A CMOS compatible ultracompact silicon photonic optical add-drop multiplexer with misaligned Sidewall Bragg gratings

We experimentally and via simulations demonstrate ultracompact single-stage and cascaded optical add-drop multiplexers using misaligned sidewall Bragg grating in a Mach-Zehnder interferometer for the silicon-on-insulator platform. The single-stage configuration has a device footprint of 400 μm × 90 μm, and the cascaded configuration has a footprint of 400 μm × 125 μm. The proposed designs have 3-dB bandwidths of 6 nm and extinction ratios of 25 dB and 51 dB, respectively, and have been fabricated for the transverse electric mode. A minimum lithographic feature size of 80 nm is used in our design, which is within the limitation of 193 nm deep ultraviolet lithography

A robust SNP barcode for typing Mycobacterium tuberculosis complex strains

Strain-specific genomic diversity in the Mycobacterium tuberculosis complex (MTBC) is an important factor in pathogenesis that may affect virulence, transmissibility, host response and emergence of drug resistance. Several systems have been proposed to classify MTBC strains into distinct lineages and families. Here, we investigate single-nucleotide polymorphisms (SNPs) as robust (stable) markers of genetic variation for phylogenetic analysis. We identify ~92k SNP across a global collection of 1,601 genomes. The SNP-based phylogeny is consistent with the gold-standard regions of difference (RD) classification system. Of the ~7k strain-specific SNPs identified, 62 markers are proposed to discriminate known circulating strains. This SNP-based barcode is the first to cover all main lineages, and classifies a greater number of sublineages than current alternatives. It may be used to classify clinical isolates to evaluate tools to control the disease, including therapeutics and vaccines whose effectiveness may vary by strain type

Foliar treatments as a strategy to control iron chlorosis in orange trees

Different foliar treatments were applied to evaluate the recovery of iron chlorosis of orange trees (Citrus sinensis (L.) Osb. cv. 'Valencia late') grown on a calcareous soil. The treatments were: Fe (II) sulphate (500 mg Fe L-1), sulphuric acid (0.5 mM H2SO4), Fe (III)-chelate (Hampiron 654 GS, 120 mg Fe L-1) and distilled water as a control. The recovery from iron chlorosis was evaluated with the SPAD-502 apparatus and the values converted to total chlorophyll concentration. The effects of treatments on the mineral composition of leaves and flowers, and the size and quality of fruits were evaluated. The residual effect of treatments was also evaluated one year later. In orange trees, the use of frequent foliar sprays with Fe was able to alleviate Fe chlorosis and prevented yield and quality losses caused by Fe chlorosis. Compared with the control, sprays of Fe (II) sulphate led to higher concentrations of chlorophyll, Fe and Zn in leaves and flowers at the end of the experimental period, and significantly improved fruit size and quality. Leaf Fe concentration increased after the sulphuric acid spray, but this treatment did not affect fruit quality parameters. The mineral composition of flowers and leaves was correlated with some fruit quality parameters obtained one year later. These results suggest that foliar sprays with Fe could help to avoid fruit quality losses caused by Fe chlorosis in citrus orchards

Optical and thermal analysis of the light-heat conversion process employing an antenna-based hybrid plasmonic waveguide for HAMR

We investigate a tapered, hybrid plasmonic waveguide which has previously been proposed as an optically efficient near-field transducer (NFT), or component thereof, in several devices which aim to exploit nanofocused light. We numerically analyze how light is transported through the waveguide and ultimately focused via effective-mode coupling and taper optimization. Crucial dimensional parameters in this optimization process are identified that are not only necessary to achieve maximum optical throughput, but also optimum thermal performance with specific application towards heat-assisted magnetic recording (HAMR). It is shown that existing devices constructed on similar waveguides may benefit from a heat spreader to avoid deformation of the plasmonic element which we achieve with no cost to the optical efficiency. For HAMR, our design is able to surpass many industry requirements in regard to both optical and thermal efficiency using pertinent figure of merits like 8.5% optical efficiency

Interwoven migration narratives: identity and social representations in the Lusophone world

