Upgrades of Genetic Programming for Data-Driven Modeling of Time Series.

In many engineering fields and scientific disciplines, the results of experiments are in the form of time series, which can be quite problematic to interpret and model. Genetic programming tools are quite powerful in extracting knowledge from data. In this work, several upgrades and refinements are proposed and tested to improve the explorative capabilities of symbolic regression (SR) via genetic programming (GP) for the investigation of time series, with the objective of extracting mathematical models directly from the available signals. The main task is not simply prediction but consists of identifying interpretable equations, reflecting the nature of the mechanisms generating the signals. The implemented improvements involve almost all aspects of GP, from the knowledge representation and the genetic operators to the fitness function. The unique capabilities of genetic programming, to accommodate prior information and knowledge, are also leveraged effectively. The proposed upgrades cover the most important applications of empirical modeling of time series, ranging from the identification of autoregressive systems and partial differential equations to the search of models in terms of dimensionless quantities and appropriate physical units. Particularly delicate systems to identify, such as those showing hysteretic behavior or governed by delayed differential equations, are also addressed. The potential of the developed tools is substantiated with both a battery of systematic numerical tests with synthetic signals and with applications to experimental data.

First spatially resolved measurements of the D-3He α-particle source with the upgraded JET gamma-ray camera.

The Joint European Torus (JET) gamma-ray camera has been recently upgraded with the installation of new gamma-ray detectors, based on LaBr3(Ce) scintillation crystals, which add spectroscopic capability to the existing system allowing measurements with good energy resolution (5% at 0.622 MeV), a dynamic range from hundreds of keV up to about 30 MeV, and high counting rate capabilities of MCps. First gamma-ray measurements during the C38 campaign of the JET have been successfully carried out, in particular, in D-3He plasmas from three-ion ion cyclotron resonance heating experiments, where the detection of 16.4 MeV γ-rays from D + 3He → γ + 5Li reactions with the gamma-ray camera upgrade allowed determining the spatial profile of alpha particles born in D + 3He fusion reactions.

Data driven theory for knowledge discovery in the exact sciences with applications to thermonuclear fusion.

In recent years, the techniques of the exact sciences have been applied to the analysis of increasingly complex and non-linear systems. The related uncertainties and the large amounts of data available have progressively shown the limits of the traditional hypothesis driven methods, based on first principle theories. Therefore, a new approach of data driven theory formulation has been developed. It is based on the manipulation of symbols with genetic computing and it is meant to complement traditional procedures, by exploring large datasets to find the most suitable mathematical models to interpret them. The paper reports on the vast amounts of numerical tests that have shown the potential of the new techniques to provide very useful insights in various studies, ranging from the formulation of scaling laws to the original identification of the most appropriate dimensionless variables to investigate a given system. The application to some of the most complex experiments in physics, in particular thermonuclear plasmas, has proved the capability of the methodology to address real problems, even highly nonlinear and practically important ones such as catastrophic instabilities. The proposed tools are therefore being increasingly used in various fields of science and they constitute a very good set of techniques to bridge the gap between experiments, traditional data analysis and theory formulation.

A comprehensive study of the uncertainties in bolometric tomography on JET using the maximum likelihood method.

Essential physical quantities of magnetically confined plasmas are derived on a routine basis from bolometric reconstructions. In the last few years at the Joint European Torus (JET), the Maximum Likelihood method has demonstrated the capability of providing reliable reconstructions for this class of ill-posed problems. The article is focused on quantifying the effects of important sources of errors, usually underestimated, that can influence both the reconstructions and the derived quantities. A complete set of phantoms has been used to test the robustness of the technique. The main sources of uncertainties investigated in this contribution are random noise, presence of outliers in the measurements, uncertainty of the position of the magnetic topology, and missing measurements from damaged or unreliable bolometers. The study provides a comprehensive quantification of the uncertainties to associate with most typical emissivities encountered in practice and constitutes a good basis for a more accurate evaluation of the power balances on the JET.

JET diagnostic enhancements testing and commissioning in preparation for DT scientific campaigns.

In order to optimize the scientific exploitation of JET (Joint European Torus) during the upcoming deuterium-tritium experiments, a set of diagnostic systems is being enhanced. These upgrades focus mainly on the experimental and operational conditions expected during tritium campaigns. It should be stressed that measurements relevant for burning plasmas are specifically targeted. Previously non-available capabilities, such as a current measurement system fully covering all poloidal field circuits, are described in detail. Instrument descriptions, performance prediction, testing, and initial commissioning results of these systems are presented.

