Singular-phase nanooptics: towards label-free single molecule detection

Non-trivial topology of phase is crucial for many important physics phenomena such as, for example, the Aharonov-Bohm effect 1 and the Berry phase 2. Light phase allows one to create "twisted" photons 3, 4 , vortex knots 5, dislocations 6 which has led to an emerging field of singular optics relying on abrupt phase changes 7. Here we demonstrate the feasibility of singular visible-light nanooptics which exploits the benefits of both plasmonic field enhancement and non-trivial topology of light phase. We show that properly designed plasmonic nanomaterials exhibit topologically protected singular phase behaviour which can be employed to radically improve sensitivity of detectors based on plasmon resonances. By using reversible hydrogenation of graphene 8 and a streptavidin-biotin test 9, we demonstrate areal mass sensitivity at a level of femto-grams per mm2 and detection of individual biomolecules, respectively. Our proof-of-concept results offer a way towards simple and scalable single-molecular label-free biosensing technologies.Comment: 19 pages, 4 figure

Azithromycin for sarcoidosis cough: an open label exploratory clinical trial

Background Chronic cough is a distressing symptom for many people with pulmonary sarcoidosis. Continuous treatment with a macrolide antibiotic may improve cough. We aimed to assess the potential efficacy of azithromycin in patients with sarcoidosis and self-reported cough.Methods We did a non-controlled, open label clinical trial of azithromycin 250 mg once daily for 3 months in patients with pulmonary sarcoidosis who reported a chronic cough. The primary outcome was number of coughs in 24 h. Secondary outcomes were cough visual analog scales and quality of life measured using the Leicester Cough Questionnaire and King's Sarcoidosis Questionnaire. Safety outcomes included QTc interval on ECG. Measurements were made at baseline and after one and 3 months of treatment.Results All 21 patients were white, median age 57 years, 9 males/12 females, median 3 years since diagnosis. Five were taking oral corticosteroids and none were taking other immunosuppressants. Twenty patients completed the trial. The median (range) number of coughs in 24 h was 228 (43–1950) at baseline, 122 (20–704) at 1 month, and 81 (16–414) at 3 months (p=0.002, Friedman's test). The median reduction in cough count at 3 months was 49.6%. There were improvements in all patient-reported outcomes. Azithromycin was well tolerated.Conclusion In a non-controlled open-label trial in people with sarcoidosis who reported a chronic cough, 3 months of treatment with azithromycin led to improvements in a range of cough metrics. Azithromycin should be tested as a treatment for sarcoidosis cough in a randomised placebo-controlled trial

Graphene-protected copper and silver plasmonics

Plasmonics has established itself as a branch of physics which promises to revolutionize data processing, improve photovoltaics, increase sensitivity of bio-detection. A widespread use of plasmonic devices is notably hindered (in addition to high losses) by the absence of stable and inexpensive metal films suitable for plasmonic applications. This may seem surprising given the number of metal compounds to choose from. Unfortunately, most of them either exhibit a strong damping of surface plasmons or easily oxidize and corrode. To this end, there has been continuous search for alternative plasmonic materials that are, unlike gold, the current metal of choice in plasmonics, compatible with complementary metal oxide semiconductor technology. Here we show that copper and silver protected by graphene are viable candidates. Copper films covered with one to a few graphene layers show excellent plasmonics characteristics surpassing those of gold films. They can be used to fabricate plasmonic devices and survive for at least a year, even in wet and corroding conditions. As a proof of concept, we use the graphene-protected copper to demonstrate dielectric loaded plasmonic waveguides and test sensitivity of surface plasmon resonances. Our results are likely to initiate a wide use of graphene-protected plasmonics.Comment: 22 pages, 5 figure

