Genome Sequences of 14 Siphophages That Infect Serratia marcescens.

We announce the complete genome sequences of 14 Serratia 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 Siphoviridae Bacteriophages That Infect Enterobacteriales.

The Enterobacteriales 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 Enterobacteriales bacteriophages (also known as the Dhillonvirus 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). Like the curvature sensor, the geometric WFS is relatively simple to implement but computationally more complex. The geometric WFS is extended by incorporating the sparse and multi-scale geometry of ridgelets, which are analyzed to optimize the performance of the geometric WFS. Ridgelets provide lower wavefront errors, in terms of root mean square error, specifically over low photon flux levels. The simulation results further show that by replacing the Radon transform of the geometric WFS with the ridgelet transform, computational complexity is reduced.

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. SCE directionality increased as field size increased from 0.5° to 4.7° diameter, although this was noted in four mild myopes and not in two emmetropes. The change with field size was supported by a geometric optics absorption model.

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. In this work, we propose a new edge detection algorithm using a combination of the wavelet transform, Shannon entropy and thresholding. The new algorithm is based on the concept that each Wavelet decomposition level has an assumed level of structure that enables the use of Shannon entropy as a measure of global image structure. The proposed algorithm is developed mathematically and compared to five popular edge detection algorithms. The results show that our solution is low redundancy, noise resilient, and well suited to real-time image processing applications.

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 2.3° fields corresponding to test (peripheral pupil) and reference (pupil centre) positions. Participants determined thresholds at 13 positions along the horizontal pupil meridian by indicating if the test field was brighter or dimmer than the reference field. Thresholds were determined by a staircase procedure after four reversals at each pupil location. After pupil dilation, seven emmetropes were tested at 0 D to 6 D accommodation stimulus levels in 2 D intervals. Data were fit by the Gaussian function, both when the fits were unforced or forced to pass through the sensitivity expected for the reference point. Directionality (ρ) and peak location values (xmax) were determined for unforced and forced fits. RESULTS: Regression slopes for ρ as a function of accommodation stimulus were not significant. There was a tendency for xmax to shift temporally with increasing accommodation across the 6 D stimulus range. This was not significant for regression fitting (-0.059 mm/D, R2  = 0.06, p = 0.20), but a paired t-test for 0 and 6 D stimuli showed a weakly significant change of 0.62 mm (p = 0.05). The differences between the two fitting approaches were small and non-significant. CONCLUSIONS: Directionality did not change with accommodation, but the pupil peak location showed a significant temporal shift of approximately 0.62 mm with 6 D accommodation stimulus. It is possible that substantial changes in the directionality and a shift in the direction of peak location might occur at very high levels of accommodation.

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. In this work, two Raspberry Pi camera types and a panchromatic astronomy camera were trialed within a pushbroom sensor to determine their utility in measuring and processing the spectrum in reflectance. Algorithmic classification of all 15 test materials exhibiting spectral phenomenology between 600 and 800 nm was easily performed. Calibration against a spectrometer considers the effects of the sensor, inherent image processing pipeline and compression. It was found that even the color Raspberry Pi cameras that are popular with STEM applications were able to record and distinguish between most minerals and, contrary to expectations, exploited the infra-red secondary transmissions in the Bayer filter to gain a wider spectral range. Such a camera without a Bayer filter can markedly improve spectral sensitivity but may not be necessary.

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. This information can be reconstructed either optically or numerically. Our hologram recording scheme utilizes working principles of the off-axis digital holographic microscope, designed for reflective micro-object investigation. The eye cornea and lens form the microscope objective. We can record in vivo digital holograms of the human eye retina with resolution after reconstruction of at least 1.3 micrometer.

