Novel method for the fabrication of spatially variant structures

Spatially varying grating structures formed at the subwave-length scale behave as a layer with an artificial effective refractive index that is dependent on the local fill fraction. We describe a novel technique to pattern gratings with a spatially varying fill fraction using a simple two-step exposure process. The first exposure forms a partial latent image of a grating in the photoresist. The resist is then saturated by overlaying an exposure with an analog spatially varying intensity, generated by using a phase-only masking technique. The cumulative exposure dose from the two steps was designed so that the point of minimum intensity will still develop the photoresist through, in all the spaces in the grating. By varying the exposure window around the saturation dose, the fill fraction of the patterned gratings was modulated; thus, the size of the space cleared at any location in the grating is a scalable function of the local cumulative dose delivered. Constant feature height is achieved across the patterned area by keeping the second exposure dose below the resist threshold exposure value. The exposure process was modeled numerically to predict the relationship between the local dose and patterned fill fraction. This technique enables rapid, low-cost fabrication of apodized grating structures for applications in diffractive optics technology

Feedback Control as a Framework for Understanding Tradeoffs in Biology

Control theory arose from a need to control synthetic systems. From regulating steam engines to tuning radios to devices capable of autonomous movement, it provided a formal mathematical basis for understanding the role of feedback in the stability (or change) of dynamical systems. It provides a framework for understanding any system with feedback regulation, including biological ones such as regulatory gene networks, cellular metabolic systems, sensorimotor dynamics of moving animals, and even ecological or evolutionary dynamics of organisms and populations. Here we focus on four case studies of the sensorimotor dynamics of animals, each of which involves the application of principles from control theory to probe stability and feedback in an organism's response to perturbations. We use examples from aquatic (electric fish station keeping and jamming avoidance), terrestrial (cockroach wall following) and aerial environments (flight control in moths) to highlight how one can use control theory to understand how feedback mechanisms interact with the physical dynamics of animals to determine their stability and response to sensory inputs and perturbations. Each case study is cast as a control problem with sensory input, neural processing, and motor dynamics, the output of which feeds back to the sensory inputs. Collectively, the interaction of these systems in a closed loop determines the behavior of the entire system.Comment: Submitted to Integr Comp Bio

Worry as a window into the lives of people who use injection drugs: a factor analysis approach

<p>Abstract</p> <p>Background</p> <p>The concept of risk dominates the HIV/AIDS literature pertaining to People Who Use Injection Drugs (PWUID). In contrast the associated concept of worry is infrequently applied, even though it can produce important perspectives of PWUID's lives. This study asked a sample (n = 105) of PWUID enrolled in a Victoria, British Columbia needle exchange program to evaluate their degree of worry about fourteen factors they may encounter in their daily lives.</p> <p>Methods</p> <p>Exploratory factor analysis was used to analyze their responses.</p> <p>Results</p> <p>Factor analysis delineated three factors: 1) overall personal security, 2) injection drug use-specific risks including overdosing and vein collapse and, 3) contracting infectious diseases associated with injection drug use (e.g. HIV/AIDS and hepatitis C).</p> <p>Conclusion</p> <p>PWUID in this study not only worry about HIV/AIDS but also about stressful factors in their daily life which have been linked to both increased HIV/AIDS risk behaviour and decreased anti-retroviral treatment adherence. The importance PWUID give to this broad range of worry/concerns emphasizes the need to place HIV/AIDS intervention, education, and treatment programs within a broader harm-reduction framework that incorporates their perspectives on both worry and risk.</p

Effectiveness of postoperative radiotherapy after radical cystectomy for locally advanced bladder cancer

BACKGROUND: Local-regional failure (LF) for locally advanced bladder cancer (LABC) after radical cystectomy (RC) is common even with chemotherapy and is associated with high morbidity/mortality. Postoperative radiotherapy (PORT) can reduce LF and may enhance overall survival (OS) but has no defined role. We hypothesized that the addition of PORT would improve OS in LABC in a large nationwide oncology database. METHODS: We identified ≥ pT3pN0-3M0 LABC patients in the National Cancer Database diagnosed 2004-2014 who underwent RC ± PORT. OS was calculated using Kaplan-Meier and Cox proportional hazards regression modeling was used to identify predictors of OS. Propensity matching was performed to match RC patients who received PORT vs those who did not. RESULTS: 15,124 RC patients were identified with 512 (3.3%) receiving PORT. Median OS was 20.0 months (95% CI, 18.2-21.8) for PORT vs 20.8 months (95% CI, 20.3-21.3) for no PORT (P = 0.178). In multivariable analysis, PORT was independently associated with improved OS: hazard ratio 0.87 (95% CI, 0.78-0.97); P = 0.008. A one-to-three propensity match yielded 1,858 patients (24.9% receiving PORT and 75.1% without). In the propensity-matched cohort, median OS was 19.8 months (95% CI, 18.0-21.6) for PORT vs 16.9 months (95% CI, 15.6-18.1) for no PORT (P = 0.030). In the propensity-matched cohort of urothelial carcinoma patients (N = 1,460), PORT was associated with improved OS for pT4, pN+, and positive margins (P \u3c 0.01 all). CONCLUSION: In this observational cohort, PORT was associated with improved OS in LABC. While the data should be interpreted cautiously, these results lend support to the use of PORT in selected patients with LABC, regardless of histology. Prospective trials of PORT are warranted

