Conceptual design of Thomson scattering diagnostics for the COMPASS-U tokamak.

The Thomson scattering (TS) diagnostic, one of the key diagnostics used on the tokamaks around the world, is planned for the COMPASS-U tokamak, which is recently under design and construction in the Institute of Plasma Physics in Prague, Czech Republic. This tokamak is supposed to be a world-unique, high magnetic field device with hot walls, allowing for the study of the plasma exhaust in advanced operational scenarios and testing cutting-edge technologies relevant to future fusion reactors, e.g., use of liquid metals. The core and edge TS systems are planned to be designed and operational, with a limited performance, already in the early stage of the tokamak operation. In this contribution, requirements and the most important constraints defining the TS system design are presented. The impact of both the possible collection lens location and spatial resolution on the plasma pedestal observation is simulated. Design considerations also take into account the high-resolution TS core and edge systems available from the COMPASS tokamak, which will be reused. The collection lenses will be newly built. Extension of the detection system will complete the plasma radius coverage in the future. The divertor TS is considered for later periods.

Thomson scattering synthetic diagnostic module for the Cherab framework.

This contribution presents a Thomson scattering module developed for the Raysect and Cherab framework. Detailed models of spectroscopic diagnostic systems can be created in the framework, which deliver synthetic data with high precision due to accurate physical treatment of ray propagation and radiation phenomena. The addition of the presented module will allow us to model Thomson scattering systems that can aid both data validation and design. Two examples of such application are given. The first example shows the application of the module on the COMPASS tokamak edge Thomson scattering diagnostic and experimental data. The second example shows the possibility to use the framework and the Thomson scattering module as a design support tool.

Microwave reflectometer for density profile and turbulence measurements on the COMPASS tokamak.

The fast microwave reflectometer system on the COMPASS tokamak consists of an O-mode polarized K-band (18 GHz-26 GHz), Ka-band (26 GHz-40 GHz), and a part of U-band (40 GHz-54 GHz). The plasma density profile from the edge plasma area is measured using a fast sweeping rate up of to 6 µs of the probing wave. The processing of the reflected signal is realized by the heterodyne detection configuration based on the I/Q modulator. Two different methods of dynamic calibration of the required linear sweep frequency, together with static frequency and dispersion calibration, were used. The electron density profile was reconstructed by a spectrogram-based method with four sweeps on average. The system has the capability to measure the mid-plane low-field side electron density profile in the density range from 4 × 1018 m-3 to 3.6 × 1019 m-3. Experimental results obtained on COMPASS discharges are presented to demonstrate the performance of the diagnostics.

Development of an ion beam detector for the atomic beam probe diagnostic.

The atomic beam probe diagnostic concept aims at measuring the edge magnetic field and through that edge current distribution in fusion plasmas by observing trajectories of an ion beam stemming from a diagnostic neutral beam. The diagnostic potentially has microsecond scale time resolution and can thus prove to be a powerful option to study fast changes in the edge plasma. A test detector has been installed on the COMPASS tokamak as an extension of the existing lithium beam diagnostic system. It employs a relatively simple concept of an array of conductive detection plates measuring the incident ion current, which is then amplified and converted to a voltage signal. The aim of the test detector is to experimentally examine the idea of the diagnostic and provide background data for design and installation of a final detector. Also, a numerical code based on the CUDA parallel computing platform has been developed for modeling lithium ion trajectories in the given COMPASS plasma discharges. We present the developments of the detector design and test measurements of the diagnostic performed both in a laboratory beam system and on the COMPASS tokamak.

Fast density reconstruction of Li-BES signal on the COMPASS tokamak.

This article describes a fast and automatic reconstruction of the edge plasma electron density from the radiation of energetic Li atoms of the diagnostic beam on the COMPASS tokamak. Radiation is detected by using a CCD camera and by using an avalanche photo-diode system with a temporal resolution of 20 ms and 2 µs, respectively. Both systems are equipped with a 670.8 nm optical filter which corresponds to the lithium 1s22s1-1s22p1 transition. A theoretical model and a data processing procedure of a raw signal to obtain the density profile are described. The reconstruction algorithm provides the absolutely calibrated electron density profiles together with the measurement error estimated from relatively calibrated light profiles; the implementation is performed in Python. Time demanding operations of the code were optimized to provide reconstruction of a single profile within less than 10 ms which makes the code applicable for processing of a large amount of data. Thanks to this calculation speed, it is possible to reconstruct electron density profiles between two consecutive shots on the COMPASS tokamak with 2 µs time resolution.

Observation and evaluation of the alignment of Thomson scattering systems.