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. Although event-based image sensors have been used in many computer vision, navigation and even space situation awareness applications, little work has been done to explore their applicability in the field of wavefront sensing. In this work, we present the integration of an event camera in a Shack-Hartmann wavefront sensor and the usage of event data to determine spot displacement and wavefront estimation. We show that it can achieve the same functionality but with substantial speed and can operate in extremely low light conditions. This makes an event-based Shack-Hartmann wavefront sensor a preferable choice for adaptive optics systems where light budget is limited or high bandwidth is required.

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. METHODS: FSW ≥18 years were recruited into a cross-sectional study using respondent-driven sampling (RDS) between October 2014-April 2015 in Port Elizabeth, South Africa. An interviewer-administered questionnaire captured information on demographics, reproductive health histories, and HIV care, including engagement in PMTCT care and ART. HIV and pregnancy testing were biologically assessed. This analysis characterizes FSW engagement in HIV prevention and treatment cascades of the four prongs of PMTCT. RESULTS: Overall, 410 FSW were enrolled. The RDS-weighted HIV prevalence was 61.5% (95% bootstrapped confidence interval 54.1-68.0). A comprehensive assessment of the four PMTCT prongs showed gaps in cascades for each of the prongs. In Prongs 1 and 2, gaps of 42% in consistent condom use with clients among HIV-negative FSW and 43% in long-term high efficacy contraceptive method use among HIV-positive FSW were observed. The analyses for prongs three and four pertained to 192 women with children < 5 years; 101/192 knew their HIV diagnosis prior to the study, of whom 85% (86/101) had their children tested for HIV after birth, but only 36% (31/86) of those who breastfed retested their children post-breastfeeding. A substantial proportion (35%, 42/120) of all HIV-positive women with children < 5 years of age were HIV-negative at their last delivery and seroconverted after delivery. Less than half (45%) of mothers with children < 5 years (45/101) were on ART and 12% (12/101) reported at least one child under five living with HIV. CONCLUSION: These findings show significant gaps in engagement in the PMTCT cascades for FSW, evidenced by sub-optimal uptake of HIV prevention and treatment in the peri/post-natal periods and insufficient prevention of unintended pregnancies among FSW living with HIV. These gaps result in elevated risks for vertical transmission among FSW and the need for PMTCT services within FSW programs.

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. Participants fixated target centers for five runs, in which each run presented the seven targets for 20 seconds each. An Eye Tribe tracker sampled eye positions at 30 Hz. Standard deviations along horizontal (σx) and vertical meridians (σy) and areas of bivariate contour ellipses (BCEAs) of fixation positions were calculated, and statistical significances of target differences for these parameters were determined. RESULTS: Average σx, σy, and BCEAs ranged from 0.26 to 0.35°, 0.38 to 0.55°, and 0.78 to 1.31 degrees, respectively. Target differences in σx (χ6 = 13.0, P = .04), (σy) (χ6 = 36.819, P < .001), and BCEA (χ6 = 34.406, P < .001) were statistically significant. There were significant post hoc differences between some of the target pairs for σy and BCEA, but not for σx. Monitor-based Bessel beam targets provided significantly smaller σy and BCEAs than the bull's eye/cross hair combination and the monitor- and laser-based Gaussian beam targets. CONCLUSIONS: Monitor-based images of Bessel beams provided better fixation targets than did a bull's eye/cross hair combination, monitor-based Gaussian images, and laser Gaussian beams, but no claim can be made that laser Bessel beams provide better fixation targets than do laser Gaussian beams. Monitor-based Bessel images should be useful for ophthalmic imaging instruments requiring stable fixation.

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. In a multivariable analysis, disclosure to clients was associated with more years of education, disclosure to non-paying partners, and meeting clients at established sex work venues, whereas a history of sexual violence was associated with less disclosure. There was also evidence of mutual disclosure with clients, however disclosure was not associated with condom use with clients or being on antiretrovirals. Safer working environments may improve FSW HIV disclosure practices, however disclosure must also be linked with protective behaviors in this population.

