| 1. |
- Adcox, K, et al.
(author)
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PHENIX detector overview
- 2003
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In: Nuclear Instruments & Methods in Physics Research. Section A: Accelerators, Spectrometers, Detectors, and Associated Equipment. - 0167-5087. ; 499:2-3, s. 469-479
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Journal article (peer-reviewed)abstract
- The PHENIX detector is designed to perform a broad study of A-A, p-A, and p-p collisions to investigate nuclear matter under extreme conditions. A wide variety of probes, sensitive to all timescales, are used to study systematic variations with species and energy as well as to measure the spin structure of the nucleon. Designing for the needs of the heavy-ion and polarized-proton programs has produced a detector with unparalleled capabilities. PHENIX measures electron and muon pairs, photons, and hadrons with excellent energy and momentum resolution. The detector consists of a large number of subsystems that are discussed in other papers in this volume. The overall design parameters of the detector are presented. (C) 2002 Elsevier Science B.V. All rights reserved.
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| 2. |
- Adler, SS, et al.
(author)
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PHENIX on-line systems
- 2003
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In: Nuclear Instruments & Methods in Physics Research. Section A: Accelerators, Spectrometers, Detectors, and Associated Equipment. - 0167-5087. ; 499:2-3, s. 560-592
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Journal article (peer-reviewed)abstract
- The PHENIX On-Line system takes signals from the Front End Modules (FEM) on each detector subsystem for the purpose of generating events for physics analysis. Processing of event data begins when the Data Collection Modules (DCM) receive data via fiber-optic links from the FEMs. The DCMs format and zero suppress the data and generate data packets. These packets go to the Event Builders (EvB) that assemble the events in final form. The Level-1 trigger (LVL1) generates a decision for each beam crossing and eliminates uninteresting events. The FEMs carry out all detector processing of the data so that it is delivered to the DCMs using a standard format. The FEMs also provide buffering for LVL1 trigger processing and DCM data collection. This is carried out using an architecture that is pipelined and deadtimeless. All of this is controlled by the Master Timing System (MTS) that distributes the RHIC clocks. A Level-2 trigger (LVL2) gives additional discrimination. A description of the components and operation of the PHENIX On-Line system is given and the solution to a number of electronic infrastructure problems are discussed. (C) 2002 Elsevier Science B.V. All rights reserved.
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| 3. |
- Alahamami, Mastour A., et al.
(author)
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Comparison of cysts in red and green images for diabetic macular edema
- 2014
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Conference paper (peer-reviewed)abstract
- Purpose: To improve the detection of macular cyst with photoscreening, we tested whether in a population of largely minority patients the red channel image from a color fundus camera visualizes cysts in diabetic macular edema better than the green channel image. In assessing diabetic retinas for clinically significant macular edema, the presence of cysts must be judged with respect to the central macula. Some grading programs use red free images, often derived from green channel images, to enhance visualization of retinal vessel damage or macular pigment, but some red and near infrared instruments have detected cysts better than short wavelength techniques. Methods: We evaluated macular cysts in 13 diabetic patients diagnosed with clinically significant macular edema, age range 33-68 years. Diabetic patients were selected from the screening study of >2000 underserved patients seen at Eastmont Wellness Center, Oakland, CA. Patients underwent photoscreening with a nonmydriatic color fundus camera (Canon Cr-DGi, Tokyo, Japan) and SD-OCT (iVue, Optovue Inc, Fremont, CA). The color fundus images for those patients were transformed into red and green channels to evaluate the appearance of macular cysts in red channel images and green channel images. The region of each cyst was compared SD-OCT scans (Adobe Photoshop CS5.1, San Jose, CA). Only cysts touching the central 1 mm around the fixation from the SD-OCT scans were sampled. Results: The average size of retinal cysts in red channel images, 124.57 µm (±106.96), was significantly greater than in green channel, 59.44 µm (±76.6), (p<0.006). Entire cysts could not be seen in 5 eyes in the green channel images. Conclusions: Our results indicate that the grading of cysts in the central macular might be improved by incorporating red channel images. There are a number of potential factors that could make cysts less visible in the green channel images, including poorer light penetration through to the deeper retina or macular pigment. Anterior segment issues impact more on green channel images. This population includes mostly minority patients who have dark fundi, and darker images.
