Low latency optical-based mode tracking with machine learning deployed on FPGAs on a tokamak.

Active feedback control in magnetic confinement fusion devices is desirable to mitigate plasma instabilities and enable robust operation. Optical high-speed cameras provide a powerful, non-invasive diagnostic and can be suitable for these applications. In this study, we process high-speed camera data, at rates exceeding 100 kfps, on in situ field-programmable gate array (FPGA) hardware to track magnetohydrodynamic (MHD) mode evolution and generate control signals in real time. Our system utilizes a convolutional neural network (CNN) model, which predicts the n = 1 MHD mode amplitude and phase using camera images with better accuracy than other tested non-deep-learning-based methods. By implementing this model directly within the standard FPGA readout hardware of the high-speed camera diagnostic, our mode tracking system achieves a total trigger-to-output latency of 17.6 µs and a throughput of up to 120 kfps. This study at the High Beta Tokamak-Extended Pulse (HBT-EP) experiment demonstrates an FPGA-based high-speed camera data acquisition and processing system, enabling application in real-time machine-learning-based tokamak diagnostic and control as well as potential applications in other scientific domains.

Tangential extreme ultraviolet and soft x-ray diagnostic system for time-resolved temperature measurement on the High Beta Tokamak-Extended Pulse.

The High Beta Tokamak-Extended Pulse has recently incorporated a tangential multi-energy extreme ultraviolet and soft x-ray diagnostic system. This system enables measurements of the electron temperature and the examination of mode dynamics within the tokamak. While other systems have been built for poloidal views over similar temperature ranges, this is the first multi-energy tangential-view system designed to work in a temperature range below 200 eV in a tokamak. To facilitate these measurements, a filter wheel comprising five distinct groups of dual-filters has been developed and implemented. By employing a combination of 0.1 µm aluminum and 0.2 µm titanium filters, the system allows estimation of electron temperature profiles through reconstruction of the emission profile using the standard "double-foil" technique. The influence of impurities and filter oxide layers on measurement outcomes is examined. Results reveal that, while the absolute electron temperature values may exhibit some deviations, key characteristics like the electron temperature profile shape and inversion radius during sawtooth events remain consistent. This consistency confirms the system's suitability for core plasma studies. This system has proven effective in detecting and analyzing internal magnetohydrodynamic phenomena, such as sawteeth.

Mode rotation control in a tokamak with a feedback-driven biased electrode.

Rotation of the plasma and MHD modes in tokamaks has been shown to stabilize resistive wall and tearing modes as well as improve confinement through suppression of edge turbulence. In this work, we control mode rotation with a biased electrode inserted into the plasma of the High Beta Tokamak-Extended Pulse's facility in conjunction with its active GPU (Graphical Processing Unit) feedback system. We first characterize a negative linear relationship between the electrode voltage and mode rotation. Using this relationship, we design, simulate, and implement a proof-of-concept, GPU-based active-control system, which shows consistent success in controlling mode rotation in both feedforward and feedback operation. Controllability is limited by operating conditions, the electrode's voltage range, and by the electrode's proximity to the vessel's walls. The final control system has a 15 µs cycle time, but the addition of various signal filters results in a full cycle latency of 200 µs.

Assessment of FTA card employment for Pasteurella multocida DNA transport and detection of virulence-associated genes in strains isolated from fowl cholera in the United States / Avaliação do emprego de cartões FTA para o transporte do DNA de Pasteurella multocida e pesquisa de genes associados à virulência em cepas isoladas de cólera aviária nos Estados Unidos

Fowl Cholera (FC) is a disease caused by Pasteurella multocida. The severity of this disease is partly caused by virulence factors. Genes encoding fimbriae, capsule, sialidases and proteins for iron metabolism may be related to P. multocida's ability to infect the host. Besides to examining DNA for the presence of virulence genes, DNA is essential for the diagnostic and FTA cards are an alternative for genetic material transport. The study aims to evaluate the viability of P. multocida DNA transport using the cards and to detect 14 virulence genes in 27 strains isolated from FC cases in the United States by multiplex-PCR. No growth was observed in any of the FTA cards, which was essential to assess the security. Furthermore, DNA detection was possible in 100% of the samples, independent of the storage period (7 to 35 days) and temperature (4°C and 37°C). ptfA, exbd-tonB, hgbA, nanB, oma87, hyaD-hyaC, sodC, hgbB, sodA, nanH and pfhA genes were detected in more than 80% of the samples. FTA cards have proven to be a viable and safe tool for DNA transport of P. multocida. A majority of genes showed a high frequency, which was similar to strains isolated from FC cases.(AU)

