Fission chamber data acquisition system for neutron flux measurements on the Mega-Amp Spherical Tokamak Upgrade.

Neutron flux measurements are important in fusion devices for both safety requirements and physics studies. A new system has been built for the Mega-Amp Spherical Tokamak Upgrade (MAST Upgrade) that provides neutron count, DC, and Campbell mode measurements for a 1 µs period at 1 MHz. The acquisition system uses a Red Pitaya board to sample current from two fission chambers mounted on the side of the MAST-U vessel. The system-on-chip design of the Zynq-7020 on the Red Pitaya also allows a web server implementation using Flask for data retrieval and diagnostic configuration over the MAST Upgrade network.

The digital mirror Langmuir probe: Field programmable gate array implementation of real-time Langmuir probe biasing.

High bandwidth, high spatial resolution measurements of electron temperature, density, and plasma potential are valuable for resolving turbulence in the boundary plasma of tokamaks. While conventional Langmuir probes can provide such measurements, either their temporal or spatial resolution is limited: the former by the sweep rate necessary for obtaining I-V characteristics and the latter by the need to use multiple electrodes, as is the case in triple and double probe configurations. The Mirror Langmuir Probe (MLP) bias technique overcomes these limitations by rapidly switching the voltage on a single electrode cycling between three bias states, each dynamically optimized for the local plasma conditions. The MLP system on Alcator C-Mod used analog circuitry to perform this function, measuring Te, VF, and Isat at 1.1 MSPS. Recently, a new prototype digital MLP controller has been implemented on a Red Pitaya Field Programmable Gate Array (FPGA) board which reproduces the functionality of the original controller and performs all data acquisition. There is also the potential to provide the plasma parameters externally for use with feedback control systems. The use of FPGA technology means the system is readily customizable at a fraction of the development time and implementation cost. A second Red Pitaya was used to test the MLP by simulating the current response of a physical probe using C-Mod experimental measurements. This project is available as a git repository to facilitate extensibility (e.g., real-time control outputs and more voltage states) and scalability through collaboration.

Elasmobranch bycatch in the demersal prawn trawl fishery in the Gulf of Papua, Papua New Guinea.

The elasmobranch bycatch of the Gulf of Papua Prawn Fishery is investigated in detail for the first time. Fisheries observers collected data on the elasmobranch bycatch from a total of 403 trawl sets (1,273 hrs) in the Gulf of Papua. A total of 40 species of elasmobranchs were recorded ranging in size from a 12 cm disc width stingray to a 350 cm total length sawfish. High mortality rates were recorded (>80%), attributed to the long trawl durations (up to 4 hours). The future inclusion of bycatch reduction devices would likely reduce the number of larger elasmobranchs being caught, based on evidence from the prawn trawl fisheries of northern Australia, and is being investigated by the PNG National Fisheries Authority. Differences in catch compositions were detected across the management zones as well as between the two monsoonal seasons (SE Monsoon and NW Monsoon). Increased monitoring and additional research is required and management plans should address the elasmobranch bycatch and in particular their high mortality rate.

Artificial neural networks and geometric morphometric methods as a means for classification: A case-study using teeth from Carcharhinus sp. (Carcharhinidae).

Over the past few decades, geometric morphometric methods have become increasingly popular and powerful tools to describe morphological data while over the same period artificial neural networks have had a similar rise in the classification of specimens to preconceived groups. However, there has been little research into how well these two systems operate together, particularly in comparison to preexisting techniques. In this study, geometric morphometric data and multilayer perceptrons, a style of artificial neural network, were used to classify shark teeth from the genus Carcharhinus to species. Three datasets of varying size and species differences were used. We compared the performance of this combination with geometric morphometric data in a linear discriminate function analysis, linear measurements in a linear discriminate function analysis, and a preexisting methodology from the literature that incorporates linear measurements and a two-layered discriminate function analysis. Across datasets, geometric morphometric data in a multilayer perceptron tended to yield modest accuracies but accuracies that varied less across species whereas other methods were able to achieve higher accuracies in some species at the expense of lower accuracies in others. Further, the performance of the two-layered discriminate function analysis illustrates that constraining what material is classified can increase the accuracy of a method. Based on this tradeoff, the best methodology will then depend on the scope of the study and the amount of material available. J. Morphol. 278:131-141, 2017. ©© 2016 Wiley Periodicals,Inc.

