Optical Phase Unwrapping in the Presence of Branch Points

Strong turbulence causes phase discontinuities known as branch points in an optical field. These discontinuities complicate the phase unwrapping necessary to apply phase corrections onto a deformable mirror in an adaptive optics (AO) system. This paper proposes a non-optimal but effective and implementable phase unwrapping method for optical fields containing branch points. This method first applies a least-squares (LS) unwrapper to the field which isolates and unwraps the LS component of the field. Four modulo-2π-equivalent non-LS components are created by subtracting the LS component from the original field and then restricting the result to differing ranges. 2π phase jumps known as branch cuts are isolated to the non-LS components and the different non-LS realizations have different branch cut placements. The best placement of branch cuts is determined by finding the non-LS realization with the lowest normalized cut length and adding it to the LS component. The result is an unwrapped field which is modulo-2π-equivalent to the original field while minimizing the effect of phase cuts on system performance. This variable-range ‘ϕLS+ϕnon-LS’ unwrapper, is found to outperform other unwrappers designed to work in the presence of branch points at a reasonable computational burden. The effect of improved unwrapping is demonstrated by comparing the performance of a system using a fixed-range ‘ϕLS+ϕnon-LS’ realization unwrapper against the variable-range ‘ϕLS+ϕnon-LS’ unwrapper in a closed-loop simulation. For the 0.5 log-amplitude variance turbulence tested, the system Strehl performance is improved by as much as 41.6 percent at points where fixed-range ‘ϕLS+ϕnon-LS’ unwrappers result in particularly poor branch cut placement. This significant improvement in previously poorly performing regions is particularly important for systems such as laser communications which require minimum Strehl ratios to operate successfully

Policy Implications of Ranking Distributions of Nitrate Runoff and Leaching by Farm, Region, and Soil Productivity

WP 1996-21 December 1996The purpose of this study is to understand the implications of farm-to-farm and regional variations in nitrogen runoff and leaching for targeting specific policies to reduce nutrient contamination. To do this, we estimate 3D-year distributions of nitrate runoff and leaching for individual soils on nearly 150 farms in three farm production regions of New York and rank the distributions according to second degree stochastic dominance criteria. Based on these rankings, it is evident that cropland across farms and regions of New York is so heterogeneous that it is impossible to target policies to reduce nitrate contamination based on farm or regional characteristics. A much clearer ranking is found if soils are grouped by productivity group as measured by corn yield. Based on the estimated elasticities of nitrate runoff and leaching with respect to nitrogen application, one can target those areas where contamination problems are I most severe by focusing on soils with potential yields greater than 125 bu.lac. For it to make sense to target lower productivity soils, the productivity of additional nitrogen application at the margin on the highest yielding soils would have to be about double that of the lower yielding group. Evidence indicates that the ratios of productivities are less than unity in all three production regions

Tracking Bacteria through the Entire Gastrointestinal Tract of a Beef Steer

Biological processes within beef cattle gastrointestinal tracts (GIT) influence animal health, and the output (feces) is an important vector for zoonotic pathogens and antibiotic resistant bacteria. Historically, outside of the rumen, little attention was paid to the bacteria along the GIT, despite their essential role in catabolizing feed into feces. Here we characterize bacteria from 15 GIT sites within a beef steer and examine the proportion of bacteria contributed by upstream compartments. This animal displayed characteristic differences between tissue and digesta communities in gastric and large-intestine, but not small-intestine, samples. The GIT sites shared between 50 and 80% of the operational taxonomic units (OTUs) with their neighboring upstream compartment, with the exception of the ileum. The ileum shared only 11% with the jejunum but displayed a similar phylum-level taxonomic distribution with the jejunum. It is unclear whether the observed changes between compartments represent a nonrandom decrease in bacterial number or rapid multiplication of certain taxa

Rapid Assessment of Breast Tumor Margins Using Deep Ultraviolet Fluorescence Scanning Microscopy

Significance: Re-excision rates for women with invasive breast cancer undergoing breast conserving surgery (or lumpectomy) have decreased in the past decade but remain substantial. This is mainly due to the inability to assess the entire surface of an excised lumpectomy specimen efficiently and accurately during surgery. Aim: The goal of this study was to develop a deep-ultraviolet scanning fluorescence microscope (DUV-FSM) that can be used to accurately and rapidly detect cancer cells on the surface of excised breast tissue. Approach: A DUV-FSM was used to image the surfaces of 47 (31 malignant and 16 normal/benign) fresh breast tissue samples stained in propidium iodide and eosin Y solutions. A set of fluorescence images were obtained from each sample using low magnification (4  ×  ) and fully automated scanning. The images were stitched to form a color image. Three nonmedical evaluators were trained to interpret and assess the fluorescence images. Nuclear–cytoplasm ratio (N/C) was calculated and used for tissue classification. Results: DUV-FSM images a breast sample with subcellular resolution at a speed of 1.0  min  /  cm2. Fluorescence images show excellent visual contrast in color, tissue texture, cell density, and shape between invasive carcinomas and their normal counterparts. Visual interpretation of fluorescence images by nonmedical evaluators was able to distinguish invasive carcinoma from normal samples with high sensitivity (97.62%) and specificity (92.86%). Using N/C alone was able to differentiate patch-level invasive carcinoma from normal breast tissues with reasonable sensitivity (81.5%) and specificity (78.5%). Conclusions: DUV-FSM achieved a good balance between imaging speed and spatial resolution with excellent contrast, which allows either visual or quantitative detection of invasive cancer cells on the surfaces of a breast surgical specimen