Cólera aviária (CA) é uma doença causada pela bactéria Pasteurella multocida e a severidade dos casos é em parte justificada por fatores de virulência. Genes codificando fímbrias, cápsulas, sialidases, dismutases e proteínas do metabolismo férrico podem ser relacionados à capacidade do agente em infectar o hospedeiro. Além da obtenção do DNA para pesquisa de genes de virulência, o material genético é fundamental para o diagnóstico, e os cartões FTA seriam uma alternativa no transporte de microrganismos. Os objetivos da presente pesquisa foram avaliar a viabilidade do transporte de DNA de P. multocida através dos cartões e detectar 14 genes de virulência em 27 cepas isoladas de CA nos Estados Unidos, por meio de multiplex-PCR. Nenhuma das amostras para análise microbiológica da segurança dos cartões apresentou crescimento. Foi possível a detecção do DNA em 100% das amostras, independentemente do tempo de estocagem (sete a 35 dias) e das temperaturas (4°C e 37°C) avaliadas. Genes ptfA, exbd-tonB, hgbA, nanB, oma87, hyaD-hyaC, sodC, hgbB, sodA, nanH e pfhA foram detectados em mais de 80% das amostras. Os cartões FTA demonstraram ser uma ferramenta viável e segura para o transporte do DNA de P. multocida. A maioria dos genes apresentou uma alta frequência, compatível com isolados de CA.(AU)

Design and installation of a ferromagnetic wall in tokamak geometry.

Low-activation ferritic steels are leading material candidates for use in next-generation fusion development experiments such as a prospective component test facility and DEMO power reactor. Understanding the interaction of plasmas with a ferromagnetic wall will provide crucial physics for these facilities. In order to study ferromagnetic effects in toroidal geometry, a ferritic wall upgrade was designed and installed in the High Beta Tokamak-Extended Pulse (HBT-EP). Several material options were investigated based on conductivity, magnetic permeability, vacuum compatibility, and other criteria, and the material of choice (high-cobalt steel) is characterized. Installation was accomplished quickly, with minimal impact on existing diagnostics and overall machine performance, and initial results demonstrate the effects of the ferritic wall on plasma stability.

Imaging free-falling particles for multipoint measurement of plasma fluctuations.

The measurement of plasma fluctuations by insertable probes is sometimes limited by the perturbation of the probe on the plasma, and some non-invasive diagnostics such as photodiode arrays can only measure integrated values. In this paper, we introduce a new approach to plasma fluctuation measurement using small, free-falling particles imaged with a fast camera to provide simultaneous multipoint measurement of visible light emissions surrounding each particle. We find that the fluctuations measured in this manner are in agreement with existing diagnostics, and the particle signals are correlated to those measured on inserted floating potential probes. Signals from multiple particles demonstrate an application of multipoint measurement of the plasma spatial structure and coherence.

Fast, multi-channel real-time processing of signals with microsecond latency using graphics processing units.

Fast, digital signal processing (DSP) has many applications. Typical hardware options for performing DSP are field-programmable gate arrays (FPGAs), application-specific integrated DSP chips, or general purpose personal computer systems. This paper presents a novel DSP platform that has been developed for feedback control on the HBT-EP tokamak device. The system runs all signal processing exclusively on a Graphics Processing Unit (GPU) to achieve real-time performance with latencies below 8 µs. Signals are transferred into and out of the GPU using PCI Express peer-to-peer direct-memory-access transfers without involvement of the central processing unit or host memory. Tests were performed on the feedback control system of the HBT-EP tokamak using forty 16-bit floating point inputs and outputs each and a sampling rate of up to 250 kHz. Signals were digitized by a D-TACQ ACQ196 module, processing done on an NVIDIA GTX 580 GPU programmed in CUDA, and analog output was generated by D-TACQ AO32CPCI modules.

