Structure determination of new algal toxins using NMR methods

Shellfish are considered a delicacy by many consumers. In NZ, as in many overseas countries, there is a now thriv¬ing shellfish industry servicing both domestic and inter-national markets. Periodically shellfish accumulate harm¬ful levels of a variety of algal toxins, including domoic acid, yessotoxins, pectenotoxins and brevetoxins. When this occurs, regulatory authorities may impose harvesting closures which have a consequential economic impact on both farmers and staff employed to harvest and market shellfish products

Measuring micro-organism gas production

Transducer, which senses pressure buildup, is easy to assemble and use, and rate of gas produced can be measured automatically and accurately. Method can be used in research, in clinical laboratories, and for environmental pollution studies because of its ability to detect and quantify rapidly the number of gas-producing microorganisms in water, beverages, and clinical samples

Optical frequency comb generation from a monolithic microresonator

Optical frequency combs provide equidistant frequency markers in the infrared, visible and ultra-violet and can link an unknown optical frequency to a radio or microwave frequency reference. Since their inception frequency combs have triggered major advances in optical frequency metrology and precision measurements and in applications such as broadband laser-based gas sensing8 and molecular fingerprinting. Early work generated frequency combs by intra-cavity phase modulation while to date frequency combs are generated utilizing the comb-like mode structure of mode-locked lasers, whose repetition rate and carrier envelope phase can be stabilized. Here, we report an entirely novel approach in which equally spaced frequency markers are generated from a continuous wave (CW) pump laser of a known frequency interacting with the modes of a monolithic high-Q microresonator13 via the Kerr nonlinearity. The intrinsically broadband nature of parametric gain enables the generation of discrete comb modes over a 500 nm wide span (ca. 70 THz) around 1550 nm without relying on any external spectral broadening. Optical-heterodyne-based measurements reveal that cascaded parametric interactions give rise to an optical frequency comb, overcoming passive cavity dispersion. The uniformity of the mode spacing has been verified to within a relative experimental precision of 7.3*10(-18).Comment: Manuscript and Supplementary Informatio

Effects of morphology on phonons of nanoscopic silver grains

The morphology of nanoscopic Ag grains significantly affects the phonons. Atomistic simulations show that realistic nanograin models display complex vibrational properties. (1) Single-crystalline grains. Nearly-pure torsional and radial phonons appear at low frequencies. For low-energy, faceted models, the breathing mode and acoustic gap (lowest frequency) are about 10% lower than predicted by elasticity theory (ET) for a continuum sphere of the same volume. The sharp edges and the atomic lattice split the ET-acoustic-gap quintet into a doublet and triplet. The surface protrusions associated with nearly spherical, high-energy models produce a smaller acoustic gap and a higher vibrational density of states (DOS) at frequencies \nu<2 THz. (2) Twined icosahedra. In contrast to the single-crystal case, the inherent strain produce a larger acoustic gap, while the core atoms yield a DOS tail extending beyond the highest frequency of single-crystalline grains. (3) Mark's decahedra, in contrast to (1) and (2), do not have a breathing mode; although twined and strained, do not exhibit a high-frequency tail in the DOS. (4) Irregular nanograins. Grain boundaries and surface disorder yield non-degenerate phonon frequencies, and significantly smaller acoustic gap. Only these nanograins exhibit a low-frequency \nu^2 DOS in the interval 1-2 THz.Comment: Version published in Phys. Rev.

A comparison of two-coloured filter systems for treating visual reading difficulties

Copyright @ 2013 Informa UK Ltd.Purpose: Visual disturbances that make it difficult to read text are often termed “visual stress”. Coloured filters in spectacles may help some children overcome reading problems that are often caused by visual stress. It has been suggested that for optimal effect each child requires an individually prescribed colour for each eye, as determined in systems such as the “Harris Foundation” coloured filters. Alternatively, it has been argued that only blue or yellow filters, as used in the “Dyslexia Research Trust” (DRT) filter system, are necessary to affect the underlying physiology. Method: A randomised, double blind trial with 73 delayed readers, was undertaken to compare changes in reading and spelling as well as irregular and non-word reading skills after 3 months of wearing either the Harris or the DRT filters. Results: Reading improved significantly after wearing either type of filter (t = −8.4, p < 0.01), with 40% of the children improving their reading age by 6 months or more during the 3 month trial. However, spelling ability (t = 2.1, p = 0.05) and non-word reading (f = 4.7, p < 0.05) improved significantly more with the DRT than with the Harris filters. Conclusion: Education and rehabilitation professionals should therefore, consider coloured filters as an effective intervention for delayed readers experiencing visual stress

Ultraplex- A rapid, flexible, all-in-one fastq demultiplexer [version 1; peer review- 1 approved]

BACKGROUND: The first step of virtually all next generation sequencing analysis involves the splitting of the raw sequencing data into separate files using sample-specific barcodes, a process known as “demultiplexing”. However, we found that existing software for this purpose was either too inflexible or too computationally intensive for fast, streamlined processing of raw, single end fastq files containing combinatorial barcodes. RESULTS: Here, we introduce a fast and uniquely flexible demultiplexer, named Ultraplex, which splits a raw FASTQ file containing barcodes either at a single end or at both 5’ and 3’ ends of reads, trims the sequencing adaptors and low-quality bases, and moves unique molecular identifiers (UMIs) into the read header, allowing subsequent removal of PCR duplicates. Ultraplex is able to perform such single or combinatorial demultiplexing on both single- and paired-end sequencing data, and can process an entire Illumina HiSeq lane, consisting of nearly 500 million reads, in less than 20 minutes. CONCLUSIONS: Ultraplex greatly reduces computational burden and pipeline complexity for the demultiplexing of complex sequencing libraries, such as those produced by various CLIP and ribosome profiling protocols, and is also very user friendly, enabling streamlined, robust data processing. Ultraplex is available on PyPi and Conda and via Github

Multi-k magnetic structures in USb_{0.9}Te_{0.1} and UAs_{0.8}Se_{0.2} observed via resonant x-ray scattering at the U M4 edge

Experiments with resonant photons at the U M4 edge have been performed on a sample of USb_{0.9}Te_{0.1}, which has an incommensurate magnetic structure with k = 0.596(2) reciprocal lattice units. The reflections of the form , as observed previously in a commensurate k = 1/2 system [N. Bernhoeft et al., Phys. Rev. B 69 174415 (2004)] are observed, removing any doubt that these occur because of multiple scattering or high-order contamination of the incident photon beam. They are clearly connected with the presence of a 3k configuration. Measurements of the reflections from the sample UAs_{0.8}Se_{0.2} in a magnetic field show that the transition at T* ~ 50 K is between a low-temperature 2k and high-temperature 3k state and that this transition is sensitive to an applied magnetic field. These experiments stress the need for quantitative theory to explain the intensities of these reflections.Comment: submitted to Phys. Rev.

Nonequilibrium plasmons and transport properties of a double--junction quantum wire

We study theoretically the current-voltage characteristics, shot noise, and full counting statistics of a quantum wire double barrier structure. We model each wire segment by a spinless Luttinger liquid. Within the sequential tunneling approach, we describe the system's dynamics using a master equation. We show that at finite bias the non-equilibrium distribution of plasmons in the central wire segment leads to increased average current, enhanced shot noise, and full counting statistics corresponding to a super-Poissonian process. These effects are particularly pronounced in the strong interaction regime, while in the non-interacting case we recover results obtained earlier using detailed balance arguments.Comment: 22 pages, RevTex 2-column, 11 figure