Crop Updates 2000 - Cereals part 2

This session covers twenty papers from different authors: DISEASE 1. Forecasting aphid and virus risk in cereals, Debbie Thackray, Jenny Hawkes and Roger Jones, Agriculture Western Australia and Centre for Legumes in Mediterranean Agriculture 2. Cereal Diagnostics, Dominie Wright, Agriculture Western Australia 3. The economic returns from spraying for leaf rust in the central wheatbelt in 1999, Peter Carlton, Trials Coordinator, Elders Limited 4. Impact and Management of Yellow Spot and Leaf Rust in the Northern Agricultural Region, Jat Bhathal and Robert Loughman, Agriculture Western Australia 5. Leaf disease management in wheat and barley in the southern agricultural region, K. Jayasena, R. Loughman and J. Majewski, Agriculture Western Australia 6. Root nematode update, R. Loughman1, S. Kelly1, G. Holloway2, N. Venn1 and D. Diepeveen1 1 Agriculture Western Australia, 2Agriculture Victoria WHEAT AGRONOMY 7. Small Grain Screenings in wheat - the agronomic issues, Brenda Shackley, Agriculture Western Australia, 8. Response of New Wheat Varieties to Seed Rate and applied Nitrogen in the North, Darshan Sharma and Wal Anderson, Agriculture Western Australia 9. Seen vigour in wheat, Darshan Sharma and Wal Anderson, Agriculture Western Australia 10. Influence of the Time of Sowing on New Wheat Varieties in the North, Darshan Sharma and Wal Anderson, Agriculture Western Australia 11, Wheat performance in a high disease season on the South Coast. 1. Disease and grain quality on the Esperance sandplain, Mohammad Amjad, Vanessa Dooley and Wal Anderson, Agriculture Western Australia 12. Wheat performance in a high disease season on the South Coast. 2. Leaf area, disease and yield at Gibson and Salmon Gums, Mohammad Amjad, Vanessa Dooley and Wal Anderson, Agriculture Western Australia 13. Agronomic Evaluation of Wheat in the Central Wheatbelt of Western Australia, Peter Burgess and Ashley Bacon, Agritech Crop Research 14. Mechanisms influencing grain susceptibility to black point in wheat, Frances Hoyle, University of Western Australia and Agriculture Western Australia 15. Improving paddock productivity using renovation cropping techniques on heavier soils, Frances Hoyle, Agriculture Western Australia 16. Improving paddock productivity using renovation cropping techniques on sandplain soils, Frances Hoyle and Keith Devenish, Agriculture Western Australia 17. Increasing profit - Is it possible using high input package approach for cereal production? M. Appelbee, IAMA Agri Services 18. Improving wheat yield, soil physical and chemical fertility by a package of deep ripping, gypsum and complete nutrients, M.A. Hamza and W.K. Anderson, Agriculture Western Australia 19. Organic Wheat - Production System Guidelines, Steven McCoy, Centre for New Industries Development 20. Durum wheat obtains a premium over bread wheat, Steven Penny, Agriculture Western Australi

Benchmarking implementations of functional languages with ‘Pseudoknot', a float-intensive benchmark

Over 25 implementations of different functional languages are benchmarked using the same program, a floating-point intensive application taken from molecular biology. The principal aspects studied are compile time and execution time for the various implementations that were benchmarked. An important consideration is how the program can be modified and tuned to obtain maximal performance on each language implementation. With few exceptions, the compilers take a significant amount of time to compile this program, though most compilers were faster than the then current GNU C compiler (GCC version 2.5.8). Compilers that generate C or Lisp are often slower than those that generate native code directly: the cost of compiling the intermediate form is normally a large fraction of the total compilation time. There is no clear distinction between the runtime performance of eager and lazy implementations when appropriate annotations are used: lazy implementations have clearly come of age when it comes to implementing largely strict applications, such as the Pseudoknot program. The speed of C can be approached by some implementations, but to achieve this performance, special measures such as strictness annotations are required by non-strict implementations. The benchmark results have to be interpreted with care. Firstly, a benchmark based on a single program cannot cover a wide spectrum of ‘typical' applications. Secondly, the compilers vary in the kind and level of optimisations offered, so the effort required to obtain an optimal version of the program is similarly varie

DIMBOA levels in hexaploid Brazilian wheat are not associated with antibiosis against the cereal aphids Rhopalosiphum padi and Sitobion avenae.

