Whole-mitochondrial genome sequencing in primary open-angle glaucoma using massively parallel sequencing identifies novel and known pathogenic variants

Purpose:The aim of this study was to determine whether mutations in mitochondrial DNA play a role in high-pressure primary open-angle glaucoma (OMIM 137760) by analyzing new data from massively parallel sequencing of mitochondrial DNA.
Methods:Glaucoma patients with high-tension primary open-angle glaucoma and ethnically matched and age-matched control subjects without glaucoma were recruited. The entire human mitochondrial genome was amplified in two overlapping fragments by long-range polymerase chain reaction and used as a template for massively parallel sequencing on an Ion Torrent Personal Genome Machine. All variants were confirmed by conventional Sanger sequencing.
Results:Whole-mitochondrial genome sequencing was performed in 32 patients with primary open-angle glaucoma from India (n = 16) and Ireland (n = 16). In 16 of the 32 patients with primary open-angle glaucoma (50% of cases), there were 22 mitochondrial DNA mutations consisting of 7 novel mutations and 8 previously reported disease-associated sequence variants. Eight of 22 (36.4%) of the mitochondrial DNA mutations were in complex I mitochondrial genes.
Conclusion:Massively parallel sequencing using the Ion Torrent Personal Genome Machine with confirmation by Sanger sequencing detected a pathogenic mitochondrial DNA mutation in 50% of the primary open-angle glaucoma cohort. Our findings support the emerging concept that mitochondrial dysfunction results in the development of glaucoma and, more specifically, that complex I defects play a significant role in primary open-angle glaucoma pathogenesis.

Low Complexity Spectral Analysis of Heart-Rate-Variability through a Wavelet based FFT

In this paper, a low complexity system for spectral analysis of heart rate variability (HRV) is presented. The main idea of the proposed approach is the implementation of the Fast-Lomb periodogram that is a ubiquitous tool in spectral analysis, using a wavelet based Fast Fourier transform. Interestingly we show that the proposed approach enables the classification of processed data into more and less significant based on their contribution to output quality. Based on such a classification a percentage of less-significant data is being pruned leading to a significant reduction of algorithmic complexity with minimal quality degradation. Indeed, our results indicate that the proposed system can achieve up-to 45% reduction in number of computations with only 4.9% average error in the output quality compared to a conventional FFT based HRV system.

BROAD-BAND EXCITATION AND EMISSION OF SURFACE-PLASMONS

The well known advantages of using surface plasmons, in particular the high sensitivity to surface adsorbates, are nearly always compromised in practice by the use of monochromatic excitation and the consequent lack of proper spectroscopic information. This limitation arises from the angle/wavelength selective nature of the surface plasmon resonance. The work described here uses an elegant broadband excitation/decay scheme in a substrate(silica)-grating profiled photoresist-Ag film geometry. Laser radiation of wavelength 488 nm, incident through the silica substrate, excites by near-field coupling a broad band of surface plasmons at the photoresist-Ag interface within the spectral range of the photoresist fluorescence. With a judicious choice of grating period this mode can cross-couple to the mode supported at the Ag-air interface. This latter mode can, in turn, couple out to light by virtue of the same grating profile. The spectral distribution of the light emitted due to this three-step process has been studied as a function of the angle of emission and depth of the grating profiled surface for each polarization. It is found that the optimum emission efficiency occurs with a groove depth in the region of 65 nm. This is considerably greater than the optimum depth of 40 nm required for surface plasmon-photon coupling at a Ag-air interface or, in other words, for the last step of the process in isolation.

Towards Multi-Sensor Spectral Alignment Through Post Measurement Calibration Correction

Semiconductor manufactures are increasing reliant on optical emission spectroscopy (OES) to source information on plasma characteristics and process change. However, nonlinearities in the response of OES sensors and errors in their calibration lead to discrepancies in observed wavelength detector response. This paper presents a technique for the retrospective spectral calibration of multiple OES sensors. Underlying methodology is given, and alignment performance is evaluated using OES recordings from a semiconductor plasma process. The paper concludes with a discussion of results and suggests avenues for future work.

Spectral gamma-ray logs and palaeoclimate change? Permian – Triassic, Persian Gulf

Spectral gamma ray (SGR) logs are used as stratigraphic tools in correlation, sequence stratigraphy and most recently, in clastic successions as a proxy for changes in hinterland palaeoweathering. In this study we analyse the spectral gamma ray signal recorded in two boreholes that penetrated the carbonate and evaporate-dominated Permian–Triassic boundary (PTB) in the South Pars Gasfield (offshore Iran, Persian Gulf) in an attempt to analyse palaeoenvironmental changes from the upper Permian (Upper Dalan Formation) and lower Triassic (Lower Kangan Formation). The results are compared to lithological changes, total organic carbon (TOC) contents and published stable isotope (δ18O, δ13C) results. This work is the first to consider palaeoclimatic effects on SGR logs from a carbonate/evaporate succession. While Th/U ratios compare well to isotope data (and thus a change to less arid hinterland climates from the Late Permian to the Early Triassic), Th/K ratios do not, suggesting a control not related to hinterland weathering. Furthermore, elevated Th/U ratios in the Early Triassic could reflect a global drawdown in U, rather than a more humid episode in the sediment hinterlands, with coincident changes in TOC. Previous work that used spectral gamma ray data in siliciclastic successions as a palaeoclimate proxy may not apply in carbonate/evaporate sedimentary rocks.

