Development of polycrystalline silicon waveguides by laser crystallization

Silicon (Si) is an excellent material for integrated photonics devices as its high refractive index allows for small device footprints. To date, most of the work in this area has leveraged the single crystal silicon-on-insulator platforms, which are relatively expensive to produce and thus drive up component costs. Here we propose an alternative method to fabricate crystalline silicon waveguides by laser processing of an amorphous starting material. As well as reducing production costs, this approach has the added advantage of removing the substrate dependence so that more flexible alternatives can be considered. This method has previously been applied to a-Si wires grown inside silica capillaries and shown to produce very large crystallites [1]. Here we demonstrate preliminary results of laser-induced crystallization of a-Si films and micro-patterned wires produced by chemical vapor deposition (CVD) on SiO2 substrates. The samples have been crystallized using a c.w. argon-ion laser at 488nm. Crystallized tracks have been written by scanning the focused beam across the samples using different laser intensities and scanning speeds. The resulting material quality is then studied using Raman spectrometry, optical and electronic microscopy and X-ray diffraction. For the planar films, we have produced crystallite sizes on the order of hundreds of nanometers to a few microns; similar to those obtained via conventional pulsed Excimer laser crystallization [2]. However, for the micro-patterned samples, we have found that it is possible to grow crystals that almost cover the entire width of the wire, over lengths of up to 18µm, considerably larger than what is typically reported for polysilicon waveguide devices [3]. Furthermore, this laser crystallization method has been observed to reform the surface of the Si wires resulting in very smooth sidewall profiles (as shown in Fig. 1) which is very important for low loss optical transmission in photonic devices

Reconstructing transmission trees for communicable diseases using densely sampled genetic data.

Whole genome sequencing of pathogens from multiple hosts in an epidemic offers the potential to investigate who infected whom with unparalleled resolution, potentially yielding important insights into disease dynamics and the impact of control measures. We considered disease outbreaks in a setting with dense genomic sampling, and formulated stochastic epidemic models to investigate person-to-person transmission, based on observed genomic and epidemiological data. We constructed models in which the genetic distance between sampled genotypes depends on the epidemiological relationship between the hosts. A data augmented Markov chain Monte Carlo algorithm was used to sample over the transmission trees, providing a posterior probability for any given transmission route. We investigated the predictive performance of our methodology using simulated data, demonstrating high sensitivity and specificity, particularly for rapidly mutating pathogens with low transmissibility. We then analyzed data collected during an outbreak of methicillin-resistant Staphylococcus aureus in a hospital, identifying probable transmission routes and estimating epidemiological parameters. Our approach overcomes limitations of previous methods, providing a framework with the flexibility to allow for unobserved infection times, multiple independent introductions of the pathogen, and within-host genetic diversity, as well as allowing forward simulation.Funding received from the following: The European Community [Mastering Hospital Antimicrobial Resistance (MOSAR) network contract LSHP-CT-2007-037941]. The National Institute of General Medical Sciences of the National Institutes of Health under award number U54GM088558. The UK Medical Research Council (Unit Programme number U105260566). The UKCRC Translational Infection Research Initiative (MRC Grant number G1000803) and Public Health England. The Medical Research Council and Department for International Development (Grant number MR/K006924/1). The Mahidol Oxford Tropical Medicine Research Unit is part of the Wellcome Trust Major Overseas Programme in SE Asia (Grant number 106698/Z/14/Z).This is the final version of the article. It first appeared from the Institute of Mathematical Statistics via http://dx.doi.org/10.1214/15-AOAS89

Effects of Different Inter-Set Rest Intervals during the Nordic Hamstring Exercise in Young Male Athletes

Context The Nordic hamstring exercise (NHE) is known to reduce hamstrings injury (HIS) risk in athletes. In order to optimise the NHE it is important to understand how acute resistance training variables influence its performance. Objective To examine the effects of different inter-set rest intervals (ISRI) on force indices during performance of the NHE. Design: Crossover Study. Setting Laboratory based. Patients or Participants Ten (age = 20.7 ± 2.3 years; height = 179.4 ± 5.5 cm; body mass = 83.9 ± 12.4 kg) well-trained young male team-sport athletes. Intervention Participants performed 2 x 6 repetitions of the NHE with either a SHORT (one-minute) or LONG (three-minute) ISRI. All sets were performed on the NordBord. Main Outcomes Measure(s) Peak force (N), average force (N), percent maintenance (%) and percent decline (%) were recorded for both dominant and non-dominant limbs as well as inter-limb force asymmetries (%) calculated. Results Analyses revealed no statistically significant interactions or main effects (p > 0.05) between conditions and sets in all variables. However, analysis of individual repetitions showed significant reductions (p < 0.05, ES = 0.58–1.28) in peak force from repetition four onwards. Conclusions Our findings suggest that a one-minute ISRI is sufficient to maintain force production qualities and inter-limb asymmetries between sets during the NHE in well-trained athletes. However, practitioners should be aware of the potentially high decrements in peak force production that may occur within the set