A 5-year retrospective report of Gallibacterium anatis and Pasteurella multocida isolates from chickens in Mississippi.

A 5-yr retrospective study (November 2006-December 2011) was conducted to determine the isolation frequency of Pasteurella multocida and Gallibacterium anatis and their antibiograms from chickens submitted to the Mississippi Poultry Research and Diagnostic Laboratory. The number of isolations of G. anatis increased over the last 5 yr in broiler and broiler breeder type chickens. For P. multocida, the number of isolations increased from 2006 to 2010, but decreased through 2011 with all isolations being from boiler breeder type chickens. Gallibacterium anatis demonstrated almost complete resistance to novobiocin, tylosin, lincosamide, and tetracycline antimicrobials with moderate to high sensitivity to sulfonamides, fluoroquinolones, and florfenicol. There was intermediate sensitivity for spectinomycin and erythromycin and variable resistance to ß-lactam and aminoglycoside antimicrobials. In sharp contrast, P. multocida showed moderate to high sensitivity to ß-lactam, novobiocin, and tetracycline antimicrobials, but had antibiograms similar to G. anatis for the other antimicrobials. Sensitivities were determined using minimum inhibitory concentration. This study examines the trends over a 5-yr period of the number of isolates of P. multocida and G. anatis and their sensitivities. These 2 pathogens produce very similar clinical signs and lesions (fowl cholera-like) in breeders despite having extremely antagonistic sensitivity patterns. This study shows the necessity for producers to attempt culture and sensitivity in suspect fowl cholera-like flocks before initiating antimicrobial treatment commonly used with P. multocida for fear that the culprit may actually be the more antimicrobial-resistant G. anatis.

In situ "artificial plasma" calibration of tokamak magnetic sensors.

A unique in situ calibration technique has been used to spatially calibrate and characterize the extensive new magnetic diagnostic set and close-fitting conducting wall of the High Beta Tokamak-Extended Pulse (HBT-EP) experiment. A new set of 216 Mirnov coils has recently been installed inside the vacuum chamber of the device for high-resolution measurements of magnetohydrodynamic phenomena including the effects of eddy currents in the nearby conducting wall. The spatial positions of these sensors are calibrated by energizing several large in situ calibration coils in turn, and using measurements of the magnetic fields produced by the various coils to solve for each sensor's position. Since the calibration coils are built near the nominal location of the plasma current centroid, the technique is referred to as an "artificial plasma" calibration. The fitting procedure for the sensor positions is described, and results of the spatial calibration are compared with those based on metrology. The time response of the sensors is compared with the evolution of the artificial plasma current to deduce the eddy current contribution to each signal. This is compared with simulations using the VALEN electromagnetic code, and the modeled copper thickness profiles of the HBT-EP conducting wall are adjusted to better match experimental measurements of the eddy current decay. Finally, the multiple coils of the artificial plasma system are also used to directly calibrate a non-uniformly wound Fourier Rogowski coil on HBT-EP.

A high-power spatial filter for Thomson scattering stray light reduction.

The Thomson scattering diagnostic on the High Beta Tokamak-Extended Pulse (HBT-EP) is routinely used to measure electron temperature and density during plasma discharges. Avalanche photodiodes in a five-channel interference filter polychromator measure scattered light from a 6 ns, 800 mJ, 1064 nm Nd:YAG laser pulse. A low cost, high-power spatial filter was designed, tested, and added to the laser beamline in order to reduce stray laser light to levels which are acceptable for accurate Rayleigh calibration. A detailed analysis of the spatial filter design and performance is given. The spatial filter can be easily implemented in an existing Thomson scattering system without the need to disturb the vacuum chamber or significantly change the beamline. Although apertures in the spatial filter suffer substantial damage from the focused beam, with proper design they can last long enough to permit absolute calibration.

Millimeter-wave radiometer diagnostics of harmonic electron cyclotron emission in the Levitated Dipole Experiment.

A 110/137 GHz radiometer pair with collimated antenna pattern is being used to diagnose optically thin harmonic electron cyclotron emission from hot electrons in LDX. Signal levels of 0.1-1 keV and 110/137 ratios of 2-4 stationary with ECRH power have been observed. The large plasma core magnetic field gradient causes all relevant harmonics to be simultaneously viewed over a angle(k,B) angular range of 0°-90° representing a unique geometry for interpretation of ECE in terms of hot electron temperature and density.