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| 4. |
- Alhamami, Mastour, et al.
(author)
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Comparison of Cysts in Red and Green Images for Diabetic Macular Edema
- 2017
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In: Optometry and Vision Science. - 1040-5488 .- 1538-9235. ; 94:2, s. 137-149
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Journal article (peer-reviewed)abstract
- Purpose: To investigate whether cysts in diabetic macular edema are better visualized in the red channel of color fundus camera images, as compared with the green channel, because color fundus camera screening methods that emphasize short-wavelength light may miss cysts in patients with dark fundi or changes to outer blood retinal barrier.Methods: Fundus images for diabetic retinopathy photoscreening were acquired for a study with Aeon Imaging, EyePACS, University of California Berkeley, and Indiana University. There were 2047 underserved, adult diabetic patients, of whom over 90% self-identified as a racial/ethnic identify other than non-Hispanic white. Color fundus images at nominally 45 degrees were acquired with a Canon Cr-DGi non-mydriatic camera (Tokyo, Japan) then graded by an EyePACS certified grader. From the 148 patients graded to have clinically significant macular edema by the presence of hard exudates in the central 1500 [mu]m of the fovea, we evaluated macular cysts in 13 patients with cystoid macular edema. Age ranged from 33 to 68 years. Color fundus images were split into red, green, and blue channels with custom Matlab software (Mathworks, Natick, MA). The diameter of a cyst or confluent cysts was quantified in the red-channel and green-channel images separately.Results: Cyst identification gave complete agreement between red-channel images and the standard full-color images. This was not the case for green-channel images, which did not expose cysts visible with standard full-color images in five cases, who had dark fundi. Cysts appeared more numerous and covered a larger area in the red channel (733 +/- 604 [mu]m) than in the green channel (349 +/- 433 [mu]m, p < 0.006).Conclusions: Cysts may be underdetected with the present fundus camera methods, particularly when short-wavelength light is emphasized or in patients with dark fundi. Longer wavelength techniques may improve the detection of cysts and provide more information concerning the early stages of diabetic macular edema or the outer blood retinal barrier.
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| 5. |
- Arthur, Edmund, et al.
(author)
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Central Macular Thickness in Diabetic Patients : A Sex-based Analysis
- 2019
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In: Optometry and Vision Science. - : American Academy of Optometry. - 1040-5488 .- 1538-9235. ; 96:4, s. 266-275
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Journal article (peer-reviewed)abstract
- SIGNIFICANCE The pathological changes in clinically significant diabetic macular edema lead to greater retinal thickening in men than in women. Therefore, male sex should be considered a potential risk factor for identifying individuals with the most severe pathological changes. Understanding this excessive retinal thickening in men may help preserve vision. PURPOSE The purpose of this study was to investigate the sex differences in retinal thickness in diabetic patients. We tested whether men with clinically significant macular edema had even greater central macular thickness than expected from sex differences without significant pathological changes. This study also aimed to determine which retinal layers contribute to abnormal retinal thickness. METHODS From 2047 underserved adult diabetic patients from Alameda County, CA, 142 patients with clinically significant macular edema were identified by EyePACS-certified graders using color fundus images (Canon CR6-45NM). First, central macular thickness from spectral domain optical coherence tomography (iVue; Optovue Inc.) was compared in 21 men versus 21 women without clinically significant macular edema. Then, a planned comparison contrasted the greater values of central macular thickness in men versus women with clinically significant macular edema as compared with those without. Mean retinal thickness and variability of central macular layers were compared in men versus women. RESULTS Men without clinically significant macular edema had a 12-μm greater central macular thickness than did women (245 ± 21.3 and 233 ± 13.4 μm, respectively; t40 = −2.18, P = .04). Men with clinically significant macular edema had a 67-μm greater central macular thickness than did women (383 ± 48.7 and 316 ± 60.4 μm, P < .001); that is, men had 55 μm or more than five times more (t20 = 2.35, P = .02). In men, the outer-nuclear-layer thickness was more variable, F10,10 = 9.34. CONCLUSIONS Underserved diabetic men had thicker retinas than did women, exacerbated by clinically significant macular edema.
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| 6. |
- Arthur, Edmund, et al.