First published online: 17 Oct 2016This article provides an exploratory analysis of the life narratives of migrants in the Portuguese-speaking world. By interweaving the life experiences of eight participants in three thematic clusters – ‘shared past’, language and sense of community – we propose a critique of the deep-seated idea of the Lusophone space as a community constructed by the harmonious conviviality of different countries and people. Drawing on contributions from cultural studies, social psychology, anthropology and sociology, we first aim to give voice to the human subjects who embark on migrations and then to understand how the engendered process of identity construction is framed by their social world, simultaneously reframing it. Thus, we aim at shedding light on the ways in which aspects of the political discourses on Lusophony are used (and are instrumental) to the migrants’ identity narrative (re)construction.This work was supported by Fundacao para a Ciencia e a Tecnologia: [Grant Number PTDC/CCI-COM/105100/2008]

Two new rapid SNP-typing methods for classifying Mycobacterium tuberculosis complex into the main phylogenetic lineages

There is increasing evidence that strain variation in Mycobacterium tuberculosis complex (MTBC) might influence the outcome of tuberculosis infection and disease. To assess genotype-phenotype associations, phylogenetically robust molecular markers and appropriate genotyping tools are required. Most current genotyping methods for MTBC are based on mobile or repetitive DNA elements. Because these elements are prone to convergent evolution, the corresponding genotyping techniques are suboptimal for phylogenetic studies and strain classification. By contrast, single nucleotide polymorphisms (SNP) are ideal markers for classifying MTBC into phylogenetic lineages, as they exhibit very low degrees of homoplasy. In this study, we developed two complementary SNP-based genotyping methods to classify strains into the six main human-associated lineages of MTBC, the 'Beijing' sublineage, and the clade comprising Mycobacterium bovis and Mycobacterium caprae. Phylogenetically informative SNPs were obtained from 22 MTBC whole-genome sequences. The first assay, referred to as MOL-PCR, is a ligation-dependent PCR with signal detection by fluorescent microspheres and a Luminex flow cytometer, which simultaneously interrogates eight SNPs. The second assay is based on six individual TaqMan real-time PCR assays for singleplex SNP-typing. We compared MOL-PCR and TaqMan results in two panels of clinical MTBC isolates. Both methods agreed fully when assigning 36 well-characterized strains into the main phylogenetic lineages. The sensitivity in allele-calling was 98.6% and 98.8% for MOL-PCR and TaqMan, respectively. Typing of an additional panel of 78 unknown clinical isolates revealed 99.2% and 100% sensitivity in allele-calling, respectively, and 100% agreement in lineage assignment between both methods. While MOL-PCR and TaqMan are both highly sensitive and specific, MOL-PCR is ideal for classification of isolates with no previous information, whereas TaqMan is faster for confirmation. Furthermore, both methods are rapid, flexible and comparably inexpensive

Mycobacterium tuberculosis lineage 4 comprises globally distributed and geographically restricted sublineages

Generalist and specialist species differ in the breadth of their ecological niches. Little is known about the niche width of obligate human pathogens. Here we analyzed a global collection of Mycobacterium tuberculosis lineage 4 clinical isolates, the most geographically widespread cause of human tuberculosis. We show that lineage 4 comprises globally distributed and geographically restricted sublineages, suggesting a distinction between generalists and specialists. Population genomic analyses showed that, whereas the majority of human T cell epitopes were conserved in all sublineages, the proportion of variable epitopes was higher in generalists. Our data further support a European origin for the most common generalist sublineage. Hence, the global success of lineage 4 reflects distinct strategies adopted by different sublineages and the influence of human migration.We thank S. Lecher, S. Li and J. Zallet for technical support. Calculations were performed at the sciCORE scientific computing core facility at the University of Basel. This work was supported by the Swiss National Science Foundation (grants 310030_166687 (S.G.) and 320030_153442 (M.E.) and Swiss HIV Cohort Study grant 740 to L.F.), the European Research Council (309540-EVODRTB to S.G.), TB-PAN-NET (FP7-223681 to S.N.), PathoNgenTrace projects (FP7-278864-2 to S.N.), SystemsX.ch (S.G.), the German Center for Infection Research (DZIF; S.N.), the Novartis Foundation (S.G.), the Natural Science Foundation of China (91631301 to Q.G.), and the National Institute of Allergy and Infectious Diseases (5U01-AI069924-05) of the US National Institutes of Health (M.E.)