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. We propose a centroid estimator based on stream processing, where the center of gravity calculation window floats with the incoming pixel from the detector. In comparison with conventional methods, we show that the proposed estimator simplifies the choice of optimized parameters, provides a unit linear coefficient response, and reduces the influence of background and noise. It is shown that the stream-based centroid estimator also works well for limited size extended sources. A hardware implementation of the proposed estimator is discussed.

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. PURPOSE: To investigate Purkinje image brightness, accuracy, and repeatability of a "Bessel" phakometer compared with those of a conventional phakometer. METHODS: Phakometers were developed with a telecentric imaging system focused at the pupil plane of the eye to capture anterior cornea, anterior lens (PIII), and posterior lens (PIV) Purkinje images. A Bessel beam was generated by a diode laser beam passing through a high-powered doublet with a central obstruction. Software was used to determine image sizes and estimate lens anterior and posterior surface radii of curvature (Ra, Rp), equivalent refractive index (RI), and equivalent power (F). The Bessel phakometer's accuracy was assessed using a model eye. Repeatability (interobserver and intraobserver) and Purkinje images brightnesses of Bessel and conventional phakometers were assessed with six participants. RESULTS: The lens parameters of the model eye determined by the Bessel phakometer were similar to those provided by the model eye's manufacturer with differences (manufacturer - Bessel) in Ra and Rp, RI, and F of +1.18 mm, 0.18 mm, +0.0053, and -0.55 D, respectively. The intraobserver repeatabilities for the Bessel and conventional phakometers were similar. The interobserver repeatabilities of Ra, Rp, and RI for the Bessel phakometer were almost half those (i.e., two times better) for the conventional phakometer. Brightnesses of PIII and PIV were approximately three times higher with the Bessel phakometer than with the conventional phakometer. CONCLUSIONS: The Bessel beam phakometer provided accurate estimates of lens parameters of a model eye and produced brighter Purkinje images and better interobserver repeatability than that 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. Interviews were used to gather information about the accessibility of sterile injecting equipment, location coordinates and movement patterns. We used the Delphi method to obtain final population size estimates for the mapped wards based on estimates from wisdom of the crowd methods, the literature and programmatic data. RESULTS: Between January and April 2015, we mapped 45 wards. Tshwane teams interviewed 39 PWID in 12 wards, resulting in an estimated number of accessible PWID ranging from 568 to 1431. In eThekwini, teams interviewed 40 PWID in 15 wards with an estimated number of accessible PWID ranging from 184 to 350. The Cape Town team interviewed 61 PWID in 18 wards with an estimated number of accessible PWID ranging between 398 and 503. Sterile needles were only available at one location. Almost all needles were bought from pharmacies. Between 80 and 86% of PWID frequented more than one location per day. PWID who reported movement visited a median of three locations a day. CONCLUSIONS: Programmatic mapping led by PWID peers can be used effectively to identify and reach PWID and build relationships where access to HIV prevention commodities for PWID is limited. PWID reported limited access to sterile injecting equipment, highlighting an important HIV prevention need. Programmatic mapping data show that outreach programmes should be flexible and account for the mobile nature of PWID populations. The PWID population size estimates can be used to develop service delivery targets and as baseline measures.

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. METHODS: FSWs ≥18 years were recruited through respondent-driven sampling into a cross-sectional study in Port Elizabeth, South Africa. Participants completed questionnaires and received HIV and syphilis testing; CD4 counts were assessed among women living with HIV. Engagement in the HIV care cascade is described, and correlates of self-reported ART use among treatment-eligible previously diagnosed FSWs were estimated using robust Poisson regression. RESULTS: Between October 2014 and April 2015, 410 FSWs participated in study activities. Overall, 261/410 were living with HIV (respondent-driven sampling-weighted prevalence 61.5% (95% bootstrapped CI 54.1% to 68.0%)). Prior diagnosis of HIV was relatively high (214/261, 82%); however, ART coverage among FSWs living with HIV was 39% (102/261). In multivariate analyses, FSWs were less likely to be on ART if they had not disclosed their HIV status to non-paying partners (adjusted prevalence ratio (aPR) 0.43, 95% CI 0.22 to 0.86, where the reference is FSWs without non-paying partners), and also if they engaged in mobile healthcare services (aPR 0.71, 95% CI 0.57 to 0.89). CONCLUSIONS: HIV testing and awareness of HIV status were high, but substantial losses in the cascade occur at treatment initiation. Given that FSWs engaged in mobile HIV testing and peer education programmes have unmet HIV treatment needs, models of decentralised treatment provision such as mobile-based ART care should be evaluated.