The AP-2 adaptor β2 appendage scaffolds alternate cargo endocytosis

The independently folded appendages of the large α and β2 subunits of the endocytic adaptor protein (AP)-2 complex coordinate proper assembly and operation of endocytic components during clathrin-mediated endocytosis. The β2 subunit appendage contains a common binding site for β-arrestin or the autosomal recessive hypercholesterolemia (ARH) protein. To determine the importance of this interaction surface in living cells, we used small interfering RNA-based gene silencing. The effect of extinguishing β2 subunit expression on the internalization of transferrin is considerably weaker than an AP-2 α subunit knockdown. We show the mild sorting defect is due to fortuitous substitution of the β2 chain with the closely related endogenous β1 subunit of the AP-1 adaptor complex. Simultaneous silencing of both β1 and β2 subunit transcripts recapitulates the strong α subunit RNA interference (RNAi) phenotype and results in loss of ARH from endocytic clathrin coats. An RNAi-insensitive β2-yellow fluorescent protein (YFP) expressed in the β1 + β2-silenced background restores cellular AP-2 levels, robust transferrin internalization, and ARH colocalization with cell surface clathrin. The importance of the β appendage platform subdomain over clathrin for precise deposition of ARH at clathrin assembly zones is revealed by a β2-YFP with a disrupted ARH binding interface, which does not restore ARH colocalization with clathrin. We also show a β-arrestin 1 mutant, which engages coated structures in the absence of any G protein-coupled receptor stimulation, colocalizes with β2-YFP and clathrin even in the absence of an operational clathrin binding sequence. These findings argue against ARH and β-arrestin binding to a site upon the β2 appendage platform that is later obstructed by polymerized clathrin. We conclude that ARH and β-arrestin depend on a privileged β2 appendage site for proper cargo recruitment to clathrin bud sites

Head-group acylation of monogalactosyldiacylglycerol is a common stress response, and the acyl-galactose acyl composition varies with the plant species and applied stress

This is the peer reviewed version of the following article: Vu, H. S., Roth, M. R., Tamura, P., Samarakoon, T., Shiva, S., Honey, S., Lowe, K., Schmelz, E. A., Williams, T. D. and Welti, R. (2014), Head-group acylation of monogalactosyldiacylglycerol is a common stress response, and the acyl-galactose acyl composition varies with the plant species and applied stress. Physiol Plantarum, 150: 517–528. doi:10.1111/ppl.12132, which has been published in final form at http://doi.org/10.1111/ppl.12132. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving.Formation of galactose-acylated monogalactosyldiacylglycerols has been shown to be induced by leaf homogenization, mechanical wounding, avirulent bacterial infection, and thawing after snap-freezing. Here, lipidomic analysis using mass spectrometry showed that galactose-acylated monogalactosyldiacylglycerols, formed in wheat (Triticum aestivum) and tomato (Solanum lycopersicum) leaves upon wounding, have acyl-galactose profiles that differ from those of wounded Arabidopsis thaliana, indicating that different plant species accumulate different acyl-galactose components in response to the same stress. Additionally, the composition of the acyl-galactose component of Arabidopsis acMGDG depends on the stress treatment. After sub-lethal freezing treatment, acMGDG contained mainly non-oxidized fatty acids esterified to galactose, whereas mostly oxidized fatty acids accumulated on galactose after wounding or bacterial infection. Compositional data are consistent with acMGDG being formed in vivo by transacylation with fatty acids from digalactosyldiacylglycerols. Oxophytodienoic acid, an oxidized fatty acid, was more concentrated on the galactosyl ring of acylated monogalactosyldiacylglycerols than in galactolipids in general. Also, oxidized fatty acid-containing acylated monogalactosyldiacylglycerols increased cumulatively when wounded Arabidopsis leaves were wounded again. These findings suggest that, in Arabidopsis, the pool of galactose-acylated monogalactosyldiacylglycerols may serve to sequester oxidized fatty acids during stress responses

A burden of proof study on alcohol consumption and ischemic heart disease

Cohort and case-control data have suggested an association between low to moderate alcohol consumption and decreased risk of ischemic heart disease (IHD), yet results from Mendelian randomization (MR) studies designed to reduce bias have shown either no or a harmful association. Here we conducted an updated systematic review and re-evaluated existing cohort, case-control, and MR data using the burden of proof meta-analytical framework. Cohort and case-control data show low to moderate alcohol consumption is associated with decreased IHD risk – specifically, intake is inversely related to IHD and myocardial infarction morbidity in both sexes and IHD mortality in males – while pooled MR data show no association, confirming that self-reported versus genetically predicted alcohol use data yield conflicting findings about the alcohol-IHD relationship. Our results highlight the need to advance MR methodologies and emulate randomized trials using large observational databases to obtain more definitive answers to this critical public health question