Measuring root system traits of wheat in 2D images to parameterize 3D root architecture models

Background and aimsThe main difficulty in the use of 3D root architecture models is correct parameterization. We evaluated distributions of the root traits inter-branch distance, branching angle and axial root trajectories from contrasting experimental systems to improve model parameterization.MethodsWe analyzed 2D root images of different wheat varieties (Triticum aestivum) from three different sources using automatic root tracking. Model input parameters and common parameter patterns were identified from extracted root system coordinates. Simulation studies were used to (1) link observed axial root trajectories with model input parameters (2) evaluate errors due to the 2D (versus 3D) nature of image sources and (3) investigate the effect of model parameter distributions on root foraging performance.ResultsDistributions of inter-branch distances were approximated with lognormal functions. Branching angles showed mean values <90°. Gravitropism and tortuosity parameters were quantified in relation to downwards reorientation and segment angles of root axes. Root system projection in 2D increased the variance of branching angles. Root foraging performance was very sensitive to parameter distribution and variance.Conclusions2D image analysis can systematically and efficiently analyze root system architectures and parameterize 3D root architecture models. Effects of root system projection (2D from 3D) and deflection (at rhizotron face) on size and distribution of particular parameters are potentially significant

Tuning the Graphene on Ir(111) adsorption regime by Fe/Ir surface-alloying

A combined scanning tunneling microscopy, x-ray photoelectron spectroscopy, angle-resolved photoemission spectroscopy, and density functional theory study of graphene on a Fe-Ir(111) alloy with variable Ir concentration is presented. Starting from an intercalated Fe layer between the graphene and Ir(111) surface we find that graphene-substrate interaction can be fine-tuned by Fe-Ir alloying at the interface. When a critical Ir-concentration close to 0.25 is reached in the Fe layer, the Dirac cone of graphene is largely restored and can thereafter be tuned across the Fermi level by further increasing the Ir content. Indeed, our study reveals an abrupt transition between a chemisorbed phase at small Ir concentrations and a physisorbed phase above the critical concentration. The latter phase is highly reminiscent of the graphene on the clean Ir(111) surface. Furthermore, the transition is accompanied by an inversion of the graphene''s induced magnetization due to the coupling with the Fe atoms from antiferromagnetic when chemisorbed to weakly ferromagnetic in the physisorption regime, with spin polarizations whose magnitude may be tuned with the amount of Fe content

Defining the Role of Ab Externo Xen Gel Stent in Glaucomatous Eyes With Prior Failed Surgical Intervention

PURPOSE: To evaluate the safety and efficacy of Xen45 Gel stent (Xen; Allergan) in eyes that have failed prior surgical intervention, compared to traditional glaucoma drainage device (GDD) or continuous-wave cyclophotocoagulation (CPC). Since this population has low expected success rates with additional surgery, it is vital to compare to standard-of-care surgical options. METHODS: Retrospective, single-center, case-control study of ab externo transconjunctival Xen shunt in eyes that have previously undergone trabeculectomy and/or GDD surgery. Postoperative data were collected for 18 months. Failure was defined as no light perception, additional glaucoma surgery required, or intraocular pressure (IOP) of \u3c 6 mmHg after 6 weeks postoperatively. RESULTS: Eighteen Xen eyes and 36 control eyes matched on both glaucoma type and previous glaucoma surgeries were included. Seventy-two percent had primary open angle glaucoma, 11% uveitic, 6% primary angle closure, 6% pseudoexfoliation, and 6% pigmentary glaucoma. Fifty-six percent of eyes in each group had prior trabeculectomy, 28% of Xen and 31% of control eyes had prior GDD, and 17% of Xen and 14% of control eyes had both. Baseline medicated IOP was lower in the Xen group (21.8 ± 7.2) compared to controls (27.5 ± 9.4, P = 0.043). The cumulative failure rate at year 1 was 17% for Xen and 20% for controls (P = 0.57). Mean survival time was 14.1 (± 1.5) months and 11.4 (± 0.6) months for controls. There was no difference in minor complication rates between groups (P = 0.65), but the Xen group had a significantly lower rate of serious complications (P = 0.043) defined as vision threatening or requiring surgical intervention in the operating room. When censored for additional glaucoma procedures, there were no differences at year 1 in IOP, change in IOP, number of IOP-lowering medications, or number of medications reduced from baseline. CONCLUSIONS: The Xen shunt provides a reasonable alternative to current standard of care, with a similar failure rate at year 1, with a noninferior IOP reduction compared to GDD and CPC, and a preferred safety profile