Using convolutional neural networks to detect edge localized modes in DIII-D from Doppler backscattering measurements.

In H-mode tokamak plasmas, the plasma is sometimes ejected beyond the edge transport barrier. These events are known as edge localized modes (ELMs). ELMs cause a loss of energy and damage the vessel walls. Understanding the physics of ELMs, and by extension, how to detect and mitigate them, is an important challenge. In this paper, we focus on two diagnostic methods-deuterium-alpha (Dα) spectroscopy and Doppler backscattering (DBS). The former detects ELMs by measuring Balmer alpha emission, while the latter uses microwave radiation to probe the plasma. DBS has the advantages of having a higher temporal resolution and robustness to damage. These advantages of DBS diagnostic may be beneficial for future operational tokamaks, and thus, data processing techniques for DBS should be developed in preparation. In sight of this, we explore the training of neural networks to detect ELMs from DBS data, using Dα data as the ground truth. With shots found in the DIII-D database, the model is trained to classify each time step based on the occurrence of an ELM event. The results are promising. When tested on shots similar to those used for training, the model is capable of consistently achieving a high f1-score of 0.93. This score is a performance metric for imbalanced datasets that ranges between 0 and 1. We evaluate the performance of our neural network on a variety of ELMs in different high confinement regimes (grassy ELM, RMP mitigated, and wide-pedestal), finding broad applicability. Beyond ELMs, our work demonstrates the wider feasibility of applying neural networks to data from DBS diagnostic.

Crohn's disease: A retrospective analysis between computed tomography enterography, colonoscopy, and histopathology.

INTRODUCTION: To investigate the spectrum of computed tomography enterography (CTE) findings of active Crohn's disease (CD) in comparison to endoscopic, histopathologic and inflammatory markers. METHODS: Hospital records of 197 patients with known or suspected CD who underwent CTE over a period of 5 years were reviewed. Eighty-nine patients fulfilled the inclusion criteria. Three-point severity scores for endoscopy, pathology, and haematologic inflammatory markers were recorded. The findings on CTE were identified by three readers and correlated with endoscopic, pathologic, and haematologic severity scores. Statistical analysis was carried out employing a Pearson Chi square test and Fisher exact test. Receiver operating characteristic (ROC), visual grading characteristic (VGC) and Cohens' kappa analyses were performed. RESULTS: The CTE findings which were significantly correlated with the severity of active disease on endoscopy include bowel wall thickening, mucosal hyperenhancement, bilaminar stratified wall enhancement, transmural wall enhancement, and mesenteric fluid adjacent to diseased bowel (p < 0.05). Only bowel wall thickening and bilaminar stratified wall enhancement correlated with the pathological severity of active CD. ROC and VGC analysis demonstrated significantly higher areas under the curve (p < 0.0001) together with excellent inter-reader agreement (k = 0.86). CONCLUSION: CTE is a reliable tool for evaluating the severity of active disease and helps in the clinical decision pathway.

Direct Observation of Nonlinear Coupling between Pedestal Modes Leading to the Onset of Edge Localized Modes.

Prior to eruptive events such as edge localized modes (ELMs), quasicoherent fluctuations, referred to as pedestal modes, are observed in the edge of fusion devices. We report on the investigations of nonlinear coupling between these modes during quasistationary inter-ELM phases leading to the ELM onset. Three dominant modes, with density and magnetic signatures, are identified as key players in the triggering mechanism of certain classes of ELMs. We demonstrate that one of these modes is amplified by the two others through three wave interactions. The amplified mode is radially shifted relative to the other two modes towards the last-closed flux surface as the ELM event approaches. Our results suggest that nonlinear coupling of pedestal modes, associated with radial distortions pushing out of the pedestal, is a possible mechanism for the triggering of low frequency ELMs relevant for future fusion devices.

First step toward a synthetic diagnostic for magnetic fluctuation measurements using cross-polarization scattering on DIII-D.