(author)
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Individual Retinal Layer Thickness in Diabetic Patients with Clinically Significant Macular Edema : A Gender Based Analysis
- 2016
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Conference paper (peer-reviewed)abstract
- Purpose: To compare segmented retinal layer thicknesses between male and female diabetics with clinically significant macular edema (CSME). This study expands our earlier analysis of central macular thickness (CMT) measurements in diabetic males vs. females. Methods: Diabetic retinopathy screening of 2080 diabetics from Alameda County, CA, indicated 142 patients with CSME, as judged by EyePACS certified graders using color fundus images (Canon CR6-45NM). Of the 2080 diabetics, 1784 were imaged with SD-OCT (Optovue iVue). From the 142 patients, we selected 11 males with good fixation, CMT > 300 µm, and no other ocular complications, along with 11 females with the greatest values of CMT while controlling for age, HbA1c and diabetes duration. Manual segmentation of retinal layers using custom software (Mathworks Matlab) of the SD-OCT images of these subjects was done. We analyzed thicknesses for regions 1 deg - 2 deg for nasal and temporal retina in a B-scan centered on the fovea. A 2 X 2 ANOVA probed the differences in thickness for gender, meridian, and their interaction. We also analyzed the central 1 mm of the outer retinal layers, and performed t-tests. Results: Males had significantly thicker nerve fiber layer (NFL) (13.30 ± 2.85 µm) than females (10.13 ± 6.13 µm) and ganglion cell layer-inner plexiform layer (GCL-IPL) (62.54 ± 21.18 µm) than females (48.07 ± 25.91 µm), p < 0.05. There was no effect of meridian and no interaction (p > 0.05). All other layers except the retinal pigment epithelium (RPE) were thicker for males than females even though these were not significant (p > 0.05). There were no significant differences for the layers of the outer retina, which were highly variable and distorted by cysts. Conclusion: Outside the fovea, NFL and GCL-IPL thicknesses were significantly higher in males than females.
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| 7. |
- Baskaran, Karthikeyan, et al.
(author)
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Stability of fixation in diabetes patients with and without clinically significant macular edema
- 2014
-
Conference paper (peer-reviewed)abstract
- Purpose - Eye diseases affecting central vision impair fixation and interfere with day-to-day tasks such as reading. Diabetic retinopathy and clinically significant macular edema (CSME) are leading causes of visual impairment in diabetes patients. The aim of this study is to find whether diabetic patients with CSME have poorer fixation stability compared to patients without CSME, by analyzing the fundus images obtained from the Laser Scanning Digital Camera (LSDC).Methods - Two hundred underserved, diabetic patients were screened for diabetic retinopathy at the Eastmont Wellness Center within the EyePACS telemedicine network, using LSDC. One eye of each patient who had diabetic retinopathy was included in this study. Non-mydriatic color fundus photos were classified for presence of CSME by two independent, certified EyePACS graders. The first 50 patients (25 males & 25 females) with CSME were selected and 50 (27 males & 23 females) diabetic patients without CSME were selected as controls. Mean age was 59 (±9) years for patients with CSME and was 55 (±10) years for patients without CSME. The subjects included 53% Hispanics, 26% African Americans and 21% other. A series of 20 images (36 deg field, 1024 X 1024 pixels, and 850 nm) were acquired at 11 fps. Eye positions were obtained by selecting a region of interest in the first image of each series and aligning the remaining images to that region by cross-correlation. The bi-contour ellipse area (BCEA) and the standard deviation of the Euclidean distance (SDED) were used to quantify fixation stability.Results - The fixation stability for patients with CSME was significantly worse than for those without CSME (t test: p < 0.001, 0.007 for BCEA and SDED, respectively). The mean fixation stability obtained by the BCEA metric was 2.74 (±0.40) log(minArc2) and 2.34 (±0.42) log(minArc2) for patients with and without CSME, respectively. For SDED the mean was 48.4 (±28.8) microns and 34.6 (±20.4) microns for patients with and without CSME, respectively. The correlation with age was not significant for either group (R2 = 0.052, 0.011).Conclusions - Diabetic patients with CSME had poorer fixation stability than patients without CSME for both metrics. Fixation stability is a potential tool for assessing macular function and could be used for tracking the treatment and progression of macular edema.The LSDC images provide one method to quantify fixation stability rapidly.
