Analysis of second harmonic generation in photonic-crystal-assisted waveguides

We study second harmonic generation in a planar dielectric waveguide having a low-index, polymer core layer, bounded by two multilayer stacks. This geometry allows exceptionally strong confinement of the light at the fundamental wavelength inside the core region with virtually zero net propagation losses for distances that exceed several centimeters, provided material and scattering losses are neglected. A phase-matched configuration of the waveguide is reported in which the pump signal is the lowest-order mode of the waveguide, and the generated second harmonic signal corresponds to the third propagation mode of the waveguide. Using a polymer waveguide core, having chi(2)=100 pm/V, we predict a conversion efficiency of approximately 90% after a propagation distance of 2 mm, using peak pump intensities inside the core of the waveguide of 1.35 GW/cm^2. If the waveguide core contains polymer layers with different glass transition temperatures, the layers can be poled independently to maximize the overlap integral, and similar pump depletions may be achieved over a distance of approximately 500 microns.Comment: 20 pages, 7 figures, 330k

Antiresonant guiding microstructured optical fibers for sensing applications

A novel refractometric sensor utilizing unique spectral properties of antiresonant-guiding microstructured optical fibers is proposed. The sensor operation is based on the wavelength shift of the transmission spectrum in response to the refractive index change of a sample loaded in the air-holes of the microstructured optical fiber. Refractive index changes on the order of 0.1% can be detected using less than a nanoliter of a sample.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/47050/1/340_2005_Article_1888.pd

Genome-wide changes in protein translation efficiency are associated with autism

We previously proposed that changes in the efficiency of protein translation are associated with autism spectrum disorders (ASDs). This hypothesis connects environmental factors and genetic factors because each can alter translation efficiency. For genetic factors, we previously tested our hypothesis using a small set of ASD-associated genes, a small set of ASD-associated variants, and a statistic to quantify by how much a single nucleotide variant (SNV) in a protein coding region changes translation speed. In this study, we confirm and extend our hypothesis using a published set of 1,800 autism quartets (parents, one affected child and one unaffected child) and genome-wide variants. Then, we extend the test statistic to combine translation efficiency with other possibly relevant variables: ribosome profiling data, presence/absence of CpG dinucleotides, and phylogenetic conservation. The inclusion of ribosome profiling abundances strengthens our results for male–male sibling pairs. The inclusion of CpG information strengthens our results for female–female pairs, giving an insight into the significant gender differences in autism incidence. By combining the single-variant test statistic for all variants in a gene, we obtain a single gene score to evaluate how well a gene distinguishes between affected and unaffected siblings. Using statistical methods, we compute gene sets that have some power to distinguish between affected and unaffected siblings by translation efficiency of gene variants. Pathway and enrichment analysis of those gene sets suggest the importance of Wnt signaling pathways, some other pathways related to cancer, ATP binding, and ATP-ase pathways in the etiology of ASDs

An electromagnetic shashlik calorimeter with longitudinal segmentation

A novel technique for longitudinal segmentation of shashlik calorimeters has been tested in the CERN West Area beam facility. A 25 tower very fine samplings e.m. calorimeter has been built with vacuum photodiodes inserted in the first 8 radiation lengths to sample the initial development of the shower. Results concerning energy resolution, impact point reconstruction and electron/pion separation are reported.Comment: 13 pages, 12 figure

Distributed XQuery-based integration and visualization of multimodality data: Application to brain mapping.

This paper addresses the need for relatively small groups of collaborating investigators to integrate distributed and heterogeneous data about the brain. Although various national efforts facilitate large-scale data sharing, these approaches are generally too “heavyweight” for individual or small groups of investigators, with the result that most data sharing among collaborators continues to be ad hoc. Our approach to this problem is to create a “lightweight” distributed query architecture, in which data sources are accessible via web services that accept arbitrary query languages but return XML results. A Distributed XQuery Processor (DXQP) accepts distributed XQueries in which subqueries are shipped to the remote data sources to be executed, with the resulting XML integrated by DXQP. A web-based application called DXBrain accesses DXQP, allowing a user to create, save and execute distributed XQueries, and to view the results in various formats including a 3-D brain visualization. Example results are presented using distributed brain mapping data sources obtained in studies of language organization in the brain, but any other XML source could be included. The advantage of this approach is that it is very easy to add and query a new source, the tradeoff being that the user needs to understand XQuery and the schemata of the underlying sources. For small numbers of known sources this burden is not onerous for a knowledgeable user, leading to the conclusion that the system helps to fill the gap between ad hoc local methods and large scale but complex national data sharing efforts

An electromagnetic shashlik calorimeter with longitudinal segmentation

A novel technique for longitudinal segmentation of shashlik calorimeters has been tested in the CERN West Area beam facility. A 25 tower e.m. calorimeter has been built with vacuum photodiodes inserted in the first 8 radiation lengths to sample the initial development of the shower. Results concerning energy resolution, impact point reconstruction and $e/\pi$ separation are reported.A novel technique for longitudinal segmentation of shashlik calorimeters has been tested in the CERN West Area beam facility. A 25 tower very fine samplings e.m. calorimeter has been built with vacuum photodiodes inserted in the first 8 radiation lengths to sample the initial development of the shower. Results concerning energy resolution, impact point reconstruction and electron/pion separation are reported

A shashlik calorimeter with longitudinal segmentation for a linear collider

Two techniques for longitudinal segmentation of shashlik calorimeters are proposed. Beam tests have demonstrated the technical feasibility of longitudinally segmented shashlik calorimeters in which longitudinal sampling is performed by lateral vacuum photodiodes or by using two scintillator types with different decay times. Results concerning energy resolution and e/π separation are presente

An Integrative Computational Approach for Prioritization of Genomic Variants

An essential step in the discovery of molecular mechanisms contributing to disease phenotypes and efficient experimental planning is the development of weighted hypotheses that estimate the functional effects of sequence variants discovered by high-throughput genomics. With the increasing specialization of the bioinformatics resources, creating analytical workflows that seamlessly integrate data and bioinformatics tools developed by multiple groups becomes inevitable. Here we present a case study of a use of the distributed analytical environment integrating four complementary specialized resources, namely the Lynx platform, VISTA RViewer, the Developmental Brain Disorders Database (DBDB), and the RaptorX server, for the identification of high-confidence candidate genes contributing to pathogenesis of spina bifida. The analysis resulted in prediction and validation of deleterious mutations in the SLC19A placental transporter in mothers of the affected children that causes narrowing of the outlet channel and therefore leads to the reduced folate permeation rate. The described approach also enabled correct identification of several genes, previously shown to contribute to pathogenesis of spina bifida, and suggestion of additional genes for experimental validations. The study demonstrates that the seamless integration of bioinformatics resources enables fast and efficient prioritization and characterization of genomic factors and molecular networks contributing to the phenotypes of interest.</p