Cross-polarization scattering (CPS) provides localized magnetic fluctuation ( B ̃ ) measurements in fusion plasmas based on the process where B ̃ scatters electromagnetic radiation into the orthogonal polarization. The CPS system on DIII-D utilizes the probe beam of a Doppler backscattering (DBS) diagnostic combined with a cross-view CPS receiver system, which allows simultaneous density and B ̃ measurements with good spatial and wavenumber coverage. The interpretation of the signals is challenging due to the complex plasma propagation of the DBS probe beam and CPS receive beams. A synthetic diagnostic for CPS is therefore essential to interpret data and perform detailed validation tests of non-linear turbulence simulations. This work reports a first step toward a synthetic diagnostic for CPS utilizing GENRAY, a 3-D ray tracing code, to simulate the propagation of the probe and scattered rays. The local B ̃ wavenumber is calculated from the local O- and X-mode wavenumbers using the wave vector matching scattering condition. The CPS wavenumber values and spatial locations are determined by a complex consideration that includes the local density and B ̃ level, receive antenna pattern and orientation, scattering volume, wavenumber values detected at the various scattering centers, and alignment of the magnetic wave vector with the plane perpendicular to the magnetic field. The issue of a spurious CPS signal due to polarization mismatches for launch and receive is also discussed. It is suggested that simultaneous O- and X-mode DBS measurements should be utilized for better understanding of the CPS signal contamination when the cutoff locations for both polarizations are close.

Quasistationary Plasma Predator-Prey System of Coupled Turbulence, Drive, and Sheared E×B Flow During High Performance DIII-D Tokamak Discharges.

A new, long-lived limit cycle oscillation (LCO) regime has been observed in the edge of near zero torque high performance DIII-D tokamak plasma discharges. These LCOs are localized and composed of density turbulence, gradient drives, and E×B velocity shear damping (E and B are the local radial electric and total magnetic fields). Density turbulence sequentially acts as a predator (via turbulence transport) of profile gradients and a prey (via shear suppression) to the E×B velocity shear. Reported here for the first time is a unique spatiotemporal variation of the local E×B velocity, which is found to be essential for the existence of this system. The LCO system is quasistationary, existing from 3 to 12 plasma energy confinement times (∼30-900 LCO cycles) limited by hardware constraints. This plasma system appears to contribute strongly to the edge transport in these high performance and transient-free plasmas, as evident from oscillations in transport relevant edge parameters at LCO time scale.

Differential desulfurization of dibenzothiophene by newly identified MTCC strains: Influence of Operon Array.

Since the sulfur specific cleavage is vital for the organic sulfur removal from fossil fuel, we explored potential bacterial strains of MTCC (Microbial Type Culture Collection) to desulfurize the Dibenzothiophene (DBT) through C-S bond cleavage (4-S pathway). MTCC strains Rhodococcus rhodochrous (3552), Arthrobacter sulfureus (3332), Gordonia rubropertincta (289), and Rhodococcus erythropolis (3951) capable of growing in 0.5 mM DBT were examined for their desulfurization ability. The presence of dsz genes as well as the metabolites was screened by polymerase chain reaction (PCR) and HPLC, respectively. All these strains showed > 99% DBT desulfurization with 10 days of incubation in minimal salt medium. From the HPLC analysis it was further revealed that these MTCC strains show differences in the end metabolites and desulfurize DBT differently following a variation in the regular 4-S pathway. These findings are also well corroborating with their respective organization of dszABC operons and their relative abundance. The above MTCC strains are capable of desulfurizing DBT efficiently and hence can be explored for biodesulfurization of petrochemicals and coal with an eco-friendly and energy economical process.

Simultaneous measurement of magnetic and density fluctuations via cross-polarization scattering and Doppler backscattering on the DIII-D tokamak.

An upgraded cross-polarization scattering (CPS) system for the simultaneous measurement of internal magnetic fluctuations B̃ and density fluctuations ñ is presented. The system has eight radial quadrature channels acquired simultaneously with an eight-channel Doppler backscattering system (measures density fluctuations ñ and flows). 3-D ray tracing calculations based on the GENRAY ray tracing code are used to illustrate the scattering and geometric considerations involved in the CPS implementation on DIII-D. A unique quasi-optical design and IF electronics system allow direct comparison of B̃ and ñ during dynamic or transient plasma events (e.g., Edge Localized Modes or ELMs, L to H-mode transitions, etc.). The system design allows the interesting possibility of both magnetic-density (B̃-ñ) fluctuation and magnetic-temperature (B̃-T̃) fluctuation cross-phase measurements suitable for detailed tests of turbulence simulations.