The Ess/Type VII secretion system of Staphylococcus aureus shows unexpected genetic diversity

We thank the core sequencing and informatics teams at the Sanger Institute for their assistance and The Wellcome Trust for its support of the Sanger Institute Pathogen Genomics and Biology groups. SRH, JP and MTGH were supported by Wellcome Trust grant 098051. Bioinformatics and Computational Biology analyses were supported by the University of St Andrews Bioinformatics Unit that is funded by a Wellcome Trust ISSF award (grant 105621/Z/14/Z). SP is funded by the UKCRC Translational Infection Research Initiative, and the NIHR Cambridge Biomedical Research Centre. CPH is supported by the Wellcome Trust (grant number 104241/z/14/z) TP is a Royal Society/Wolfson Merit Award Holder.BACKGROUND: Type VII protein secretion (T7SS) is a specialised system for excreting extracellular proteins across bacterial cell membranes and has been associated with virulence in Staphylococcus aureus. The genetic diversity of the ess locus, which encodes the T7SS, and the functions of proteins encoded within it are poorly understood. RESULTS: We used whole genome sequence data from 153 isolates representative of the diversity of the species to investigate the genetic variability of T7SS across S. aureus. The ess loci were found to comprise of four distinct modules based on gene content and relative conservation. Modules 1 and 4, comprising of the 5' and 3' modules of the ess locus, contained the most conserved clusters of genes across the species. Module 1 contained genes encoding the secreted protein EsxA, and the EsaAB and EssAB components of the T7SS machinery, and Module 4 contained two functionally uncharacterized conserved membrane proteins. Across the species four variants of Module 2 were identified containing the essC gene, each of which was associated with a specific group of downstream genes. The most diverse module of the ess locus was Module 3 comprising a highly variable arrangement of hypothetical proteins. RNA-Seq was performed on representatives of the four Module 2 variants and demonstrated strain-specific differences in the levels of transcription in the conserved Module 1 components and transcriptional linkage Module 2, and provided evidence of the expression of genes the variable regions of the ess loci. CONCLUSIONS: The ess locus of S. aureus exhibits modularity and organisational variation across the species and transcriptional variation. In silico analysis of ess loci encoded hypothetical proteins identified potential novel secreted substrates for the T7SS. The considerable variety in operon arrangement between otherwise closely related isolates provides strong evidence for recombination at this locus. Comparison of these recombination regions with each other, and with the genomes of other Staphylococcal species, failed to identify evidence of intra- and inter-species recombination, however the analysis identified a novel T7SS in another pathogenic staphylococci, Staphylococcus lugdunensis.Publisher PDFPeer reviewe

Duration of exposure to multiple antibiotics is associated with increased risk of VRE bacteraemia: a nested case-control study.

BACKGROUND: VRE bacteraemia has a high mortality and continues to defy control. Antibiotic risk factors for VRE bacteraemia have not been adequately defined. We aimed to determine the risk factors for VRE bacteraemia focusing on duration of antibiotic exposure. METHODS: A retrospective matched nested case-control study was conducted amongst hospitalized patients at Cambridge University Hospitals NHS Foundation Trust (CUH) from 1 January 2006 to 31 December 2012. Cases who developed a first episode of VRE bacteraemia were matched 1:1 to controls by length of stay, year, specialty and ward type. Independent risk factors for VRE bacteraemia were evaluated using conditional logistic regression. RESULTS: Two hundred and thirty-five cases were compared with 220 controls. Duration of exposure to parenteral vancomycin, fluoroquinolones and meropenem was independently associated with VRE bacteraemia. Compared with patients with no exposure to vancomycin, those who received courses of 1-3 days, 4-7 days or >7 days had a stepwise increase in risk of VRE bacteraemia [conditional OR (cOR) 1.2 (95% CI 0.4-3.8), 3.8 (95% CI 1.2-11.7) and 6.6 (95% CI 1.9-22.8), respectively]. Other risk factors were: presence of a central venous catheter (CVC) [cOR 8.7 (95% CI 2.6-29.5)]; neutropenia [cOR 15.5 (95% CI 4.2-57.0)]; hypoalbuminaemia [cOR 8.5 (95% CI 2.4-29.5)]; malignancy [cOR 4.4 (95% CI 1.6-12.0)]; gastrointestinal disease [cOR 12.4 (95% CI 4.2-36.8)]; and hepatobiliary disease [cOR 7.9 (95% CI 2.1-29.9)]. CONCLUSIONS: Longer exposure to vancomycin, fluoroquinolones or meropenem was associated with VRE bacteraemia. Antimicrobial stewardship interventions targeting high-risk antibiotics are required to complement infection control procedures against VRE bacteraemia

The Optimal Taxation of Asset Income when Government Consumption is Endogenous: Theory, Estimation and Welfare