The objective of this study was to evaluate the natural levels of the plant defence compound DIMBOA in young leaves of eight hexaploid Brazilian wheat genotypes and the impact of the genotypes upon development of cereal aphids, Rhopalosiphum padi and Sitobion avenae. HPLC Analysis revealed that the DIMBOA levels varied from 5.376 (in BRS Guabiju) to 30.651 mmol/kgFW (in BRS Timbaúva) with two genotypes outperforming Solstice, a UK variety used as reference. Bioassays were conducted to evaluate the development and fecundity of both aphids when grown on the wheat genotypes. Although BRS Guabiju and BRS Timbaúva were among the genotypes showing the highest and lowest susceptibility respectively, against both aphids, no correlation could be found between DIMBOA levels and antibiosis effects. The cultivar BRS 327 that was among the genotypes showing lower intrinsic rate of population increase for the two aphid species. Elucidating the role of secondary metabolites in plant resistance to aphids and the characterisation of the genotypes that allowed reduced aphid development are important steps to achieve a better natural resistance in hexaploid Brazilian wheat

Hypergraph models of biological networks to identify genes critical to pathogenic viral response

Background: Representing biological networks as graphs is a powerful approach to reveal underlying patterns, signatures, and critical components from high-throughput biomolecular data. However, graphs do not natively capture the multi-way relationships present among genes and proteins in biological systems. Hypergraphs are generalizations of graphs that naturally model multi-way relationships and have shown promise in modeling systems such as protein complexes and metabolic reactions. In this paper we seek to understand how hypergraphs can more faithfully identify, and potentially predict, important genes based on complex relationships inferred from genomic expression data sets. Results: We compiled a novel data set of transcriptional host response to pathogenic viral infections and formulated relationships between genes as a hypergraph where hyperedges represent significantly perturbed genes, and vertices represent individual biological samples with specific experimental conditions. We find that hypergraph betweenness centrality is a superior method for identification of genes important to viral response when compared with graph centrality. Conclusions: Our results demonstrate the utility of using hypergraphs to represent complex biological systems and highlight central important responses in common to a variety of highly pathogenic viruses

Seropositivity to Herpes Simplex Virus Antibodies and Risk of Alzheimer's Disease: A Population-Based Cohort Study

International audienceBACKGROUND: Herpes Simplex Virus (HSV) infection has been proposed as a possible risk factor of Alzheimer's Disease (AD) notably because it is neurotropic, ubiquitous in the general population and able to establish lifelong latency in the host. The fact that HSV was present in elderly subjects with AD suggests that the virus could be a co-factor of the disease. We investigated the risk of developing AD in anti-HSV immunoglobulin G (IgG) positive subjects (indicator of a lifelong infection to HSV) and IgM-positive subjects (indicator of primary infection or reactivation of the virus) in a longitudinal population-based cohort of elderly subjects living in the community. METHODS: Cox proportional hazard models were used to study the risk of developing AD according to the presence or not of anti-HSV IgG and IgM antibodies, assessed in the sera of 512 elderly initially free of dementia followed for 14 years. RESULTS: During the follow-up, 77 incident AD cases were diagnosed. Controlled for age, gender, educational level and Apolipoprotein E4 (APOE4) status, IgM-positive subjects showed a significant higher risk of developing AD (HR = 2.55; 95% CI [1.38-4.72]), although no significant increased risk was observed in IgG-positive subjects (HR = 1.67; 95%CI [0.75-3.73]). No modification effect with APOE4 status was found. CONCLUSION: Reactivation of HSV seropositivity is highly correlated with incident AD. HSV chronic infection may therefore be contributive to the progressive brain damage characteristic of AD