The upgraded JET gamma-ray cameras based on high resolution/high count rate compact spectrometers.

The JET gamma-ray cameras have been recently upgraded within the gamma-ray camera upgrade project in support of development of JET high performance deuterium plasma scenarios and in preparation of deuterium-tritium experiments. New, dedicated detectors based on a LaBr3 crystal and silicon photo-multipliers have been developed and replaced pre-existing CsI detectors in all 19 channels. The new instrument gives opportunity of making two-dimensional gamma-ray measurements with a counting rate capability exceeding 1 MCounts/s (MCps) and energy resolution better than 5% at 1.1 MeV. The upgrade is of relevance for fast ion and runaway electron physics studies in high performance deuterium discharges and also in plasmas with tritium at neutron yields in the range up to about 5 × 1017 n/s.

First neutron spectroscopy measurements with a pixelated diamond detector at JET.

A prototype Single crystal Diamond Detector (SDD) was installed at the Joint European Torus (JET) in 2013 along an oblique line of sight and demonstrated the possibility to carry out neutron spectroscopy measurements with good energy resolution and detector stability in discharges heated by neutral beam injection and radio-frequency waves. Starting from these positive results, within the Vertical Neutron Spectrometer project of the Joint European Torus, we have developed a pixelated instrument consisting of a matrix of 12 independent SDDs, called the Diamond Vertical Neutron Spectrometer (DVNS), which boosts the detection efficiency of a single SDD by an order of magnitude. In this paper we describe the main features of the DVNS, including the detector design, energy resolution, and data acquisition system for on-line processing. Preliminary spectroscopy measurements of 2.5 MeV neutrons from the present deuterium plasma at JET are finally presented.

JET diagnostic enhancements in preparation for DT operations.

In order to complete the exploitation of the JET ITER-like Wall and to take full benefit from deuterium-tritium experiments on JET, a set of diagnostic system refurbishments or upgrades is in progress. These diagnostic enhancements focus mainly on neutron, gamma, fast ions, instabilities, and operations support. These efforts intend to provide better spatial, temporal, and energy resolution while increasing measurement coverage. Also previously non-existing capabilities, such as Doppler reflectometry is now available for scientific exploitation. Guaranteeing diagnostic reliability and consistency during the expected DT conditions is also a critical objective of the work and systems being implemented. An overview of status and scope of the ongoing projects is presented.

Performance of the prototype LaBr3 spectrometer developed for the JET gamma-ray camera upgrade.

In this work, we describe the solution developed by the gamma ray camera upgrade enhancement project to improve the spectroscopic properties of the existing JET γ-ray camera. Aim of the project is to enable gamma-ray spectroscopy in JET deuterium-tritium plasmas. A dedicated pilot spectrometer based on a LaBr3 crystal coupled to a silicon photo-multiplier has been developed. A proper pole zero cancellation network able to shorten the output signal to a length of 120 ns has been implemented allowing for spectroscopy at MHz count rates. The system has been characterized in the laboratory and shows an energy resolution of 5.5% at Eγ = 0.662 MeV, which extrapolates favorably in the energy range of interest for gamma-ray emission from fast ions in fusion plasmas.

The use of Ocimum americanum essential oil against the pathogens Aeromonas hydrophila and Gyrodactylus sp. in silver catfish (Rhamdia quelen).

