Experimental demonstration of TM lateral leakage in a standard SOI photonics platform

We provide an experimental demonstration of the width dependent losses of the fundamental TM guided mode in fabricated silicon-on-insulator shallow etched ridge waveguides

Microwave and RF Applications for Micro-resonator based Frequency Combs

Photonic integrated circuits that exploit nonlinear optics in order to generate and process signals all-optically have achieved performance far superior to that possible electronically - particularly with respect to speed. We review the recent achievements based in new CMOS-compatible platforms that are better suited than SOI for nonlinear optics, focusing on radio frequency (RF) and microwave based applications that exploit micro-resonator based frequency combs. We highlight their potential as well as the challenges to achieving practical solutions for many key applications. These material systems have opened up many new capabilities such as on-chip optical frequency comb generation and ultrafast optical pulse generation and measurement. We review recent work on a photonic RF Hilbert transformer for broadband microwave in-phase and quadrature-phase generation based on an integrated frequency optical comb. The comb is generated using a nonlinear microring resonator based on a CMOS compatible, high-index contrast, doped-silica glass platform. The high quality and large frequency spacing of the comb enables filters with up to 20 taps, allowing us to demonstrate a quadrature filter with more than a 5-octave (3 dB) bandwidth and an almost uniform phase response.Comment: 10 pages, 6 figures, 68 references. arXiv admin note: substantial text overlap with arXiv:1512.0174

Neuropsychiatric manifestation of confusional psychosis due to Cryptococcus neoformans var. grubii in an apparently immunocompetent host: a case report

Cognitive disorders like dementia, delirium, depression, anxiety, psychosis and mania are the commonest neuropsychiatric manifestations. We discuss here a case of an adult women presenting with neuropsychiatric manifestations of confusional psychosis owing to Cryptococcosis. The principal cause was consequently established by culturing Cryptococcus neoformans from the cerebrospinal fluid confirmed as C. neoformans var. grubii (Serotype A) by genotypic methods. Antifungal therapy with IV Amphotericin B lead to sustained improvement and recovery of the patient from behavioural disorders. The case discussed here invokes the need for the vigilance it demands in delineating organic brain syndromes for a favourable treatment outcome

Automated Analysis of Cryptococcal Macrophage Parasitism Using GFP-Tagged Cryptococci

The human fungal pathogens Cryptococcus neoformans and C. gattii cause life-threatening infections of the central nervous system. One of the major characteristics of cryptococcal disease is the ability of the pathogen to parasitise upon phagocytic immune effector cells, a phenomenon that correlates strongly with virulence in rodent models of infection. Despite the importance of phagocyte/Cryptococcus interactions to disease progression, current methods for assaying virulence in the acrophage system are both time consuming and low throughput. Here, we introduce the first stable and fully characterised GFP–expressing derivatives of two widely used cryptococcal strains: C. neoformans serotype A type strain H99 and C. gattii serotype B type strain R265. Both strains show unaltered responses to environmental and host stress conditions and no deficiency in virulence in the macrophage model system. In addition, we report the development of a method to effectively and rapidly investigate macrophage parasitism by flow cytometry, a technique that preserves the accuracy of current approaches but offers a four-fold improvement in speed

Microevolution of serial clinical isolates of Cryptococcus neoformans var. grubii and C. gattii

This is the final version. Available from the publisher via the DOI in this record.The pathogenic species of Cryptococcus are a major cause of mortality owing to severe infections in immunocompromised as well as immunocompetent individuals. Although antifungal treatment is usually effective, many patients relapse after treatment, and in such cases, comparative analyses of the genomes of incident and relapse isolates may reveal evidence of determinative, microevolutionary changes within the host. Here, we analyzed serial isolates cultured from cerebrospinal fluid specimens of 18 South African patients with recurrent cryptococcal meningitis. The time between collection of the incident isolates and collection of the relapse isolates ranged from 124 days to 290 days, and the analyses revealed that, during this period within the patients, the isolates underwent several genetic and phenotypic changes. Considering the vast genetic diversity of cryptococcal isolates in subSaharan Africa, it was not surprising to find that the relapse isolates had acquired different genetic and correlative phenotypic changes. They exhibited various mechanisms for enhancing virulence, such as growth at 39°C, adaptation to stress, and capsule production; a remarkable amplification of ERG11 at the native and unlinked locus may provide stable resistance to fluconazole. Our data provide a deeper understanding of the microevolution of Cryptococcus species under pressure from antifungal chemotherapy and host immune responses. This investigation clearly suggests a promising strategy to identify novel targets for improved diagnosis, therapy, and prognosis.Wellcome TrustNational Institute of Allergy and Infectious Disease

Mixture of experts models to exploit global sequence similarity on biomolecular sequence labeling