Transport induced by large scale convective structures in a dipole-confined plasma.

Convective structures characterized by E×B motion are observed in a dipole-confined plasma. Particle transport rates are calculated from density dynamics obtained from multipoint measurements and the reconstructed electrostatic potential. The calculated transport rates determined from the large-scale dynamics and local probe measurements agree in magnitude, show intermittency, and indicate that the particle transport is dominated by large-scale convective structures.

A digital control system for external magnetohydrodynamic modes in tokamak plasmas.

A feedback system for controlling external, long-wavelength magnetohydrodynamic activity is described. The system is comprised of a network of localized magnetic pickup and control coils driven by four independent, low-latency field-programable gate array controllers. The control algorithm incorporates digital spatial filtering to resolve low mode number activity, temporal filtering to correct for frequency-dependent amplitude and phase transfer effects in the control hardware, and a Kalman filter to distinguish the unstable plasma mode from noise.

A novel Henneguya species from channel catfish described by morphological, histological, and molecular characterization.

Channel catfish Ictalurus punctatus from a commercial farming operation in the Mississippi Delta were submitted for examination for the presence of infection by the trematode Bolbophorus damnificus. The fish were instead found to possess skin nodules suggestive of Henneguya pellis, a species previously described in the blue catfish I. furcatus. Despite the dermal location and distribution of lesions, morphological characteristics of the myxospores were inconsistent with H. pellis. Spores possessed a lanceolate spore body 15.4 +/- 1.5 microm (mean +/- SD; range = 12.2-19.3 microm) in length and 5.5 +/- 0.6 microm (range = 4.5-6.8 microm) in width in valvular view, and 4.7 +/- 0.2 microm (range = 4.2-5.0 microm) in width in sutural view. Polar capsules were pyriform and unequal in both length and width and contained polar filaments with six coils. Polar capsules measured 6.1 +/- 0.8 microm (range = 4.0-7.9 microm) long and 1.7 +/- 0.3 microm (range = 1.0-2.2 microm) wide. The caudal appendages were 50.5 +/- 8.3 microm (range = 34.8-71.4 micorm) long and the total length of the spore was 65.9 +/- 8.6 microm (range = 48.2-90.0 microm). The "blister like" plasmodia were round or ovoid, up to 2 mm in diameter, and randomly distributed throughout the epidermis of the fish. Histologically, plasmodia were confined to the dermis and elicited no inflammatory reaction from the fish. A blast search of the 18S small subunit rDNA sequence obtained by polymerase chain reaction amplification resulted in no identical sequence matches but indicated a close relationship to H. gurlei, H. ictaluri, and H. exilis. The unique host record, spore morphology, and novel genetic sequence derived from this isolate lead us to propose this isolate as a novel species, H. sutherlandi.

Genetic and virulence characterization of Flavobacterium columnare from channel catfish (Ictalurus punctatus).

AIM: To develop a method for conducting pulsed-field gel electrophoresis (PFGE) on Flavobacterium columnare, to use PFGE to characterize F. columnare channel catfish isolates, and to determine whether variation in pathogenic potential exists in F. columnare isolates from channel catfish. METHODS AND RESULTS: On the basis of PFGE-derived profiles, similarity dendrograms constructed for more than 30 F. columnare isolates showed two major genetic groups with more than 60% similarity. Channel catfish fingerlings challenged with PFGE group A isolates by bath immersion had significantly higher average mortalities (>60%) than fish challenged with PFGE group B isolates (<9%). However, abrasion and skin mucus removal made channel catfish fingerlings susceptible to disease caused by group B isolates following immersion exposure. CONCLUSION: Our results suggest that two genetic divisions of F. columnare channel catfish isolates exist, and that isolates in PFGE group A isolates tend to be more pathogenic to immunocompetent channel catfish fingerlings than PFGE group B isolates. SIGNIFICANCE AND IMPACT OF THE STUDY: PFGE is a potentially useful tool for determining whether F. columnare isolates are more likely to be primary or secondary pathogens. Pathogenesis research for columnaris disease in catfish should focus on pathogenic isolates from PFGE group A.