UNLABELLED: The bactericidal activity (minimum inhibitory concentration (MIC)-test) of Ocimum americanum (inflorescences) essential oil (OAEO) against Aeromonas hydrophila was determined in this study. Also investigated was the potential of OAEO and the main compound found in the oil (linalool) at subinhibitory concentrations to be inhibitors of haemolysis caused by Aer. hydrophila in fish erythrocytes. An in vivo experiment was conducted to evaluate the survival of fish (Rhamdia quelen) experimentally infected with Aer. hydrophila and exposed to OAEO. A second experiment was conducted to evaluate the in vitro and in vivo activity of OAEO (mix from inflorescences and leaves) against the parasite Gyrodactylus sp. The OAEO showed weak in vitro activity against Aer. hydrophila (6400 µg ml(-1) ). Subinhibitory concentrations of OAEO (100 µg ml(-1) ) inhibited haemolysis (90%) caused by Aer. hydrophila in fish erythrocytes, however, linalool did not inhibit haemolysis activity. At the low concentrations (10 and 20 mg l(-1) ) added to the water, OAEO promoted the survival of fish experimentally infected with Aer. hydrophila. Lastly, the OAEO mix (50 mg l(-1) ) was effective against Gyrodactylus sp., significantly reducing (60%) the number of parasites in the fish. SIGNIFICANCE AND IMPACT OF THE STUDY: Phytochemicals, such as essential oils (EOs) are a great source of new molecules and have shown potential to be used in aquaculture systems. However, additional studies focused on the in vivo efficacy, mode of action and identification of the active compounds are needed. This study determined the potential of Ocimum americanum EO for use against two important fish pathogens, Aeromonas hydrophila and Gyrodactylus sp., as well as providing preliminary information about the role of the main EO compound (linalool) against Aer. hydrophila virulence.

Automatic location of disruption times in JET.

The loss of stability and confinement in tokamak plasmas can induce critical events known as disruptions. Disruptions produce strong electromagnetic forces and thermal loads which can damage fundamental components of the devices. Determining the disruption time is extremely important for various disruption studies: theoretical models, physics-driven models, or disruption predictors. In JET, during the experimental campaigns with the JET-C (Carbon Fiber Composite) wall, a common criterion to determine the disruption time consisted of locating the time of the thermal quench. However, with the metallic ITER-like wall (JET-ILW), this criterion is usually not valid. Several thermal quenches may occur previous to the current quench but the temperature recovers. Therefore, a new criterion has to be defined. A possibility is to use the start of the current quench as disruption time. This work describes the implementation of an automatic data processing method to estimate the disruption time according to this new definition. This automatic determination allows both reducing human efforts to locate the disruption times and standardizing the estimates (with the benefit of being less vulnerable to human errors).

UMEL: a new regression tool to identify measurement peaks in LIDAR/DIAL systems for environmental physics applications.

Recently, surveying large areas in an automatic way, for early detection of both harmful chemical agents and forest fires, has become a strategic objective of defence and public health organisations. The Lidar and Dial techniques are widely recognized as a cost-effective alternative to monitor large portions of the atmosphere. To maximize the effectiveness of the measurements and to guarantee reliable monitoring of large areas, new data analysis techniques are required. In this paper, an original tool, the Universal Multi Event Locator, is applied to the problem of automatically identifying the time location of peaks in Lidar and Dial measurements for environmental physics applications. This analysis technique improves various aspects of the measurements, ranging from the resilience to drift in the laser sources to the increase of the system sensitivity. The method is also fully general, purely software, and can therefore be applied to a large variety of problems without any additional cost. The potential of the proposed technique is exemplified with the help of data of various instruments acquired during several experimental campaigns in the field.

Tomographic analysis of neutron and gamma pulse shape distributions from liquid scintillation detectors at Joint European Torus.

The Joint European Torus (JET, Culham, UK) is the largest tokamak in the world devoted to nuclear fusion experiments of magnetic confined Deuterium (D)/Deuterium-Tritium (DT) plasmas. Neutrons produced in these plasmas are measured using various types of neutron detectors and spectrometers. Two of these instruments on JET make use of organic liquid scintillator detectors. The neutron emission profile monitor implements 19 liquid scintillation counters to detect the 2.45 MeV neutron emission from D plasmas. A new compact neutron spectrometer is operational at JET since 2010 to measure the neutron energy spectra from both D and DT plasmas. Liquid scintillation detectors are sensitive to both neutron and gamma radiation but give light responses of different decay time such that pulse shape discrimination techniques can be applied to identify the neutron contribution of interest from the data. The most common technique consists of integrating the radiation pulse shapes within different ranges of their rising and/or trailing edges. In this article, a step forward in this type of analysis is presented. The method applies a tomographic analysis of the 3-dimensional neutron and gamma pulse shape and pulse height distribution data obtained from liquid scintillation detectors such that n/γ discrimination can be improved to lower energies and additional information can be gained on neutron contributions to the gamma events and vice versa.

Improved equilibrium reconstructions by advanced statistical weighting of the internal magnetic measurements.