Background: Identification of functionally important sites in biomolecular sequences has broad applications ranging from rational drug design to the analysis of metabolic and signal transduction networks. Experimental determination of such sites lags far behind the number of known biomolecular sequences. Hence, there is a need to develop reliable computational methods for identifying functionally important sites from biomolecular sequences. Results: We present a mixture of experts approach to biomolecular sequence labeling that takes into account the global similarity between biomolecular sequences. Our approach combines unsupervised and supervised learning techniques. Given a set of sequences and a similarity measure defined on pairs of sequences, we learn a mixture of experts model by using spectral clustering to learn the hierarchical structure of the model and by using bayesian techniques to combine the predictions of the experts. We evaluate our approach on two biomolecular sequence labeling problems: RNA-protein and DNA-protein interface prediction problems. The results of our experiments show that global sequence similarity can be exploited to improve the performance of classifiers trained to label biomolecular sequence data. Conclusion: The mixture of experts model helps improve the performance of machine learning methods for identifying functionally important sites in biomolecular sequences.This is a proceeding from IEEE International Conference on Bioinformatics and Biomedicine (BIBM) 10 (2009): S4, doi: 10.1186/1471-2105-10-S4-S4. Posted with permission.</p

Quantifying the effect of testate amoeba decomposition on peat-based water-table reconstructions

This is the author accepted manuscript. The final version is available from Elsevier via the DOI in this record.Testate amoebae are a widely-used tool for palaeohydrological reconstruction from peatlands. However, it has been observed that weak idiosomic siliceous tests (WISTs) are common in uppermost peats, but very rarely found as subfossils deeper in the peat profile. This taphonomic problem has been noted widely and it has been established that WISTs disaggregate and/or dissolve in the low pH condition of ombrotrophic peatlands. Here we investigate the effect of this taphonomic problem on water-table reconstructions from thirty European peatlands through the comparison of reconstructions based on all taxa and those with WISTs removed. In almost all cases the decomposition of WISTs does not introduce discernible bias to peatland water-table reconstructions. However, some discrepancy is apparent when large abundances of Corythion-Trinema type are present (9−12 cm deviation with 50–60% abundance of this particular taxon). We recommend that WISTs should be removed before carrying out water-table reconstructions, and that the minimum count of testate amoebae per sample should exclude WISTs to ensure the development of robust reconstructions

Effect of Biodiversity Changes in Disease Risk: Exploring Disease Emergence in a Plant-Virus System

The effect of biodiversity on the ability of parasites to infect their host and cause disease (i.e. disease risk) is a major question in pathology, which is central to understand the emergence of infectious diseases, and to develop strategies for their management. Two hypotheses, which can be considered as extremes of a continuum, relate biodiversity to disease risk: One states that biodiversity is positively correlated with disease risk (Amplification Effect), and the second predicts a negative correlation between biodiversity and disease risk (Dilution Effect). Which of them applies better to different host-parasite systems is still a source of debate, due to limited experimental or empirical data. This is especially the case for viral diseases of plants. To address this subject, we have monitored for three years the prevalence of several viruses, and virus-associated symptoms, in populations of wild pepper (chiltepin) under different levels of human management. For each population, we also measured the habitat species diversity, host plant genetic diversity and host plant density. Results indicate that disease and infection risk increased with the level of human management, which was associated with decreased species diversity and host genetic diversity, and with increased host plant density. Importantly, species diversity of the habitat was the primary predictor of disease risk for wild chiltepin populations. This changed in managed populations where host genetic diversity was the primary predictor. Host density was generally a poorer predictor of disease and infection risk. These results support the dilution effect hypothesis, and underline the relevance of different ecological factors in determining disease/infection risk in host plant populations under different levels of anthropic influence. These results are relevant for managing plant diseases and for establishing conservation policies for endangered plant species

Experimental demonstration of two-dimensional hybrid waveguide-integrated plasmonic crystals on silicon-on-insulator platform

Nanoscale plasmonic structures can offer unique functionality due to extreme sub-wavelength optical confinement, but the realization of complex plasmonic circuits is hampered by high propagation losses. Hybrid approaches can potentially overcome this limitation, but only few practical approaches based on either single or few element arrays of nanoantennas on dielectric nanowire have been experimentally demonstrated. In this paper, we demonstrate a two dimensional hybrid photonic plasmonic crystal interfaced with a standard silicon photonic platform. Off resonance, we observe low loss propagation through our structure, while on resonance we observe strong propagation suppression and intense concentration of light into a dense lattice of nanoscale hot-spots on the surface providing clear evidence of a hybrid photonic plasmonic crystal bandgap. This fully integrated approach is compatible with established silicon-on-insulator (SOI) fabrication techniques and constitutes a significant step toward harnessing plasmonic functionality within SOI photonic circuits