| 1. |
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| 2. |
- Duncanson, Laura, et al.
(author)
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Aboveground biomass density models for NASA's Global Ecosystem Dynamics Investigation (GEDI) lidar mission
- 2022
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In: Remote Sensing of Environment. - : Elsevier BV. - 0034-4257 .- 1879-0704. ; 270
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Journal article (peer-reviewed)abstract
- NASA's Global Ecosystem Dynamics Investigation (GEDI) is collecting spaceborne full waveform lidar data with a primary science goal of producing accurate estimates of forest aboveground biomass density (AGBD). This paper presents the development of the models used to create GEDI's footprint-level (~25 m) AGBD (GEDI04_A) product, including a description of the datasets used and the procedure for final model selection. The data used to fit our models are from a compilation of globally distributed spatially and temporally coincident field and airborne lidar datasets, whereby we simulated GEDI-like waveforms from airborne lidar to build a calibration database. We used this database to expand the geographic extent of past waveform lidar studies, and divided the globe into four broad strata by Plant Functional Type (PFT) and six geographic regions. GEDI's waveform-to-biomass models take the form of parametric Ordinary Least Squares (OLS) models with simulated Relative Height (RH) metrics as predictor variables. From an exhaustive set of candidate models, we selected the best input predictor variables, and data transformations for each geographic stratum in the GEDI domain to produce a set of comprehensive predictive footprint-level models. We found that model selection frequently favored combinations of RH metrics at the 98th, 90th, 50th, and 10th height above ground-level percentiles (RH98, RH90, RH50, and RH10, respectively), but that inclusion of lower RH metrics (e.g. RH10) did not markedly improve model performance. Second, forced inclusion of RH98 in all models was important and did not degrade model performance, and the best performing models were parsimonious, typically having only 1-3 predictors. Third, stratification by geographic domain (PFT, geographic region) improved model performance in comparison to global models without stratification. Fourth, for the vast majority of strata, the best performing models were fit using square root transformation of field AGBD and/or height metrics. There was considerable variability in model performance across geographic strata, and areas with sparse training data and/or high AGBD values had the poorest performance. These models are used to produce global predictions of AGBD, but will be improved in the future as more and better training data become available.
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| 3. |
- Klionsky, Daniel J., et al.
(author)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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In: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Research review (peer-reviewed)abstract
- In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
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| 4. |
- Letcher, Susan G., et al.
(author)
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Environmental gradients and the evolution of successional habitat specialization : a test case with 14 Neotropical forest sites
- 2015
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In: Journal of Ecology. - : Wiley. - 0022-0477 .- 1365-2745. ; 103:5
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Journal article (peer-reviewed)abstract
- * Successional gradients are ubiquitous in nature, yet few studies have systematically examined the evolutionary origins of taxa that specialize at different successional stages. Here we quantify successional habitat specialization in Neotropical forest trees and evaluate its evolutionary lability along a precipitation gradient. Theoretically, successional habitat specialization should be more evolutionarily conserved in wet forests than in dry forests due to more extreme microenvironmental differentiation between early and late-successional stages in wet forest. * We applied a robust multinomial classification model to samples of primary and secondary forest trees from 14 Neotropical lowland forest sites spanning a precipitation gradient from 788 to 4000 mm annual rainfall, identifying species that are old-growth specialists and secondary forest specialists in each site. We constructed phylogenies for the classified taxa at each site and for the entire set of classified taxa and tested whether successional habitat specialization is phylogenetically conserved. We further investigated differences in the functional traits of species specializing in secondary vs. old-growth forest along the precipitation gradient, expecting different trait associations with secondary forest specialists in wet vs. dry forests since water availability is more limiting in dry forests and light availability more limiting in wet forests. * Successional habitat specialization is non-randomly distributed in the angiosperm phylogeny, with a tendency towards phylogenetic conservatism overall and a trend towards stronger conservatism in wet forests than in dry forests. However, the specialists come from all the major branches of the angiosperm phylogeny, and very few functional traits showed any consistent relationships with successional habitat specialization in either wet or dry forests. * Synthesis. The niche conservatism evident in the habitat specialization of Neotropical trees suggests a role for radiation into different successional habitats in the evolution of species-rich genera, though the diversity of functional traits that lead to success in different successional habitats complicates analyses at the community scale. Examining the distribution of particular lineages with respect to successional gradients may provide more insight into the role of successional habitat specialization in the evolution of species-rich taxa.
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| 5. |
- 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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| 6. |
- 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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| 7. |
- 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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| 8. |
- 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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| 9. |
- 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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| 10. |
- Celander, Malin C., 1962, et al.
(author)
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Resistance to Cyp3a induction by polychlorinated biphenyls, including non-dioxin-like PCB153, in gills of killifish (Fundulus heteroclitus) from New Bedford Harbor
- 2021
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In: Environmental Toxicology and Pharmacology. - : Elsevier BV. - 1382-6689. ; 83
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Journal article (peer-reviewed)abstract
- Previous reports suggested that non-dioxin-like (NDL) PCB153 effects on cytochrome P450 3A (Cyp3a) expression in Atlantic killifish (Fundulus heteroclitus) gills differed between F0 generation fish from a PCB site (New Bedford Harbor; NBH) and a reference site (Scorton Creek; SC). Here, we examined effects of PCB153, dioxin-like (DL) PCB126, or a mixture of both, on Cyp3a56 mRNA in killifish generations removed from the wild, without environmental PCB exposures. PCB126 effects in liver and gills differed between populations, as expected. Gill Cyp3a56 was not affected by either congener in NBH F2 generation fish, but was induced by PCB153 in SC F1 fish, with females showing a greater response. PCB153 did not affect Cyp3a56 in liver of either population. Results suggest a heritable resistance to NDL-PCBs in killifish from NBH, in addition to that reported for DL PCBs. Induction of Cyp3a56 in gills may be a biomarker of exposure to NDL PCBs in fish populations that are not resistant to PCBs.
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