In a Tokamak the configuration of the magnetic fields remains the key element to improve performance and to maximise the scientific exploitation of the device. On the other hand, the quality of the reconstructed fields depends crucially on the measurements available. Traditionally in the least square minimisation phase of the algorithms, used to obtain the magnetic field topology, all the diagnostics are given the same weights, a part from a corrective factor taking into account the error bars. This assumption unduly penalises complex diagnostics, such as polarimetry, which have a limited number of highly significant measurements. A completely new method to choose the weights, to be given to the internal measurements of the magnetic fields for improved equilibrium reconstructions, is presented in this paper. The approach is based on various statistical indicators applied to the residuals, the difference between the actual measurements and their estimates from the reconstructed equilibrium. The potential of the method is exemplified using the measurements of the Faraday rotation derived from JET polarimeter. The results indicate quite clearly that the weights have to be determined carefully, since the inappropriate choice can have significant repercussions on the quality of the magnetic reconstruction both in the edge and in the core. These results confirm the limitations of the assumption that all the diagnostics have to be given the same weight, irrespective of the number of measurements they provide and the region of the plasma they probe.

Influence of plasma diagnostics and constraints on the quality of equilibrium reconstructions on Joint European Torus.

One of the main approaches to thermonuclear fusion relies on confining high temperature plasmas with properly shaped magnetic fields. The determination of the magnetic topology is, therefore, essential for controlling the experiments and for achieving the required performance. In Tokamaks, the reconstruction of the fields is typically formulated as a free boundary equilibrium problem, described by the Grad-Shafranov equation in toroidal geometry and axisymmetric configurations. Unfortunately, this results in mathematically very ill posed problems and, therefore, the quality of the equilibrium reconstructions depends sensitively on the measurements used as inputs and on the imposed constraints. In this paper, it is shown how the different diagnostics (Magnetics Measurements, Polarimetry and Motional Stark Effect), together with the edge current density and plasma pressure constraints, can have a significant impact on the quality of the equilibrium on JET. Results show that both the Polarimetry and Motional Stark Effect internal diagnostics are crucial in order to obtain reasonable safety factor profiles. The impact of the edge current density constraint is significant when the plasma is in the H-mode of confinement. In this plasma scenario the strike point positions and the plasma last closed flux surface can change even by centimetres, depending on the edge constraints, with a significant impact on the remapping of the equilibrium-dependent diagnostics and of pedestal physics studies. On the other hand and quite counter intuitively, the pressure constraint can severely affect the quality of the magnetic reconstructions in the core. These trends have been verified with several JET discharges and consistent results have been found. An interpretation of these results, as interplay between degrees of freedom and available measurements, is provided. The systematic analysis described in the paper emphasizes the importance of having sufficient diagnostic inputs and of properly validating the results of the codes with independent measurements.

AVE 0991, a non-peptide mimic of angiotensin-(1-7) effects, attenuates pulmonary remodelling in a model of chronic asthma.

BACKGROUND AND PURPOSE: AVE 0991 (AVE) is a non-peptide compound, mimic of the angiotensin (Ang)-(1-7) actions in many tissues and pathophysiological states. Here, we have investigated the effect of AVE on pulmonary remodelling in a murine model of ovalbumin (OVA)-induced chronic allergic lung inflammation. EXPERIMENTAL APPROACH: We used BALB/c mice (6-8 weeks old) and induced chronic allergic lung inflammation by OVA sensitization (20 µg·mouse(-1) , i.p., four times, 14 days apart) and OVA challenge (1%, nebulised during 30 min, three times per·week, for 4 weeks). Control and AVE groups were given saline i.p and challenged with saline. AVE treatment (1 mg·kg(-1) ·per day, s.c.) or saline (100 µL·kg(-1) ·per day, s.c.) was given during the challenge period. Mice were anaesthetized 72 h after the last challenge and blood and lungs collected. In some animals, primary bronchi were isolated to test contractile responses. Cytokines were evaluated in bronchoalveolar lavage (BAL) and lung homogenates. KEY RESULTS: Treatment with AVE of OVA sensitised and challenged mice attenuated the altered contractile response to carbachol in bronchial rings and reversed the increased airway wall and pulmonary vasculature thickness and right ventricular hypertrophy. Furthermore, AVE reduced IL-5 and increased IL-10 levels in the BAL, accompanied by decreased Ang II levels in lungs. CONCLUSIONS AND IMPLICATIONS: AVE treatment prevented pulmonary remodelling, inflammation and right ventricular hypertrophy in OVA mice, suggesting that Ang-(1-7) receptor agonists are a new possibility for the treatment of pulmonary remodelling induced by chronic asthma.