Modifications to the synthetic aperture microwave imaging diagnostic.

The synthetic aperture microwave imaging diagnostic has been operating on the MAST experiment since 2011. It has provided the first 2D images of B-X-O mode conversion windows and showed the feasibility of conducting 2D Doppler back-scattering experiments. The diagnostic heavily relies on field programmable gate arrays to conduct its work. Recent successes and newly gained experience with the diagnostic have led us to modify it. The enhancements will enable pitch angle profile measurements, O and X mode separation, and the continuous acquisition of 2D DBS data. The diagnostic has also been installed on the NSTX-U and is acquiring data since May 2016.

Non-centralised service for palliative stenting of malignant gastric outlet obstruction.

INTRODUCTION: Malignant gastric outlet obstruction (GOO) is a common, debilitating and frequently pre-terminal symptom of intra-abdominal malignancies. Traditional 'gold standard' treatment has been palliative surgical gastro-enterostomy. Over the past two decades, use of self-expanding metallic stents (SEMSs) to relieve malignant GOO has become first-line treatment. We present the results from a single district general hospital in the UK in which malignant GOO was treated with SEMSs over a six-year period. METHODS: All patients who underwent palliative stenting for malignant gastro-duodenal tumours in our centre for six years up to January 2013 were assessed retrospectively. Outcomes were assessed with regard to: technical and clinical success; return to oral nutrition; prevalence of complications and re-intervention; and overall survival. RESULTS: Thirty-two stents were implanted in 29 patients. Technical success was 100%. Clinical success and return to oral nutrition were both 91%. The prevalence of complications was 16%. The prevalence of re-intervention was 13%. Mean survival was 91 (range, 5-392) days. Median wait from decision to implant a stent to stent implantation was 1 (range, 0-14) day. Overall, 25 covered and nine uncovered stents were implanted. CONCLUSION: Stent implantation for GOO in this patient group is an established and preferable alternative to surgical intervention. Much of the treatment for malignancies of the upper gastrointestinal tract has now been centralised. Our data showed comparable results with published data for these procedures, with a high prevalence of success and low prevalence of major complications. It is of considerable benefit to these patients not to have to travel to a regional centre for stent implantation.

Design of a real-time two-color interferometer for MAST Upgrade.

A single chord two-color CO2/HeNe (10.6/0.633 µm) heterodyne laser interferometer has been designed to measure the line integral electron density along the mid-plane of the MAST Upgrade tokamak, with a typical error of 1 × 10(18) m(-3) (∼2° phase error) at 4 MHz temporal resolution. To ensure this diagnostic system can be restored from any failures without stopping MAST Upgrade operations, it has been located outside of the machine area. The final design and initial testing of this system, including details of the optics, vibration isolation, and a novel phase detection scheme are discussed in this paper.

Edge Thomson scattering diagnostic on COMPASS tokamak: installation, calibration, operation, improvements.

The core Thomson scattering diagnostic (TS) on the COMPASS tokamak was put in operation and reported earlier. Implementation of edge TS, with spatial resolution along the laser beam up to ∼1/100 of the tokamak minor radius, is presented now. The procedure for spatial calibration and alignment of both core and edge systems is described. Several further upgrades of the TS system, like a triggering unit and piezo motor driven vacuum window shutter, are introduced as well. The edge TS system, together with the core TS, is now in routine operation and provides electron temperature and density profiles.

A field programmable gate array unit for the diagnosis and control of neoclassical tearing modes on MAST.