Measurement of local, internal magnetic fluctuations via cross-polarization scattering in the DIII-D tokamak (invited).

We present new measurements of internal magnetic fluctuations obtained with a novel eight channel cross polarization scattering (CPS) system installed on the DIII-D tokamak. Measurements of internal, localized magnetic fluctuations provide a window on an important physics quantity that we heretofore have had little information on. Importantly, these measurements provide a new ability to challenge and test linear and nonlinear simulations and basic theory. The CPS method, based upon the scattering of an incident microwave beam into the opposite polarization by magnetic fluctuations, has been significantly extended and improved over the method as originally developed on the Tore Supra tokamak. A new scattering geometry, provided by a unique probe beam, is utilized to improve the spatial localization and wavenumber range. Remotely controllable polarizer and mirror angles allow polarization matching and wavenumber selection for a range of plasma conditions. The quasi-optical system design, its advantages and challenges, as well as important physics validation tests are presented and discussed. Effect of plasma beta (ratio of kinetic to magnetic pressure) on both density and magnetic fluctuations is studied and it is observed that internal magnetic fluctuations increase with beta. During certain quiescent high confinement operational regimes, coherent low frequency modes not detected by magnetic probes are detected locally by CPS diagnostics.

Lanthanum induced B-to-Z transition in self-assembled Y-shaped branched DNA structure.

Controlled conversion of right-handed B-DNA to left-handed Z-DNA is one of the greatest conformational transitions in biology. Recently, the B-Z transition has been explored from nanotechnological points of view and used as the driving machinery of many nanomechanical devices. Using a combination of CD spectroscopy, fluorescence spectroscopy, and PAGE, we demonstrate that low concentration of lanthanum chloride can mediate B-to-Z transition in self-assembled Y-shaped branched DNA (bDNA) structure. The transition is sensitive to the sequence and structure of the bDNA. Thermal melting and competitive dye binding experiments suggest that La(3+) ions are loaded to the major and minor grooves of DNA and stabilize the Z-conformation. Our studies also show that EDTA and EtBr play an active role in reversing the transition from Z-to-B DNA.

MaxMod: a hidden Markov model based novel interface to MODELLER for improved prediction of protein 3D models.

Modeling the three-dimensional (3D) structures of proteins assumes great significance because of its manifold applications in biomolecular research. Toward this goal, we present MaxMod, a graphical user interface (GUI) of the MODELLER program that combines profile hidden Markov model (profile HMM) method with Clustal Omega program to significantly improve the selection of homologous templates and target-template alignment for construction of accurate 3D protein models. MaxMod distinguishes itself from other existing GUIs of MODELLER software by implementing effortless modeling of proteins using templates that bear modified residues. Additionally, it provides various features such as loop optimization, express modeling (a feature where protein model can be generated directly from its sequence, without any further user intervention) and automatic update of PDB database, thus enhancing the user-friendly control of computational tasks. We find that HMM-based MaxMod performs better than other modeling packages in terms of execution time and model quality. MaxMod is freely available as a downloadable standalone tool for academic and non-commercial purpose at http://www.immt.res.in/maxmod/.

Estrogens control inflammation in experimental colitis.

There is now a wealth of experimental evidence indicating that the deficit in endogenous estrogen facilitates the onset of inflammation that can be antagonized by estrogen replacement therapy. This work investigated the role of estrogen in the control of intestinal inflammation in a panel of colitis models, focusing on the morphological changes, the activity of mast cells, the expression of cytokines (IL-1beta, IL-6, and TNF-alpha), fibronectin and reactive oxygen species. Two hundred adult male rats were divided into 4 groups: colitis was induced in Group I and Group II but only the latter was treated with estrogen; Group III received estrogen only, and Group IV saline. Colitis was induced in 4 models using: iodoacetamide; iodoacetamide + enteropathogenic E. coli; 2, 4, 6-Trinitrobenzene sulfonic acid; and dextran sulfate sodium salt. Macroscopic and microscopic evaluations of abdominal structures as well as molecular analysis were made on days 7, 14, 28 and 56. There was a significant improvement in the health condition of the estrogen-treated rats: the inflammation scores were reduced by at least 10-15%, the number of mast cells in the colon decreased by 30%, fibronectin expression was only 50% and reactive oxygen species decreased by 30%. In addition, there was a significant decrease in TNF-alpha, IL-6 and IL-1beta expression by about 25%. In conclusion, there was an improvement in the inflammatory status in all estrogen-treated groups through the duration of the experiment at all-time points. In addition, there was less tissue necrosis as depicted by less fibronectin and a marked antioxidant effect.