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| 8. |
- Edwards, Robert A., et al.
(author)
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Global phylogeography and ancient evolution of the widespread human gut virus crAssphage
- 2019
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In: Nature Microbiology. - : Springer Science and Business Media LLC. - 2058-5276. ; 4:10, s. 1727-1736
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Journal article (peer-reviewed)abstract
- Microbiomes are vast communities of microorganisms and viruses that populate all natural ecosystems. Viruses have been considered to be the most variable component of microbiomes, as supported by virome surveys and examples of high genomic mosaicism. However, recent evidence suggests that the human gut virome is remarkably stable compared with that of other environments. Here, we investigate the origin, evolution and epidemiology of crAssphage, a widespread human gut virus. Through a global collaboration, we obtained DNA sequences of crAssphage from more than one-third of the world's countries and showed that the phylogeography of crAssphage is locally clustered within countries, cities and individuals. We also found fully colinear crAssphage-like genomes in both Old-World and New-World primates, suggesting that the association of crAssphage with primates may be millions of years old. Finally, by exploiting a large cohort of more than 1,000 individuals, we tested whether crAssphage is associated with bacterial taxonomic groups of the gut microbiome, diverse human health parameters and a wide range of dietary factors. We identified strong correlations with different clades of bacteria that are related to Bacteroidetes and weak associations with several diet categories, but no significant association with health or disease. We conclude that crAssphage is a benign cosmopolitan virus that may have coevolved with the human lineage and is an integral part of the normal human gut virome.
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| 9. |
- Green, Jason J. A., et al.
(author)
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Retina Artery to Vein Intensity Ratio as a Function of Wavelength and Dark-Field Offset With Low Cost Ophthalmoscope
- 2014
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Conference paper (peer-reviewed)abstract
- PurposeTo quantify light return from retinal vessels for oxygenation status. To use a low-cost Digital Light Ophthalmoscope (DLO) based on a novel structured light pattern Digital Light Projector for quantitative retinal imaging. MethodsFive normal subjects of ages 27-63 and various eye colors were imaged without mydriasis. The DLO produced a progressively scanning 6 pixel wide stripe, 96 stripe illumination pattern (85 μm stripe width at retina) with LEDs at 635 +/- 25nm (Red) and 535 +/- 70nm (Green) with a constant fixation target location across tests. The illumination was synchronized to a 13.2 Hz rolling shutter CMOS sensor (11 μm resolution at retina). To collect the light return from the retina at varying light multiply scattered levels, aperture offset was varied in position with respect to the illumination centerline: dark-field mode was obtained with large offsets and confocal mode had small offsets, where offset was varied from -517 μm (row start 30) to 1353 μm (row start 200). Multiple images of 12 bit dynamic range were captured in sequence, aligned with translational cross correlation, then time averaged to reduce noise. The artery and vein gray scale intensity level was measured at vessel centers for: 1) both vessels over background retina and 2) artery over the optic disc and vein over background. Mean-to-mean intensity ratios were then compared. ResultsWith an aperture width of 704 μm, intensity varied by 2.60 bits (a factor of 4.5) for each subject per condition: red, green, artery, and vein, 3.39 bits if same subject and condition (2.3% Red A/V ratio CoV σ/μ), and by 5.07 bits over all tests. Yet, the ratio (Red/Green Artery)/(Red/Green Vein) was close to unity across offsets and linear fits had an R^2 regression of, for case 1: 0.72, 0.06, 0.25, 0.18, and 0.49, and case 2: 0.0005, 0.89, 0.75, 0.50, and 0.18. The Artery/Vein ratio trend slopes, intercept points, and inversions varied between subjects, i.e. contrast reversals were observed. ConclusionsThe DLO can be utilized electronically to effectively perform quantitative fundus imaging at both Red and Green wavelengths, which is a step towards performing oximetry. 77 is zero offset
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| 10. |
- Ingling, Allen W, et al.