A real-time system has been developed to trigger both the MAST Thomson scattering (TS) system and the plasma control system on the phase and amplitude of neoclassical tearing modes (NTMs), extending the capabilities of the original system. This triggering system determines the phase and amplitude of a given NTM using magnetic coils at different toroidal locations. Real-time processing of the raw magnetic data occurs on a low cost field programmable gate array (FPGA) based unit which permits triggering of the TS lasers on specific amplitudes and phases of NTM evolution. The MAST plasma control system can receive a separate trigger from the FPGA unit that initiates a vertical shift of the MAST magnetic axis. Such shifts have fully removed m∕n = 2∕1 NTMs instabilities on a number of MAST discharges.

Laser system for high resolution Thomson scattering diagnostics on the COMPASS tokamak.

A new Thomson scattering diagnostic has been designed and is currently being installed on the COMPASS tokamak in IPP Prague in the Czech Republic. The requirements for this system are very stringent with approximately 3 mm spatial resolution at the plasma edge. A critical part of this diagnostic is the laser source. To achieve the specified parameters, a multilaser solution is utilized. Two 30 Hz 1.5 J Nd:YAG laser systems, used at the fundamental wavelength of 1064 nm, are located outside the tokamak area at a distance of 20 m from the tokamak. The design of the laser beam transport path is presented. The approach leading to a final choice of optimal focusing optics is given. As well as the beam path to the tokamak, a test path of the same optical length was built. Performance tests of the laser system carried out using the test path are described.

A 130 point Nd:YAG Thomson scattering diagnostic on MAST.

A Thomson scattering diagnostic designed to measure both edge and core physics has been implemented on MAST. The system uses eight Nd:YAG lasers, each with a repetition rate of 30 Hz. The relative and absolute timing of the lasers may be set arbitrarily to produce fast bursts of measurements to suit the time evolution of the physics being studied. The scattered light is collected at F/6 by a 100 kg six element lens system with an aperture stop of 290 mm. The collected light is then transferred to 130 polychromators by 130 independent fiber bundles. The data acquisition and processing are based on a distributed computer system of dual core processors embedded in 26 chassis. Each chassis is standalone and performs data acquisition and processing for five polychromators. This system allows data to be available quickly after the MAST shot and has potential for real-time operations.

MAST YAG Thomson scattering upgrade alignment system.

The recent upgrade to the MAST YAG Thomson scattering while enhancing the diagnostic capabilities increased the complexity of the system. There are eight YAG lasers now operational, doubling the number from the previous setup. This means alignment between each laser individually and reference points is essential to guarantee data quality and diagnostic reliability. To address this issue an alignment system was recently installed. It mimics the beams alignment in MAST by sampling 1% of the laser beam that is sent into a telescope which demagnifies by a factor of 8. The demagnified beam is viewed with a CCD camera. By scanning the camera the profile and position of the beams in the scattering zone and in a range of several meters inside MAST can be determined. Therefore alignment is checked along the beam path without having to sample it inside the vessel. The experimental apparatus and test procedures are described.

Laser beam combiner for Thomson scattering core LIDAR.

The light detection and ranging Thomson scattering (TS) diagnostic is advantageous since it only requires a single view port into the tokamak. This technique requires a short pulse laser at high energy, usually showing a limited repetition rate. Having multiple lasers will increase the repetition rate. This paper presents a scanning mirror as a laser beam combiner. Measurements of the position accuracy and jitter show that the pointing stability of the laser beam is within ±25 µrad for over tens of seconds. A control feedback loop is implemented to demonstrate the long term stability. Such a system could be applied for ITER and JET.

Synchronization of Thomson scattering measurements on MAST using an FPGA based "Smart" trigger unit.