Development of a mirror-based endoscope for divertor spectroscopy on JET with the new ITER-like wall (invited).

A new endoscope with optimised divertor view has been developed in order to survey and monitor the emission of specific impurities such as tungsten and the remaining carbon as well as beryllium in the tungsten divertor of JET after the implementation of the ITER-like wall in 2011. The endoscope is a prototype for testing an ITER relevant design concept based on reflective optics only. It may be subject to high neutron fluxes as expected in ITER. The operating wavelength range, from 390 nm to 2500 nm, allows the measurements of the emission of all expected impurities (W I, Be II, C I, C II, C III) with high optical transmittance (≥ 30% in the designed wavelength range) as well as high spatial resolution that is ≤ 2 mm at the object plane and ≤ 3 mm for the full depth of field (± 0.7 m). The new optical design includes options for in situ calibration of the endoscope transmittance during the experimental campaign, which allows the continuous tracing of possible transmittance degradation with time due to impurity deposition and erosion by fast neutral particles. In parallel to the new optical design, a new type of possibly ITER relevant shutter system based on pneumatic techniques has been developed and integrated into the endoscope head. The endoscope is equipped with four digital CCD cameras, each combined with two filter wheels for narrow band interference and neutral density filters. Additionally, two protection cameras in the λ > 0.95 µm range have been integrated in the optical design for the real time wall protection during the plasma operation of JET.

Neutron field parameter measurements on the JET tokamak by means of super-heated fluid detectors.

The neutron field parameters (fluence and energy distribution) at a specific location outside the JET Torus Hall have been measured by means of super-heated fluid detectors (or "bubble detectors") in combination with an independent, time-of-flight, technique. The bubble detector assemblies were placed at the end of a vertical line of sight at about 16 m from the tokamak mid plane. Spatial distributions of the neutron fluence along the radial and toroidal directions have been obtained using two-dimensional arrays of bubble detectors. Using a set of three bubble detector spectrometers the neutron energy distribution was determined over a broad energy range, from about 10 keV to above 10 MeV, with an energy resolution of about 30% at 2.5 MeV. The very broad energy response allowed for the identification of energy features far from the main fusion component (around 2.45 MeV for deuterium discharges).

Introducing minimum Fisher regularisation tomography to AXUV and soft x-ray diagnostic systems of the COMPASS tokamak.

The contribution focuses on plasma tomography via the minimum Fisher regularisation (MFR) algorithm applied on data from the recently commissioned tomographic diagnostics on the COMPASS tokamak. The MFR expertise is based on previous applications at Joint European Torus (JET), as exemplified in a new case study of the plasma position analyses based on JET soft x-ray (SXR) tomographic reconstruction. Subsequent application of the MFR algorithm on COMPASS data from cameras with absolute extreme ultraviolet (AXUV) photodiodes disclosed a peaked radiating region near the limiter. Moreover, its time evolution indicates transient plasma edge cooling following a radial plasma shift. In the SXR data, MFR demonstrated that a high resolution plasma positioning independent of the magnetic diagnostics would be possible provided that a proper calibration of the cameras on an x-ray source is undertaken.

Spectral broadening of characteristic γ-ray emission peaks from 12C(3He,pγ)14N reactions in fusion plasmas.

The spectral broadening of characteristic γ-ray emission peaks from the reaction (12)C((3)He,pγ)(14)N was measured in D((3)He) plasmas of the JET tokamak with ion cyclotron resonance heating tuned to the fundamental harmonic of (3)He. Intensities and detailed spectral shapes of γ-ray emission peaks were successfully reproduced using a physics model combining the kinetics of the reacting ions with a detailed description of the nuclear reaction differential cross sections for populating the L1-L8 (14)N excitation levels yielding the observed γ-ray emission. The results provide a paradigm, which leverages knowledge from areas of physics outside traditional plasma physics, for the development of nuclear radiation based methods for understanding and controlling fusion burning plasmas.