWFS heavily depends on the position and size of the detector for each spot and the distortions introduced by other aberrations. In this paper, we propose a method to measure the intensity of each spot by setting a threshold to select effective pixels and using the weighted average intensity within a selected window.

Optical test-benches for multiple source wavefront propagation and spatiotemporal point-spread function emulation.

Precise measurement of aberrations within an optical system is essential to mitigate combined effects of user-generated aberrations for the study of anisoplanatic imaging using optical test benches. The optical system point spread function (PSF) is first defined, and methods to minimize the effects of the optical system are discussed. User-derived aberrations, in the form of low-order Zernike ensembles, are introduced using a liquid crystal spatial light modulator (LC-SLM), and dynamic phase maps are used to study the spatiotemporal PSF.