Microalga Scenedesmus sp.: A potential low-cost green machine for silver nanoparticle synthesis.

Bionanotechnology has revolutionized nanomaterial synthesis by providing a green synthetic platform using biological systems. Among such biological systems, microalgae have tremendous potential to take up metal ions and produce nanoparticles by a detoxification process. The present study explores the intracellular and extracellular biogenic syntheses of silver nanoparticles (SNPs) using the unicellular green microalga Scenedesmus sp. Biosynthesized SNPs were characterized by AAS, UV-Vis spectroscopy, TEM, XRD, FTIR, DLS, and TGA studies and finally checked for antibacterial activity. Intracellular nanoparticle biosynthesis was initiated by a high rate of Ag(+) ion accumulation in the microalgal biomass and subsequent formation of spherical crystalline SNPs (average size, 15-20 nm) due to the biochemical reduction of Ag(+) ions. The synthesized nanoparticles were intracellular, as confirmed by the UV-Vis spectra of the outside medium. Furthermore, extracellular synthesis using boiled extract showed the formation of well scattered, highly stable, spherical SNPs with an average size of 5-10 nm. The size and morphology of the nanoparticles were confirmed by TEM. The crystalline nature of the SNPs was evident from the diffraction peaks of XRD and bright circular ring pattern of SAED. FTIR and UV-Vis spectra showed that biomolecules, proteins and peptides, are mainly responsible for the formation and stabilization of SNPs. Furthermore, the synthesized nanoparticles exhibited high antimicrobial activity against pathogenic gram-negative and gram-positive bacteria. Use of such a microalgal system provides a simple, cost-effective alternative template for the biosynthesis of nanomaterials in a large-scale system that could be of great use in biomedical applications.

Parametric appraisal of process parameters for adhesion of plasma sprayed nanostructured YSZ coatings using Taguchi experimental design.

This paper presents the application of the Taguchi experimental design in developing nanostructured yittria stabilized zirconia (YSZ) coatings by plasma spraying process. This paper depicts dependence of adhesion strength of as-sprayed nanostructured YSZ coatings on various process parameters, and effect of those process parameters on performance output has been studied using Taguchi's L16 orthogonal array design. Particle velocities prior to impacting the substrate, stand-off-distance, and particle temperature are found to be the most significant parameter affecting the bond strength. To achieve retention of nanostructure, molten state of nanoagglomerates (temperature and velocity) has been monitored using particle diagnostics tool. Maximum adhesion strength of 40.56 MPa has been experimentally found out by selecting optimum levels of selected factors. The enhanced bond strength of nano-YSZ coating may be attributed to higher interfacial toughness due to cracks being interrupted by adherent nanozones.

Effect of dissimilatory Fe(III) reducers on bio-reduction and nickel-cobalt recovery from Sukinda chromite-overburden.

The effect of an adapted dissimilatory iron reducing bacterial consortium (DIRB) towards bio-reduction of Sukinda chromite overburden (COB) with enhanced recovery of nickel and cobalt is being reported for the first time. The remarkable ability of DIRB to utilize Fe(III) as terminal electron acceptor reducing it to Fe(II) proved beneficial for treatment of COB as compared to previous reports for nickel leaching. XRD studies showed goethite as the major iron-bearing phase in COB. Under facultative anaerobic conditions, goethite was reduced to hematite and magnetite with the exposure of nickel oxide. FESEM studies showed DIRB to be associated with COB through biofilm formation with secondary mineral precipitates of magnetite deposited as tiny globular clusters on the extra polymeric substances. The morphological and mineralogical changes in COB, post DIRB application, yielded a maximum of 68.5% nickel and 80.98% cobalt in 10 days using 8M H2SO4.