Gp41-targeted antibodies restore infectivity of a fusion-deficient HIV-1 envelope glycoprotein

The HIV-1 envelope glycoprotein (Env) mediates viral entry via conformational changes associated with binding the cell surface receptor (CD4) and coreceptor (CCR5/CXCR4), resulting in subsequent fusion of the viral and cellular membranes. While the gp120 Env surface subunit has been extensively studied for its role in viral entry and evasion of the host immune response, the gp41 transmembrane glycoprotein and its role in natural infection are less well characterized. Here, we identified a primary HIV-1 Env variant that consistently supports \u3e300% increased viral infectivity in the presence of autologous or heterologous HIV-positive plasma. However, in the absence of HIV-positive plasma, viruses with this Env exhibited reduced infectivity that was not due to decreased CD4 binding. Using Env chimeras and sequence analysis, we mapped this phenotype to a change Q563R, in the gp41 heptad repeat 1 (HR1) region. We demonstrate that Q563R reduces viral infection by disrupting formation of the gp41 six-helix bundle required for virus-cell membrane fusion. Intriguingly, antibodies that bind cluster I epitopes on gp41 overcome this inhibitory effect, restoring infectivity to wild-type levels. We further demonstrate that the Q563R change increases HIV-1 sensitivity to broadly neutralizing antibodies (bNAbs) targeting the gp41 membrane-proximal external region (MPER). In summary, we identify an HIV-1 Env variant with impaired infectivity whose Env functionality is restored through the binding of host antibodies. These data contribute to our understanding of gp41 residues involved in membrane fusion and identify a mechanism by which host factors can alleviate a viral defect

GroEL provides a folding pathway with lower apparent activation energy compared to spontaneous refolding of human carbonic anhydrase II

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/117184/1/feb2s0014579397006637.pd

Existence of families of spacetimes with a Newtonian limit

J\"urgen Ehlers developed \emph{frame theory} to better understand the relationship between general relativity and Newtonian gravity. Frame theory contains a parameter $\lambda$, which can be thought of as $1/c^2$, where $c$ is the speed of light. By construction, frame theory is equivalent to general relativity for $\lambda >0$, and reduces to Newtonian gravity for $\lambda =0$. Moreover, by setting \ep=\sqrt{\lambda}, frame theory provides a framework to study the Newtonian limit \ep \searrow 0 (i.e. $c\to \infty$). A number of ideas relating to frame theory that were introduced by J\"urgen have subsequently found important applications to the rigorous study of both the Newtonian limit and post-Newtonian expansions. In this article, we review frame theory and discuss, in a non-technical fashion, some of the rigorous results on the Newtonian limit and post-Newtonian expansions that have followed from J\"urgen's work

Effect of Citrus Byproducts on Survival of O157:H7 and Non-O157 \u3ci\u3eEscherichia coli\u3c/i\u3e Serogroups within \u3ci\u3eIn Vitro\u3c/i\u3e Bovine Ruminal Microbial Fermentations

Citrus byproducts (CBPs) are utilized as a low cost nutritional supplement to the diets of cattle and have been suggested to inhibit the growth of both Escherichia coli O157:H7 and Salmonella. The objective of this study was to examine the effects in vitro that varying concentrations of CBP in the powdered or pelleted variety have on the survival of Shiga-toxin Escherichia coli (STEC) serotypes O26:H11, O103:H8, O111:H8, O145:H28, and O157:H7 in bovine ruminal microorganism media. The O26:H11, O111:H8, O145:H28, and O157:H7 serotypes did not exhibit a change in populations in media supplemented with CBP with either variety. The O103:H8 serotype displayed a general trend for an approximate 1 log10 reduction in 5% powdered CBP and 20% pelleted CBP over 6 h. There was a trend for reductions in populations of a variant form of O157:H7 mutated in the stx1 and stx2 genes in higher concentrations of CBP. These results suggest that variations exist in the survival of these serotypes of STEC within mixed ruminal microorganism fluid media when supplemented with CBP. Further research is needed to determine why CBPs affect STEC serotypes differently