Latanoprost for open-angle glaucoma (UKGTS): a randomised, multicentre, placebo-controlled trial

Background
Treatments for open-angle glaucoma aim to prevent vision loss through lowering of intraocular pressure, but to our knowledge no placebo-controlled trials have assessed visual function preservation, and the observation periods of previous (unmasked) trials have typically been at least 5 years. We assessed vision preservation in patients given latanoprost compared with those given placebo.

Methods
In this randomised, triple-masked, placebo-controlled trial, we enrolled patients with newly diagnosed open-angle glaucoma at ten UK centres (tertiary referral centres, teaching hospitals, and district general hospitals). Eligible patients were randomly allocated (1:1) with a website-generated randomisation schedule, stratified by centre and with a permuted block design, to receive either latanoprost 0·005% (intervention group) or placebo (control group) eye drops. Drops were administered from identical bottles, once a day, to both eyes. The primary outcome was time to visual field deterioration within 24 months. Analyses were done in all individuals with follow-up data. The Data and Safety Monitoring Committee (DSMC) recommended stopping the trial on Jan 6, 2011 (last patient visit July, 2011), after an interim analysis, and suggested a change in primary outcome from the difference in proportions of patients with incident progression between groups to time to visual field deterioration within 24 months. This trial is registered, number ISRCTN96423140.

Findings
We enrolled 516 individuals between Dec 1, 2006, and March 16, 2010. Baseline mean intraocular pressure was 19·6 mm Hg (SD 4·6) in 258 patients in the latanoprost group and 20·1 mm Hg (4·8) in 258 controls. At 24 months, mean reduction in intraocular pressure was 3·8 mm Hg (4·0) in 231 patients assessed in the latanoprost group and 0·9 mm Hg (3·8) in 230 patients assessed in the placebo group. Visual field preservation was significantly longer in the latanoprost group than in the placebo group: adjusted hazard ratio (HR) 0·44 (95% CI 0·28–0·69; p=0·0003). We noted 18 serious adverse events, none attributable to the study drug.

Interpretation
This is the first randomised placebo-controlled trial to show preservation of the visual field with an intraocular-pressure-lowering drug in patients with open-angle glaucoma. The study design enabled significant differences in vision to be assessed in a relatively short observation period

A quality-scalable and energy-efficient approach for spectral analysis of heart rate variability

Today there is a growing interest in the integration of health monitoring applications in portable devices necessitating the development of methods that improve the energy efficiency of such systems. In this paper, we present a systematic approach that enables energy-quality trade-offs in spectral analysis systems for bio-signals, which are useful in monitoring various health conditions as those associated with the heart-rate. To enable such trade-offs, the processed signals are expressed initially in a basis in which significant components that carry most of the relevant information can be easily distinguished from the parts that influence the output to a lesser extent. Such a classification allows the pruning of operations associated with the less significant signal components leading to power savings with minor quality loss since only less useful parts are pruned under the given requirements. To exploit the attributes of the modified spectral analysis system, thresholding rules are determined and adopted at design- and run-time, allowing the static or dynamic pruning of less-useful operations based on the accuracy and energy requirements. The proposed algorithm is implemented on a typical sensor node simulator and results show up-to 82% energy savings when static pruning is combined with voltage and frequency scaling, compared to the conventional algorithm in which such trade-offs were not available. In addition, experiments with numerous cardiac samples of various patients show that such energy savings come with a 4.9% average accuracy loss, which does not affect the system detection capability of sinus-arrhythmia which was used as a test case. 

Coherent spectral enhancement of carrier-envelope-phase stable continua with dual-gas high harmonic generation

Attosecond science is enabled by the ability to convert femtosecond near-infrared laser light into coherent harmonics in the extreme ultraviolet spectral range. While attosecond sources have been utilized in experiments that have not demanded high intensities, substantially higher photon flux would provide a natural link to the next significant experimental breakthrough. Numerical simulations of dual-gas high harmonic generation indicate that the output in the cutoff spectral region can be selectively enhanced without disturbing the single-atom gating mechanism. Here, we summarize the results of these simulations and present first experimental findings to support these predictions. (c) 2012 Optical Society of America

Evidence of plasma polarization shift of Ti He-alpha resonance line in high density laser produced plasmas