Concerning plasma diagnostics based on Thomson scattering (TS), precise adjustment and proper alignment is of great importance in order to provide reliable and accurate measurements. Any misalignment could result in an incorrectly determined plasma density or prevent the measurement with this type of diagnostic altogether. Suitable means of alignment monitoring should be integrated into each TS diagnostic system. Variations of commonly used methods are discussed in this article. Correlation of results from alignment control with performed measurements of vibrations on the COMPASS tokamak is presented. Various techniques of optimization of alignment monitoring are shown. The optimal technique, which could be accommodated during the construction of TS diagnostic systems in future fusion devices, is proposed.

Filamentary probe on the COMPASS tokamak.

This paper describes a new filamentary probe recently introduced on the COMPASS tokamak. It allows the measurement of electrostatic and magnetic properties of the filaments and their changes in dependence on distance from the separatrix in the region between a divertor and midplane. The probe head is mounted on a manipulator moving the probe radially on a shot-to-shot basis. This configuration is suitable for the long term statistical measurement of the plasma filaments and the measurement of their evolution during their propagation from the separatrix to the wall. The basics of the filamentary probe construction, the evolution of the plasma parameters, and first conditional averages of the plasma filaments in the scrape-off layer of the COMPASS tokamak during the L-mode regime are presented.

Fitting of the Thomson scattering density and temperature profiles on the COMPASS tokamak.

A new technique for fitting the full radial profiles of electron density and temperature obtained by the Thomson scattering diagnostic in H-mode discharges on the COMPASS tokamak is described. The technique combines the conventionally used modified hyperbolic tangent function for the edge transport barrier (pedestal) fitting and a modification of a Gaussian function for fitting the core plasma. Low number of parameters of this combined function and their straightforward interpretability and controllability provide a robust method for obtaining physically reasonable profile fits. Deconvolution with the diagnostic instrument function is applied on the profile fit, taking into account the dependence on the actual magnetic configuration.

Profile measurements of the electron temperature on the ASDEX Upgrade, COMPASS, and ISTTOK tokamak using Thomson scattering, triple, and ball-pen probes.

The ball-pen probe (BPP) technique is used successfully to make profile measurements of the electron temperature on the ASDEX Upgrade (Axially Symmetric Divertor Experiment), COMPASS (COMPact ASSembly), and ISTTOK (Instituto Superior Tecnico TOKamak) tokamak. The electron temperature is provided by a combination of the BPP potential (ΦBPP) and the floating potential (Vfl) of the Langmuir probe (LP), which is compared with the Thomson scattering diagnostic on ASDEX Upgrade and COMPASS. Excellent agreement between the two diagnostics is obtained for circular and diverted plasmas and different heating mechanisms (Ohmic, NBI, ECRH) in deuterium discharges with the same formula Te = (ΦBPP - Vfl)/2.2. The comparative measurements of the electron temperature using BPP/LP and triple probe (TP) techniques on the ISTTOK tokamak show good agreement of averaged values only inside the separatrix. It was also found that the TP provides the electron temperature with significantly higher standard deviation than BPP/LP. However, the resulting values of both techniques are well in the phase with the maximum of cross-correlation function being 0.8.

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.

Use of soft x-ray diagnostic on the COMPASS tokamak for investigations of sawteeth crash neighborhood and of plasma position using fast inversion methods.

The soft x-ray diagnostic is suitable for monitoring plasma activity in the tokamak core, e.g., sawtooth instability. Moreover, spatially resolved measurements can provide information about plasma position and shape, which can supplement magnetic measurements. In this contribution, fast algorithms with the potential for a real-time use are tested on the data from the COMPASS tokamak. In addition, the soft x-ray data are compared with data from other diagnostics in order to discuss possible connection between sawtooth instability on one side and the transition to higher confinement mode, edge localized modes and productions of runaway electrons on the other side.

Dichloroacetate induces autophagy in colorectal cancer cells and tumours.