Maximizing biomass productivity and CO2 biofixation of microalga, Scenedesmus sp. by using sodium hydroxide.

A series of experiments were carried out with three native strains of microalgae to measure growth rates, biomass, and lipid productivities. Scenedesmus sp. IMMTCC-6 had better biomass growth rate and higher lipid production. The growth, lipid accumulation, and carbon dioxide (CO2) consumption rate of Scenedesmus sp. IMMTCC-6 were tested under different NaOH concentrations in modified BBM. The algal strain showed the maximum specific growth rate (0.474/day), biomass productivity (110.9 mg l(-1) d(-1)), and CO2 consumption rate (208.4 mg l(-1) d(-1)) with an NaOH concentration of 0.005 M on the 8(th) day of cultivation. These values were 2.03-, 6.89-, and 6.88-fold more than the algal cultures grown in control conditions (having no NaOH and CO2). The CO2 fixing efficiency of the microalga with other alternative carbon sources like Na2CO3 and NaHCO3 was also investigated and compared. The optimized experimental parameters at shake-flask scale were implemented for scaling up the process in a self-engineered photobioreactor. A significant increase in lipid accumulation (14.23% to 31.74%) by the algal strain from the logarithmic to stationary phases was obtained. The algal lipids were mainly composed of C16/C18 fatty acids, and are desirable for biodiesel production. The study suggests that microalga Scenedesmus sp. IMMTCC-6 is an efficient strain for biodiesel production and CO2 biofixation using stripping solution of NaOH in a cyclic process.

Ultrafast laser-induced microstructure/nanostructure replication and optical properties.

This paper demonstrates replication of ultrafast laser-induced micro/nano surface textures on poly(dimethylsiloxane) (PDMS). The surface texture replication process reduces the processing steps for microtexturing while improving light trapping. Two methods are demonstrated to replicate surface microtexture, a simple mold method and an embossing method. The laser microtextured silicon and titanium surfaces with micro to nanoscale features have been successfully replicated. Optical characterization of the replicated microtextured PDMS surfaces is performed and the results agree with model predictions. The replicated microtextured PDMS film is applied on a silicon surface and optical characterization shows that surface reflectance can be suppressed over 55% compared to the control value.

Micro texturing of silicon using pulsed N(2)-laser and formation mechanism.

A low-cost pulsed N(2)-laser has been used to successfully demonstrate the formation of self-organized conical microtexture in Si. The process is demonstrated in vacuum environment to avoid the use of SF(6) gas and sulfur incorporation. The microtexture is formed with an average structure height of ~15 um, base diameter ~10 µm, and tip-to-tip separation ~8 µm. Energy dispersive x-ray spectroscopy of individual conelike structure shows that the material remains free from impurity incorporation. We have shown that the laser-induced-damage-related absorption can be successfully restored after an hour annealing at 1000 °C, making the material an ideal candidate for photovoltaic and other photonic applications.

Self-organized 2D periodic arrays of nanostructures in silicon by nanosecond laser irradiation.

We report a phenomenon of spontaneous formation of self-organized 2D periodic arrays of nanostructures (protrusions) by directly exposing a silicon surface to multiple nanosecond laser pulses. These self-organized 2D periodic nanostructures are produced toward the edge as an annular region around the circular laser spot. The heights of these nanostructures are around 500 nm with tip diameter ~100 nm. The period of the nanostructures is about 1064 nm, the wavelength of the incident radiation. In the central region of the laser spot, nanostructures are destroyed because of the higher laser intensity (due to the Gaussian shape of the laser beam) and accumulation of large number of laser pulses. Optical diffraction from these nanostructures indicates a threefold symmetry, which is in accordance with the observed morphological symmetries of these nanostructures.

Laser-textured silicon photodiode with broadband spectral response.

A femtosecond-laser-textured Si photodetector is reported. Broadband spectral optical response is detected from UV to NIR. A quantum efficiency of greater than 80% from 490 nm to 780 nm has been achieved. The quantum efficiency at 245 nm is 62%, which is comparable to UV-enhanced Si photodiodes. The bandwidth of a 250-µm-diameter device is 60 MHz.