This paper derives the Ramsey optimal policy for taxing asset income in a model where government expenditure is a function of net output or the inputs that produce it. Extending Judd (1999), I demonstrate that the canonical result that the optimal tax on capital income is zero in the medium to long term is a special case of a more general model. Employing a vector error correction model to estimate the relationship between government consumption and net output or the factor inputs that generate it for the United States between 1948Q1 to 2015Q4, I demonstrate that this special case is empirically implausible, and show how a cointegrating vector can be used to determine the optimal tax schedule. I simulate a version of the model using the empirical estimates to measure the welfare implications of changing the tax rate on asset income, and contrast these results with those generated in a version of the model where government consumption is purely exogenous. The shifting pattern of welfare measurements con rms the theoretical results. I calculate that the prevailing effective tax rate on net asset income in the US between 1970 and 2014 averaged 0.449. Hence abolishing the tax completely does generate welfare improvements, though only by the equivalent of between 1.103 and 1.616% percent permanent increase in consumption - well under half the implied welfare benefit when the endogeneity of the government consumption is ignored. The maximum welfare improvement from shifting part of the burden of tax from capital to labor is the equivalent of a permanent increase in consumption of between only 1.491 and 1.858%, and is attained when the tax rate on asset income is lowered to between 0.148 and 0.186. Allowing the tax rate to vary over time raises the maximum welfare bene t to 1.865%. All the results are very robust to a wide range of elasticities of labor supply

Chiral separation of substituted phenylalanine analogues using chiral palladium phosphine complexes with enantioselective liquid–liquid extraction

Chiral palladium phosphine complexes have been employed in the chiral separation of amino acids and phenylalanine analogues in particular. The use of (S)-xylyl-BINAP as a ligand for the palladium complex in enantioselective liquid–liquid extraction allowed the separation of the phenylalanine analogues with the highest operational selectivity reported to date. 31P NMR, FTIR, FIR, UV-Vis, CD and Raman spectroscopy methods have been applied to gain insight into the binding mechanism of the amino acid substrates with the chiral palladium phosphine complexes. A complexation in a bidentate fashion is proposed.

The influence of vernalization and daylength on expression of flowering-time genes in the shoot apex and leaves of barley (Hordeum vulgare).

Responses to prolonged low-temperature treatment of imbibed seeds (vernalization) were examined in barley (Hordeum vulgare). These occurred in two phases: the perception of prolonged cold, which occurred gradually at low temperatures, and the acceleration of reproductive development, which occurred after vernalization. Expression of the VERNALIZATION1 gene (HvVRN1) increased gradually in germinating seedlings during vernalization, both at the shoot apex and in the developing leaves. This occurred in darkness, independently of VERNALIZATION2 (HvVRN2), consistent with the hypothesis that expression of HvVRN1 is induced by prolonged cold independently of daylength flowering-response pathways. After vernalization, expression of HvVRN1 was maintained in the shoot apex and leaves. This was associated with accelerated inflorescence initiation and with down-regulation of HvVRN2 in the leaves. The largest determinant of HvVRN1 expression levels in vernalized plants was the length of seed vernalization treatment. Daylength did not influence HvVRN1 expression levels in shoot apices and typically did not affect expression in leaves. In the leaves of plants that had experienced a saturating seed vernalization treatment, expression of HvVRN1 was higher in long days, however. HvFT1 was expressed in the leaves of these plants in long days, which might account for the elevated HvVRN1 expression. Long-day up-regulation of HvVRN1 was not required for inflorescence initiation, but might accelerate subsequent stages of inflorescence development. Similar responses to seed vernalization were also observed in wheat (Triticum aestivum). These data support the hypothesis that VRN1 is induced by cold during winter to promote spring flowering in vernalization-responsive cereals

The WiggleZ Dark Energy Survey: the transition to large-scale cosmic homogeneity

We have made the largest-volume measurement to date of the transition to large-scale homogeneity in the distribution of galaxies. We use the WiggleZ survey, a spectroscopic survey of over 200,000 blue galaxies in a cosmic volume of ~1 (Gpc/h)^3. A new method of defining the 'homogeneity scale' is presented, which is more robust than methods previously used in the literature, and which can be easily compared between different surveys. Due to the large cosmic depth of WiggleZ (up to z=1) we are able to make the first measurement of the transition to homogeneity over a range of cosmic epochs. The mean number of galaxies N(<r) in spheres of comoving radius r is proportional to r^3 within 1%, or equivalently the fractal dimension of the sample is within 1% of D_2=3, at radii larger than 71 \pm 8 Mpc/h at z~0.2, 70 \pm 5 Mpc/h at z~0.4, 81 \pm 5 Mpc/h at z~0.6, and 75 \pm 4 Mpc/h at z~0.8. We demonstrate the robustness of our results against selection function effects, using a LCDM N-body simulation and a suite of inhomogeneous fractal distributions. The results are in excellent agreement with both the LCDM N-body simulation and an analytical LCDM prediction. We can exclude a fractal distribution with fractal dimension below D_2=2.97 on scales from ~80 Mpc/h up to the largest scales probed by our measurement, ~300 Mpc/h, at 99.99% confidence.Comment: 21 pages, 16 figures, accepted for publication in MNRA