Coupled-mode theory for periodic side-coupled microcavity and photonic crystal structures

We use a phenomenological Hamiltonian approach to derive a set of coupled mode equations that describe light propagation in waveguides that are periodically side-coupled to microcavities. The structure exhibits both Bragg gap and (polariton like) resonator gap in the dispersion relation. The origin and physical significance of the two types of gaps are discussed. The coupled-mode equations derived from the effective field formalism are valid deep within the Bragg gaps and resonator gaps.Comment: 13 pages, 6 figure

Electric Field-Driven Water Dipoles: Nanoscale Architecture of Electroporation

<div><p>Electroporation is the formation of permeabilizing structures in the cell membrane under the influence of an externally imposed electric field. The resulting increased permeability of the membrane enables a wide range of biological applications, including the delivery of normally excluded substances into cells. While electroporation is used extensively in biology, biotechnology, and medicine, its molecular mechanism is not well understood. This lack of knowledge limits the ability to control and fine-tune the process. In this article we propose a novel molecular mechanism for the electroporation of a lipid bilayer based on energetics analysis. Using molecular dynamics simulations we demonstrate that pore formation is driven by the reorganization of the interfacial water molecules. Our energetics analysis and comparisons of simulations with and without the lipid bilayer show that the process of poration is driven by field-induced reorganization of water dipoles at the water-lipid or water-vacuum interfaces into more energetically favorable configurations, with their molecular dipoles oriented in the external field. Although the contributing role of water in electroporation has been noted previously, here we propose that interfacial water molecules are the main players in the process, its initiators and drivers. The role of the lipid layer, to a first-order approximation, is then reduced to a relatively passive barrier. This new view of electroporation simplifies the study of the problem, and opens up new opportunities in both theoretical modeling of the process and experimental research to better control or to use it in new, innovative ways.</p></div

Transgenic plant-derived siRNAs can suppress propagation of influenza virus in mammalian cells

As an example of the cost-effective large-scale generation of small-interfering RNA (siRNAs), we have created transgenic tobacco plants that produce siRNAs targeted to the mRNA of the non-structural protein NS1 from the influenza A virus subtype H1N1. We have investigated if these siRNAs, specifically targeted to the 5 ′-portion of the NS1 transcripts (5mNS1), would suppress viral propagation in mammalian cells. Agroinfiltration of transgenic tobacco with an Agrobacterium strain harboring a 5mNS1-expressing binary vector caused a reduction in 5mNS1 transcripts in the siRNA-accumulating transgenic plants. Further, H1N1 infection of siRNA-transfected mammalian cells resulted in significant suppression of viral replication. These results demonstrate that plant-derived siRNAs can inhibit viral propagation through RNA interference and could potentially be applied in control of viral-borne diseases. © 2004 Published by Elsevier B.V. on behalf of the Federation of European Biochemical Societies.postprin

MF2293

Fadi Aramouni et al, Food safety, Kansas State University, October 1997

IPD-MHC 2.0:An improved inter-species database for the study of the major histocompatibility complex

The IPD-MHC Database project (http://www.ebi.ac.uk/ipd/mhc/) collects and expertly curates sequences of the major histocompatibility complex from non-human species and provides the infrastructure and tools to enable accurate analysis. Since the first release of the database in 2003, IPD-MHC has grown and currently hosts a number of specific sections, with more than 7000 alleles from 70 species, including non-human primates, canines, felines, equids, ovids, suids, bovins, salmonids and murids. These sequences are expertly curated and made publicly available through an open access website. The IPD-MHC Database is a key resource in its field, and this has led to an average of 1500 unique visitors and more than 5000 viewed pages per month. As the database has grown in size and complexity, it has created a number of challenges in maintaining and organizing information, particularly the need to standardize nomenclature and taxonomic classification, while incorporating new allele submissions. Here, we describe the latest database release, the IPD-MHC 2.0 and discuss planned developments. This release incorporates sequence updates and new tools that enhance database queries and improve the submission procedure by utilizing common tools that are able to handle the varied requirements of each MHC-group

Characteristics of Fine Particulate Matter (PM2.5) over urban, suburban and rural areas of Hong Kong

In urban areas, Fine Particulate Matter (PM2.5) associated with local vehicle emissions can cause respiratory and cardiorespiratory disease and increased mortality rates, but less in rural areas. However, Hong Kong may be a special case since the whole territory often suffers from regional haze from nearby mainland China, as well as local sources. Therefore, to understand which areas of Hong Kong may be affected by damaging levels of fine particulates, PM2.5 data were obtained from March 2005 to February 2009 for urban, suburban and rural air quality monitoring stations; namely Central (city area, commercial area, and urban populated area), Tsuen Wan (city area, commercial area, urban populated, and residential area), Tung Chung (suburban and residential area), Yuen Long (urban and residential area), and Tap Mun (remote rural area). To evaluate the relative contributions of regional and local pollution sources, the study aims to test the influence of weather conditions on PM2.5 concentrations. Thus meteorological parameters including temperature, relative humidity, wind speed, and wind directions were obtained from the Hong Kong Observatory.. The results showed that Hong Kong’s air quality is mainly affected by regional aerosol emissions, either transported from the land or ocean, as similar patterns of variations in PM2.5 concentrations were observed over urban, suburban, and rural areas of Hong Kong. Only slightly higher PM2.5 concentrations were observed over urban sites, such as Central, compared to suburban and rural sites, which could be attributed to local automobile emissions. Results showed that meteorological parameters have potential to explain 80% of the variability in daily mean PM2.5 concentrations at Yuen Long, 77% at Tung Chung, 72% at Central, 71% at Tsuen Wan, and 67% at Tap Mun during the spring to summer part of the year. The results provide not only a better understanding of the impact of regional long-distance transport of air pollutants on Hong Kong’s air quality but also a reference for future regional-scale collaboration on air quality management

RNA Sequencing Identifies Transcriptionally Viable Gene Fusions in Esophageal Adenocarcinomas

Esophageal adenocarcinoma (EAC) is a deadly cancer with increasing incidence in the U.S., but mechanisms underlying pathogenesis are still mostly elusive. In addressing this question, we assessed gene-fusion landscapes by comprehensive RNA sequencing (RNAseq) of 55 pre-treatment EAC and 49 non-malignant biopsy tissues from patients undergoing endoscopy for Barrett’s esophagus. In this cohort, we identified 21 novel candidate EAC-associated fusions occurring in 3.33%-11.67% of EACs. Two candidate fusions were selected for validation by PCR and Sanger sequencing in an independent set of pre-treatment EAC (N=115) and non-malignant (N=183) biopsy tissues. In particular, we observed RPS6KB1–VMP1 gene fusion as a recurrent event occurring in ~10% of EAC cases. Notably, EAC cases harboring RPS6KB1–VMP1 fusions exhibited significantly poorer overall survival as compared to fusion-negative cases. Mechanistic investigations established that the RPS6KB1–VMP1 transcript coded for a fusion protein which significantly enhanced the growth rate of non-dysplastic Barrett’s esophagus cells. Compared to the wild-type VMP1 protein, which mediates normal cellular autophagy, RPS6KB1–VMP1 fusion exhibited aberrant subcellular localization and was relatively ineffective in triggering autophagy. Overall, our findings identified RPS6KB1–VMP1 as a genetic fusion that promotes EAC by modulating autophagy-related processes, offering new insights into the molecular pathogenesis of esophageal adenocarcinomas

A reassessment of primary thyroid lymphoma: high-grade MALT-type lymphoma as a distinct subtype of diffuse large B-cell lymphoma

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/73362/1/j.1365-2559.2000.00941.x.pd