A spectroscopic study of the He-alpha (1s(2) S-1(0) - 1s2p P-1(1)) line emission (4749.73 eV) from high density plasma was conducted. The plasma was produced by irradiating Ti targets with intense (I approximate to 1x10(19) W/cm(2)), 400nm wavelength high contrast, short (45fs) p-polarized laser pulses at an angle of 45 degrees. A line shift up to 3.4 +/- 1.0 eV (1.9 +/- 0.55 m angstrom) was observed in the He-alpha line. The line width of the resonance line at FWHM was measured to be 12.1 +/- 0.6 eV (6.7 +/- 0.35 m angstrom). For comparison, we looked into the emission of the same spectral line from plasma produced by irradiating the same target with laser pulses of reduced intensities (approximate to 10(17) W/cm(2)): we observed a spectral shift of only 1.8 +/- 1.0 eV (0.9 +/- 0.55m angstrom) and the line-width measures up to 5.8 +/- 0.25 eV (2.7 +/- 0.35 m angstrom). These data provide evidence of plasma polarization shift of the Ti He-alpha line.

Polarization spectral synthesis for Type Ia supernova explosion models

We present a Monte Carlo radiative transfer technique for calculating synthetic spectropolarimetry for multidimensional supernova explosion models. The approach utilizes 'virtual-packets' that are generated during the propagation of the Monte Carlo quanta and used to compute synthetic observables for specific observer orientations. Compared to extracting synthetic observables by direct binning of emergent Monte Carlo quanta, this virtual-packet approach leads to a substantial reduction in the Monte Carlo noise. This is not only vital for calculating synthetic spectropolarimetry (since the degree of polarization is typically very small) but also useful for calculations of light curves and spectra. We first validate our approach via application of an idealized test code to simple geometries. We then describe its implementation in the Monte Carlo radiative transfer code ARTIS and present test calculations for simple models for Type Ia supernovae. Specifically, we use the well-known one-dimensional W7 model to verify that our scheme can accurately recover zero polarization from a spherical model, and to demonstrate the reduction in Monte Carlo noise compared to a simple packet-binning approach. To investigate the impact of aspherical ejecta on the polarization spectra, we then use ARTIS to calculate synthetic observables for prolate and oblate ellipsoidal models with Type Ia supernova compositions.

Late-time spectral line formation in Type IIb supernovae, with application to SN 1993J, SN 2008ax, and SN 2011dh

We investigate line formation processes in Type IIb supernovae (SNe) from 100 to 500 days post-explosion using spectral synthesis calculations. The modelling identifies the nuclear burning layers and physical mechanisms that produce the major emission lines, and the diagnostic potential of these. We compare the model calculations with data on the three best observed Type IIb SNe to-date - SN 1993J, SN 2008ax, and SN 2011dh. Oxygen nucleosynthesis depends sensitively on the main-sequence mass of the star and modelling of the [O I] lambda lambda 6300, 6364 lines constrains the progenitors of these three SNe to the M-ZAMS = 12-16 M-circle dot range (ejected oxygen masses 0.3-0.9 M-circle dot), with SN 2011dh towards the lower end and SN 1993J towards the upper end of the range. The high ejecta masses from M-ZAMS greater than or similar to 17 M-circle dot progenitors give rise to brighter nebular phase emission lines than observed. Nucleosynthesis analysis thus supports a scenario of low-to-moderate mass progenitors for Type IIb SNe, and by implication an origin in binary systems. We demonstrate how oxygen and magnesium recombination lines may be combined to diagnose the magnesium mass in the SN ejecta. For SN 2011dh, a magnesium mass of 0.02-0.14 M-circle dot is derived, which gives a Mg/O production ratio consistent with the solar value. Nitrogen left in the He envelope from CNO burning gives strong [N II] lambda lambda 6548, 6583 emission lines that dominate over Ha emission in our models. The hydrogen envelopes of Type IIb SNe are too small and dilute to produce any noticeable H alpha emission or absorption after similar to 150 days, and nebular phase emission seen around 6550 angstrom is in many cases likely caused by [N II] lambda lambda 6548, 6583. Finally, the influence of radiative transport on the emergent line profiles is investigated. Significant line blocking in the metal core remains for several hundred days, which affects the emergent spectrum. These radiative transfer effects lead to early-time blueshifts of the emission line peaks, which gradually disappear as the optical depths decrease with time. The modelled evolution of this effect matches the observed evolution in SN 2011dh.

Forward and backward least angle regression for nonlinear system identification

A forward and backward least angle regression (LAR) algorithm is proposed to construct the nonlinear autoregressive model with exogenous inputs (NARX) that is widely used to describe a large class of nonlinear dynamic systems. The main objective of this paper is to improve model sparsity and generalization performance of the original forward LAR algorithm. This is achieved by introducing a replacement scheme using an additional backward LAR stage. The backward stage replaces insignificant model terms selected by forward LAR with more significant ones, leading to an improved model in terms of the model compactness and performance. A numerical example to construct four types of NARX models, namely polynomials, radial basis function (RBF) networks, neuro fuzzy and wavelet networks, is presented to illustrate the effectiveness of the proposed technique in comparison with some popular methods.