A piscirickettsiosis-like syndrome in cultured Nile tilapia in Latin America with Francisella spp. as the pathogenic agent.

In 2004, cultured Nile tilapia Oreochromis niloticus in several Latin America farms began to succumb to a disease similar to the piscirickettsiosis-like syndrome previously reported in tilapia in Taiwan and the United States. Mortality increased during 2005; reductions in tilapia biomass ranged from 5% to 80% in individual ponds and averaged 50% overall. All ages of fish have been involved. Clinical signs include lethargy, loss of appetite, petechia, exophthalmia, and abnormal swimming behavior. Gross lesions have included splenomegaly, renomegaly, and numerous white nodules observed in the spleen, kidney, testes, heart, ovaries, and occasionally the liver. A previously unreported black granulomatous lesion was reported in up to 30% of the fillets. Histologically, granulomatous infiltrates were observed in the kidney, spleen, liver, testes, ovary, and choroid gland, and rarely in the brain and heart. A small pleomorphic bacterium was observed in Giemsa-stained blood smears and spleen imprints. The bacterium did not grow on standard microbiological media and has not been isolated in cell culture. We obtained a near-complete 16S ribosomal DNA sequence with high similarity to Francisella spp. sequences previously identified in tilapias Oreochromis spp. (Taiwan), Atlantic cod Gadus morhua (Norway), and three-line grunts Parapristipoma trilineatum (Japan).

Observation of centrifugally driven interchange instabilities in a plasma confined by a magnetic dipole.

Centrifugally driven interchange instabilities are observed in a laboratory plasma confined by a dipole magnetic field. The instabilities appear when an equatorial mesh is biased to drive a radial current that causes rapid axisymmetric plasma rotation. The observed instabilities are quasicoherent in the laboratory frame of reference; they have global radial mode structures and low azimuthal mode numbers, and they are modified by the presence of energetic, magnetically confined electrons. Results from a self-consistent nonlinear simulation reproduce the measured mode structures.

Observation of nonlinear frequency-sweeping suppression with rf diffusion.

Nonlinear frequency sweeping of unstable waves in a laboratory plasma is suppressed upon application of rf fields. Frequency sweeping is driven by a population of energetic electrons trapped in a magnetic dipole field that excite drift-resonant potential fluctuations and create coherent structures in phase space. Self-consistent numerical simulation reproduces the suppression and suggests an explanation due to rf scattering of energetic electrons that destroys the phase-space structures.

Endometritis in postparturient cattle associated with bovine herpesvirus-4 infection: 15 cases.

Suppurative, ulcerative endometritis associated with bovine herpesvirus-4 (BHV-4) infection was identified in 15 postparturient dairy cows from 5 separate dairies. Characteristic eosinophilic to amphophilic intranuclear viral inclusion bodies were identified within degenerate endometrial lining epithelium and endothelial cells. Bovine herpesvirus-4 was confirmed as the etiology by a combination of fluorescent antibody assays, viral isolation, heminested PCR, ultrastructural examination of the uterus and inoculated tissue culture cells, and negative-stain electron microscopy of tissue culture supernatant. Viral particles measuring 70-95 nm were demonstrated in uterine epithelial and endothelial cells by electron microscopy. Bacteria including Arcanobacterium pyogenes, Escherichia coli, and an alpha-Streptococcus isolate were isolated from all uteri. Bovine herpesvirus-4-associated endometritis has been previously reported in sporadic cases in Europe but has not been previously reported in the United States. Endometritis associated with BHV-4 appears to be an emerging syndrome in Georgia dairy herds.

A functional cra gene is required for Salmonella enterica serovar typhimurium virulence in BALB/c mice.

A minitransposon mutant of Salmonella enterica serovar Typhimurium SR-11, SR-11 Fad(-), is unable to utilize gluconeogenic substrates as carbon sources and is avirulent and immunogenic when administered perorally to BALB/c mice (M. J. Utley et al., FEMS Microbiol. Lett., 163:129-134, 1998). Here, evidence is presented that the mutation in SR-11 Fad(-) that renders the strain avirulent is in the cra gene, which encodes the Cra protein, a regulator of central carbon metabolism.