The MAST Thomson scattering diagnostic has recently been upgraded to make electron density and temperature measurements at 130 points across the 1.5 m diameter of the plasma. The new system is able to take 240 measurements per second using eight Nd:YAG lasers, each running at 30 Hz. The exact firing time of these lasers is adjusted with 100 ns precision using a field programmable gate array based trigger unit. Trigger pulses are produced to fire the lamps of all lasers and the Q switches with the appropriate delay depending on the warm-up status. The lasers may be fired in rapid bursts so as to achieve a high temporal resolution over eight points separated down to the microsecond level. This trigger unit receives optical trigger events and signals from external sources, allowing the trigger sequences to be resynchronized to the start of the plasma pulse and further events during the shot such as the entry of a fuelling pellet or randomly occurring plasma events. This resynchronization of the laser firing sequence allows accurate and reproducible measurements of fast plasma phenomena.

Absolute calibration of LIDAR Thomson scattering systems by rotational Raman scattering.

Absolute calibration of LIDAR Thomson scattering systems on large fusion devices may be achieved using rotational Raman scattering. The choice of calibrating gas molecule presents different options and design trade-offs and is likely to be strongly dependent on the laser wavelength selected. Raman scattering of hydrogenic molecules produces a very broad spectrum, however, with far fewer scattered photons than scattering from nitrogen or oxygen at the same gas pressure. Lower laser wavelengths have the advantage that the Raman cross section increases, sigma(Raman) proportional to 1/lambda(0)(4), but the disadvantage that the spectral width of the scattered spectrum decreases, Deltalambda(Raman) proportional to lambda(0)(2). This narrower spectrum makes measurement closer to the laser wavelength necessary. The design of the calibration technique presents a number of challenges. Some of these challenges are generic to all Thomson scattering systems. These include detecting a sufficient number of photoelectrons and designing filters that measure close to the laser wavelength while simultaneously achieving adequate blocking of the laser wavelength. An issue specific to LIDAR systems arises since the collection optics operates over a wide range of depth of field. This wide depth of field has the effect of changing the angle of light incident on the optical interference filter with plasma major radius. The angular distribution then determines the effective spectral transmission function of the interference filter and hence impacts on the accuracy of the absolute calibration. One method that can be used to increase absolute calibration accuracy is collecting both Stokes and anti-Stokes lines with optical filter transmission bands specifically designed to reduce systematic uncertainty.

Magnetic reconnection triggering magnetohydrodynamic instabilities during a sawtooth crash in a Tokamak plasma.

Thomson scattering measurements with subcentimeter spatial resolution have been made during a sawtooth crash in a Mega Ampere Spherical Tokamak fusion plasma. The unparalleled resolution of the temperature profile has shed new light on the mechanisms that underlie the sawtooth. As magnetic reconnection occurs, the temperature gradient at the island boundary increases. The increased local temperature gradient is sufficient to make the helical core unstable to ideal magnetohydrodynamic instabilities, thought to be responsible for the rapidity of the collapse.

Design and implementation of a full profile sub-cm ruby laser based Thomson scattering system for MAST.

A major upgrade to the ruby Thomson scattering (TS) system has been designed and implemented on the Mega-ampere spherical tokamak (MAST). MAST is equipped with two TS systems, a Nd:YAG laser system and a ruby laser system. Apart from common collection optics each system provides independent measurements of the electron temperature and density profile. This paper focuses on the recent upgrades to the ruby TS system. The upgraded ruby TS system measures 512 points across the major radius of the MAST vessel. The ruby laser can deliver one 10 J 40 ns pulse at 1 Hz or two 5 J pulses separated by 100-800 µs. The Thomson scattered light is collected at F/15 over 1.4 m. This system can resolve small (7 mm) structures at 200 points in both the electron temperature and density channels at high optical contrast; ∼50% modulated transfer function. The system is fully automated for each MAST discharge and requires little adjustment. The estimated measurement error for a 7 mm radial point is <4% of T(e) and <3% of n(e) in the range of 40 eV to 2 keV, for a density of n(e)=2×10(19) m(-3). The photon statistics at lower density can be increased by binning in the radial direction as desired. A new intensified CCD camera design allows the ruby TS system to take two snapshots separated with a minimum time of 230 µs. This is exploited to measure two density and temperature profiles or to measure the plasma background light.