BACKGROUND: Dichloroacetate (DCA) has been found to have antitumour properties. METHODS: We investigated the cellular and metabolic responses to DCA treatment and recovery in human colorectal (HT29, HCT116 WT and HCT116 Bax-ko), prostate carcinoma cells (PC3) and HT29 xenografts by flow cytometry, western blotting, electron microscopy, (1)H and hyperpolarised (13)C-magnetic resonance spectroscopy. RESULTS: Increased expression of the autophagy markers LC3B II was observed following DCA treatment both in vitro and in vivo. We observed increased production of reactive oxygen species (ROS) and mTOR inhibition (decreased pS6 ribosomal protein and p4E-BP1 expression) as well as increased expression of MCT1 following DCA treatment. Steady-state lactate excretion and the apparent hyperpolarised [1-(13)C] pyruvate-to-lactate exchange rate (k(PL)) were decreased in DCA-treated cells, along with increased NAD(+)/NADH ratios and NAD(+). Steady-state lactate excretion and k(PL) returned to, or exceeded, control levels in cells recovered from DCA treatment, accompanied by increased NAD(+) and NADH. Reduced k(PL) with DCA treatment was found in HT29 tumour xenografts in vivo. CONCLUSIONS: DCA induces autophagy in cancer cells accompanied by ROS production and mTOR inhibition, reduced lactate excretion, reduced k(PL) and increased NAD(+)/NADH ratio. The observed cellular and metabolic changes recover on cessation of treatment.

High-resolution Thomson scattering system on the COMPASS tokamak: evaluation of plasma parameters and error analysis.

The electron density and temperature profiles measured by the Thomson scattering diagnostic on the COMPASS tokamak are used for estimation of electron kinetic energy, energy confinement time, and effective charge number Z(eff). Data are compared with the line-integrated electron density measured by a microwave interferometer in an ohmically heated plasma with a circular cross section. An error analysis of both electron temperature and density are performed by two methods-a constant chi-square boundaries method and a Monte Carlo simulation, determining asymmetrical error bars for the electron temperature.

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.

Progress of development of Thomson scattering diagnostic system on COMPASS.

A new Thomson scattering diagnostic system has been designed and is being built now on the COMPASS tokamak at the Institute of Plasma Physics ASCR in Prague (IPP Prague) in the Czech Republic. This contribution focuses on design, development, and installation of the light collection and detection system. High spatial resolution of 3 mm will be achieved by a combination of design of collection optics and connected polychromators. Imaging characteristics of both core and edge plasma collection objectives are described and fiber backplane design is presented. Several calibration procedures are discussed. The operational deployment of the Thomson scattering diagnostic is planned by the end of 2010.

Screening to prevent polyoma virus nephropathy in kidney transplantation: a cost analysis.

Polyoma virus nephropathy is an important cause of graft dysfunction in kidney transplant recipients and screening to prevent disease has been advocated. Although screening incurs new costs, our hypothesis is that savings from less immunosuppression in those with positive screening tests could pay for overall costs of screening. In 134 consecutive recipients, polyoma virus (positive decoy cells) was detected in the urine of 34 (25.4%) individuals over a 2-year follow-up. Of these 34, 11 had a plasma BK PCR of >7700 copies/mL. Immunosuppression was reduced stepwise in these patients until viral loads fell <1000/mL. Overall screening costs (including extra plasma PCR testing) were estimated at $33,450. Those with positive PCR had greater reductions in annual immunosuppression costs by year 2 ($6452 vs. $2799, p = 0.0015) compared to those with negative screens. At the end of the 2-year period, 61% of the screening costs were covered by less immunosuppressant costs. At the end of 30 months there were net savings. In summary, reductions in immunosuppression cover the cost of screening for polyoma viral infection. Longer-term follow-up is needed to ensure patient outcomes remain acceptable.

Access to the kidney transplant wait list.

The study examines selection for kidney transplantation and determines who are referred, how many had contraindications and whether comorbidity indices predict transplant status. Of 113 consecutive adult incident end-stage renal disease (ESRD) patients at this single center 47 (41.6%) were referred. Using published guidelines, 48 (42.5%) had a specific contraindication. However 26 (23%) were neither referred nor had contraindications. An ESRD mortality score, acute renal failure status and albumin were independent predictors of referral but only the mortality score was predictive of contraindication status. The Charlson and ESRD comorbidity indices were less predictive of contraindication or referral status. In a comparison of patients who were Candidates (referred and no contraindication, n = 39) compared to those who were Neither (not referred and no contraindications, n = 26), age was the most discriminating factor (c = 0.99, 95% CI 0.97-1.00). Comorbidity and mortality indices were inferior. Neither patients were older (75 +/- 7 years) and had comorbidity scores that were higher than Candidates but similar to those with contraindications (ESRD index; Neither 3.3 +/- 2.5, Candidate 1.4 +/- 1.8, and contraindication 4.1 +/- 3.4). Comorbitity indices do not help explain selection practices whereas age is an important discriminator. How many Neither patients would benefit from transplantation is not known.

Survey of porcine rotavirus G and P genotype in Poland and the United States using RT-PCR.