(author)
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Fixation stability readily obtained from confocal color fundus imaging
- 2015
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In: Investigative Ophthalmology and Visual Science. - 0146-0404 .- 1552-5783. ; 56:7, s. 515-515
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Journal article (peer-reviewed)abstract
- PurposeStabile fixation underpins most visual tasks such as reading, and is important for accurate assessment of visual function and treatment. Retinal imaging instruments average images over time to improve the signal to noise ratio, discarding useful eye movement data. We determined whether the frame-to-frame motion of the retina during non-mydriatic color fundus imaging could provide fixation stability measures, e.g. Bivariate Contour Ellipse Area (BCEA). MethodsNon-mydriatic color fundus images were acquired using the Digital Light Ophthalmoscope (DLO). Twenty subjects with varied fundus pigmentation were tested without mydriasis. The DLO uses a digital light projector with LED light sources to provide the illumination for both confocal imaging and fixation stimuli. The DLO projects a series of lines across the fundus that is synchronized to the 2D CMOS sensor, providing high contrast confocal imaging. Monochromatic 40 deg images were acquired with alternating red and green LED illumination at 14.3 Hz and overlayed to present a pseudo-color image to the operator in real time. To reduce pupil constriction and patient discomfort, the green LED was long-pass filtered with a 570 nm filter. A 1.5mm entrance pupil and time-averaged power of <30 uW were used. Images were aligned automatically with custom software (MATLAB) using cross-correlation and 2D translation. A canvas of twice the image size was used to allow image alignment despite moderate eye movements. Blinks and large saccades were discarded and BCEA was computed. ResultsThe image alignment algorithm successfully aligned nearly all the frames, rejecting 3.7%, and allowing fixation stability to be computed from color fundus image data. The BCEA for 1 standard deviation was 2.97 log minarc2 for all subjects and both the red and yellow-orange illumination. There was no difference between the BCEA for red or yellow-orange illumination (t = .86). ConclusionsThe color DLO records sufficiently high quality images to reliably calculate measures of fixation stability. Despite recruiting an especially challenging population that included dark fundi, small pupils, high refractive errors, and media issues, we achieved success in all subjects tested to date.
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| 11. |
- Muller, Matthew S, et al.
(author)
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Non-mydriatic color fundus imaging with the Digital Light Ophthalmoscope
- 2015
-
Conference paper (peer-reviewed)abstract
- Purpose To provide non-mydriatic confocal color fundus imaging of sufficient quality for screening for diabetic retinopathy despite dark fundus pigmentation, small pupil, high refractive error, or other anterior segment issues. MethodsNon-mydriatic color fundus images of 34 volunteers (aged 39.2 ± 13.2 yr) were acquired using the Digital Light Ophthalmoscope (DLO). 10 subjects had dark fundi and/or high refractive errors, as well as other anterior segment issues. Unique to retinal cameras, the Digital Light Ophthalmoscope (DLO) uses a digital light projector with LED light sources to provide the illumination for both confocal imaging and fixation stimuli. The DLO projects a series of lines across the fundus that is synchronized to the electronic rolling shutter read-out on a 2D CMOS sensor, providing high contrast confocal imaging that is highly customizable through software. Monochromatic 40 deg field images were acquired with alternating red and green LED illumination at 14.3 Hz and overlayed to present a pseudo-color image to the operator in real time. To reduce pupil constriction and patient discomfort while maintaining strong blood absorption, the green illumination was long-pass filtered with a 570 nm filter, and a 1.5mm entrance pupil and time-averaged power of <30 uW was used. ResultsThe DLO provided gradable quality non-mydriatic fundus images in all tested subjects, including those with dark fundi or pupils < 2 mm, as judged by an EyePACS certified grader. The use of long pass filters in the green LED permitted high contrast, non-mydriatic images with illumination wavelengths >570 nm and limited pupil constriction. Retinal vessels at the 4th branch or smaller, as well as neovascularization in diabetic retinopathy, could be seen. Hyperpigmentation was clearly seen both peripherally as bear tracks and centrally at the posterior pole. The aperture width and color balance can be adjusted to provide high contrast and yet relatively uniform and natural color across the image. ConclusionsThe DLO provides confocal color fundus images in real time without the use of short (< 570nm) wavelength light. Despite recruiting an especially challenging population that included dark fundi, small pupils, high refractive errors, and media issues, we achieved a 100% success rate in obtaining gradable images for screening.
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