Design of a new Nd:YAG Thomson scattering system for MAST.

A new infrared Thomson scattering system has been designed for the MAST tokamak. The system will measure at 120 spatial points with approximately 10 mm resolution across the plasma. Eight 30 Hz 1.6 J Nd:YAG lasers will be combined to produce a sampling rate of 240 Hz. The lasers will follow separate parallel beam paths to the MAST vessel. Scattered light will be collected at approximately f/6 over scattering angles ranging from 80 degrees to 120 degrees. The laser energy and lens size, relative to an existing 1.2 J f/12 system, greatly increases the number of scattered photons collected per unit length of laser beam. This is the third generation of this polychromator to be built and a number of modifications have been made to facilitate mass production and to improve performance. Detected scattered signals will be digitized at a rate of 1 GS/s by 8 bit analog to digital converters (ADCs.) Data may be read out from the ADCs between laser pulses to allow for real-time analysis.

Why does Japan have a high incidence of gastric cancer? Comparison of gastritis between UK and Japanese patients.

BACKGROUND AND AIMS: The incidence of gastric cancer in Japan is four times higher than in the UK. It usually arises in a stomach with corpus predominant or pangastritis that has undergone extensive atrophy and intestinal metaplasia. We hypothesised that a Japanese population would have a more severe gastritis with a corpus predominant or pangastritis pattern and a greater degree of atrophy and intestinal metaplasia than that found in the UK. To test this we designed a comparative trial. METHODS: A total of 252 age matched consecutive patients were recruited from the endoscopy services in Leeds and Tokyo. In each centre, 21 patients were prospectively selected from each decennial, between the ages of 20-80 years. All had epigastric discomfort as their predominant symptom. Patients with peptic ulcer, cancer, and oesophagitis were excluded. Five gastric biopsies were examined by two histopathologists using the updated Sydney system. Helicobacter pylori infection was assessed by histology and culture of biopsies and enzyme linked immunosorbent assay and immunoblot of plasma. RESULTS: Gastritis was found by both pathologists in 59 (47%) UK and 76 (60%) Japanese patients (chi(2) test, p = 0.04). In those patients with gastritis, corpus predominant or pangastritis was commoner in the Japanese (63% Japan v 36% in the UK (chi(2) test, p = 0.003) Atrophy and intestinal metaplasia were more extensive and severe (Mann-Whitney U test, p<0.001) and chronic inflammation and polymorph activity were also greater, especially in the corpus (Mann-Whitney U test, p<0.001). Fifty three of 59 UK gastritis patients (90%) and 67/76 (88%) (chi(2) test, p = 1) Japanese gastritis patients were positive for H pylori. Using a previously described "gastric cancer risk index" among H pylori positive patients, there were significantly more Japanese than UK subjects with a "high risk" score. CONCLUSION: In Japanese as opposed to English patients, gastritis is more prevalent and severe with more corpus predominant atrophy and intestinal metaplasia. These differences may partially explain the higher incidence of gastric cancer in Japan.

Digit preference in Goldmann applanation tonometry: the hedgehog effect.

PURPOSE: Digit preference is a subconscious bias towards numbers that end in certain digits. We conducted a study to assess for digit preference in intraocular pressure measurement using the Goldmann applanation tonometer. DESIGN: Prospective study with masked and unmasked phases. METHODS: The study was conducted in general ophthalmic clinics in a District General Hospital in Blackpool, United Kingdom, by 6 clinical ophthalmologists. Consecutive right eye intraocular pressure measurements were collected for a 2-month period for the masked phase and were repeated for the unmasked phase. The proportion of even numbers was the main outcome measure. RESULTS: Six ophthalmologists completed both phases: 555 of 917 readings were even in the masked phase (P = .075), and 679 of 1056 readings were even in the unmasked phase (P = .022). CONCLUSIONS: Our results suggest that digit preference influences measurements from the Goldmann applanation tonometer and that this persists when observers are aware of digit preference. This bias may influence both clinical decision-making and trial results.