Porcine rotaviruses are a common cause of gastroenteritis. Several serotypes have been detected based on the two surface proteins VP4 (P-types) and VP7 (G-types). However, limited studies have been performed on the relative frequency of rotavirus types in diarrhetic pigs primarily because of the lack of availability of suitable methods. In this study, we describe a reverse transcriptase-polymerase chain reaction (RT-PCR) method for the typing of P and G types of rotavirus. This method allowed to detect G and P types in 96.8 and 87.1% of isolates collected in the United States, respectively and in 54.5 and 38.6% of isolates collected in Poland, respectively. Within the US specimens the G3, G4, G5, G9 and G10 types were detected in combination with P6 and P7 types while among Polish specimens only G3, G4 and G5 types in combination with P6 and P7 types were identified. In both instances the G4 and G5 were the most prevalent types. These studies show that a RT-PCR typing method is suitable for molecular epidemiological studies and that there is more diversity among porcine rotavirus than previously reported.

p21-activated kinase-1 (PAK1) inhibition of the human scavenger receptor class B, type I promoter in macrophages is independent of PAK1 kinase activity, but requires the GTPase-binding domain.

Scavenger receptor class B, type I (SR-BI), is a high density lipoprotein receptor that mediates the flux of cholesterol between high density lipoprotein and cells. Recent evidence suggests that SR-BI plays a role in atherosclerosis and that inflammatory mediators down-regulate SR-BI in the macrophage. The purpose of this study was to evaluate the ability of lipopolysaccharide (LPS) to down-regulate the activity of the human SR-BI promoter in the macrophage and to delineate the mechanisms involved. Experiments with cultured cells and in vivo derived macrophages showed that LPS has a powerful suppressive effect on SR-BI expression both in vitro and in vivo. Transient transfection studies demonstrated that LPS represses SR-BI promoter activity in the macrophage cell line RAW 264.7. Cotransfection with either a constitutively active p21-activated protein kinase-1 (PAK1) construct (T423E) or a kinase-deficient PAK1 construct (K299R) resulted in repression of the SR-BI promoter, similar to LPS. These results demonstrate that PAK1-mediated down-regulation of the SR-BI promoter is independent of PAK1 kinase activity and suggest that PAK1 mediates the LPS-induced decrease in promoter activity. Cotransfection with constitutively active Cdc42 or Rac expression constructs also resulted in down-regulation of the promoter; whereas the dominant-negative Cdc42 and Rac constructs elevated basal promoter activity and blunted the LPS response. Cotransfection of PAK1 constructs containing mutations in both the kinase domain and the Cdc42/Rac-binding domain attenuated the PAK1-mediated down-regulation of the promoter, suggesting that Rac and Cdc42 are required for PAK1-mediated decreases in SR-BI promoter activity. 5'-Deletion analysis and gel shift data suggest that LPS inhibits binding of a novel transcription factor to a myeloid zing finger protein-1-like element (-476 to -456) in the human SR-BI promoter. These results demonstrate that the PAK1 pathway down-regulates the SR-BI promoter and suggest that activation of this pathway may play an important role in cholesterol trafficking in the vessel wall.

Soluble 2-substituted aminopyrido[2,3-d]pyrimidin-7-yl ureas. Structure-activity relationships against selected tyrosine kinases and exploration of in vitro and in vivo anticancer activity.

In continuing our search for medicinal agents to treat proliferative diseases, we have discovered 2-substituted aminopyrido[2,3-d]pyrimidin-7-yl ureas as a novel class of soluble, potent, broadly active tyrosine kinase (TK) inhibitors. An efficient route was developed that enabled the synthesis of a wide variety of analogues with substitution on several positions of the template. From the lead structure 1, several series of analogues were made that examined the C-6 aryl substituent, a variety of water solublizing substitutents at the C-2 position, and urea or other acyl functionality at the N-7 position. Compounds of this series were competitive with ATP and displayed submicromolar to low nanomolar potency against a panel of TKs, including receptor (platelet-derived growth factor, PDGFr; fibroblast growth factor, FGFr;) and nonreceptor (c-Src) classes. Several of the most potent compounds displayed submicromolar inhibition of PDGF-mediated receptor autophosphorylation in rat aortic vascular smooth muscle cells and low micromolar inhibition of cellular growth in five human tumor cell lines. One of the more thoroughly evaluated members, 32, with IC50 values of 0.21 microM (PDGFr), 0.049 microM (bFGFr), and 0.018 microM (c-Src), was evaluated in in vivo studies against a panel of five human tumor xenografts, with known and/or inferred dependence on the EGFr, PDGFr, and c-Src TKs. Compound 32 produced a tumor growth delay of 14 days against the Colo-205 colon xenograft model.