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. In order to ensure a high-quality clinical diagnosis, US images must be restored by reducing their speckle noise and blur. In general, speckle noise is modeled as a multiplicative noise following a Rayleigh distribution and blur as a Gaussian function. Hereto, we propose an intelligent estimator based on artificial neural networks (ANNs) to estimate the variances of noise and blur, which, in turn, are used to obtain an image without discernible distortions. A set of statistical features computed from the image and its complex wavelet sub-bands are used as input to the ANN. In the proposed method, we solve the inverse Rayleigh function numerically for speckle reduction and use the Richardson-Lucy algorithm for de-blurring. The performance of this method is compared with that of the traditional methods by applying them to a synthetic, physical phantom and clinical data, which confirms better restoration results by the proposed method.

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. To bias resolution and detection to the short-wavelength cone system, a blue (450 nm) test stimulus was presented against a bright yellow background that desensitized the M- and L-cones. Participants were three trichromatic males with normal visual functions. With green stimuli, resolution showed a steep central-peripheral gradient that was similar between participants, whereas the detection gradient was shallower and patterns were different between participants. Detection and resolution with blue stimuli were poorer than for green stimuli. The detection of blue stimuli was superior to resolution across the horizontal visual field and the patterns were different between participants. The mid-/long-wavelength cone system's resolution is limited by midget ganglion cell spacing and its detection is limited by the size of the M- and L-cone photoreceptors, consistent with previous observations. We found that no such simple relationships occur for the short-wavelength cone system between resolution and the bistratified ganglion cell spacing, nor between detection and the S-cone photoreceptor sizes.

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. The approach consists of four steps. First, a frame selection strategy is employed by proposing an unsupervised k-means clustering technique. Second, a B-spline-based nonrigid image registration is carried out to suppress geometric distortions. Third, a spatiotemporal kernel regression is proposed by introducing the local sharp patch concept to fuse the registered frame sequences into an image. Finally, a blind deconvolution technique is employed to deblur the fused image. Experiments are carried out with synthetic and real-world turbulence-degraded data by implementing the proposed method and two recently reported methods. The proposed method demonstrates significant improvement over the two reported methods in terms of alleviating blur and distortions, as well as improving visual quality.

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. It reduces dependency on the operator and provides better qualitative and quantitative information for an effective diagnosis. Furthermore, it provides a 3D view, which allows the observation of volume information. The major shortcoming of any type of US imaging is the presence of speckle noise. Hence, speckle reduction is vital in providing a better clinical diagnosis. The key objective of any speckle-reduction algorithm is to attain a speckle-free image while preserving the important anatomical features. In this paper we introduce a nonlinear multi-scale complex wavelet-diffusion based algorithm for speckle reduction and sharp-edge preservation of 2D and 3D US images. In the proposed method we use a Rayleigh and Maxwell-mixture model for 2D and 3D US images, respectively, where a genetic algorithm is used in combination with an expectation maximization method to estimate mixture parameters. Experimental results using both 2D and 3D synthetic, physical phantom, and clinical data demonstrate that our proposed algorithm significantly reduces speckle noise while preserving sharp edges without discernible distortions. The proposed approach performs better than the state-of-the-art approaches in both qualitative and quantitative measures.