Studying fast-ion populations using oscillations in solid-state neutral-particle analyzer signal and neutral-beam injection power.

A method for determining the fast-ion population density in magnetically confined plasmas as a function of pitch-radius, (λ, R), using a solid-state neutral-particle analyzer (ssNPA) signal and neutral-beam injection (NBI) power-output data has been developed. Oscillations in the NBI power output are replicated only in the active part of the ssNPA signal, allowing this to be separated from the passive and background signals, which usually complicate data from this diagnostic. Results obtained using this method are compared with those from standard techniques using data from the Mega-Amp Spherical Tokamak Upgrade spherical tokamak.

3D surface reconstruction of cellular cryo-soft X-ray microscopy tomograms using semisupervised deep learning.

Cryo-soft X-ray tomography (cryo-SXT) is a powerful method to investigate the ultrastructure of cells, offering resolution in the tens of nanometer range and strong contrast for membranous structures without requiring labeling or chemical fixation. The short acquisition time and the relatively large field of view leads to fast acquisition of large amounts of tomographic image data. Segmentation of these data into accessible features is a necessary step in gaining biologically relevant information from cryo-soft X-ray tomograms. However, manual image segmentation still requires several orders of magnitude more time than data acquisition. To address this challenge, we have here developed an end-to-end automated 3D segmentation pipeline based on semisupervised deep learning. Our approach is suitable for high-throughput analysis of large amounts of tomographic data, while being robust when faced with limited manual annotations and variations in the tomographic conditions. We validate our approach by extracting three-dimensional information on cellular ultrastructure and by quantifying nanoscopic morphological parameters of filopodia in mammalian cells.

Design elements and first data from a new Doppler backscattering system on the MAST-U spherical tokamak.

A new Doppler backscattering (DBS) system has been installed and tested on the MAST-U spherical tokamak. It utilizes eight simultaneous fixed frequency probe beams (32.5, 35, 37.5, 40, 42.5, 45, 47.5, and 50 GHz). These frequencies provide a range of radial positions from the edge plasma to the core depending on plasma conditions. The system utilizes a combination of novel features to provide remote control of the probed density wavenumber, the launched polarization (X vs O-mode), and the angle of the launched DBS to match the magnetic field pitch angle. The range of accessible density turbulence wavenumbers (kθ) is reasonably large with normalized wavenumbers kθρs ranging from ≤0.5 to 9 (ion sound gyroradius ρs = 1 cm). This wavenumber range is relevant to a variety of instabilities believed to be important in establishing plasma transport (e.g., ion temperature gradient, trapped electron, electron temperature gradient, micro-tearing, kinetic ballooning modes). The system is specifically designed to address the requirement of density fluctuation wavevector alignment which can significantly reduce the SNR if not accounted for.

Validating and optimizing mismatch tolerance of Doppler backscattering measurements with the beam model (invited).

We use the beam model of Doppler backscattering (DBS), which was previously derived from beam tracing and the reciprocity theorem, to shed light on mismatch attenuation. This attenuation of the backscattered signal occurs when the wavevector of the probe beam's electric field is not in the plane perpendicular to the magnetic field. Correcting for this effect is important for determining the amplitude of the actual density fluctuations. Previous preliminary comparisons between the model and Mega-Ampere Spherical Tokamak (MAST) plasmas were promising. In this work, we quantitatively account for this effect on DIII-D, a conventional tokamak. We compare the predicted and measured mismatch attenuation in various DIII-D, MAST, and MAST-U plasmas, showing that the beam model is applicable in a wide variety of situations. Finally, we performed a preliminary parameter sweep and found that the mismatch tolerance can be improved by optimizing the probe beam's width and curvature at launch. This is potentially a design consideration for new DBS systems.

Spatially clustered count data provide more efficient search strategies in invasion biology and disease control.

Geographic profiling, a mathematical model originally developed in criminology, is increasingly being used in ecology and epidemiology. Geographic profiling boasts a wide range of applications, such as finding source populations of invasive species or breeding sites of vectors of infectious disease. The model provides a cost-effective approach for prioritizing search strategies for source locations and does so via simple data in the form of the positions of each observation, such as individual sightings of invasive species or cases of a disease. In doing so, however, classic geographic profiling approaches fail to make the distinction between those areas containing observed absences and those areas where no data were recorded. Absence data are generated via spatial sampling protocols but are often discarded during the inference process. Here we construct a geographic profiling model that resolves these issues by making inferences via count data, analyzing a set of discrete sentinel locations at which the number of encounters has been recorded. Crucially, in our model this number can be zero. We verify the ability of this new model to estimate source locations and other parameters of practical interest via a Bayesian power analysis. We also measure model performance via real-world data in which the model infers breeding locations of mosquitoes in bromeliads in Miami-Dade County, Florida, USA. In both cases, our novel model produces more efficient search strategies by shifting focus from those areas containing observed absences to those with no data, an improvement over existing models that treat these areas equally. Our model makes important improvements upon classic geographic profiling methods, which will significantly enhance real-world efforts to develop conservation management plans and targeted interventions.

Descriptive epidemiology of coronavirus disease 2019 in Nigeria, 27 February-6 June 2020.

The objective of this study was to describe the epidemiology of COVID-19 in Nigeria with a view of generating evidence to enhance planning and response strategies. A national surveillance dataset between 27 February and 6 June 2020 was retrospectively analysed, with confirmatory testing for COVID-19 done by real-time polymerase chain reaction (RT-PCR). The primary outcomes were cumulative incidence (CI) and case fatality (CF). A total of 40 926 persons (67% of total 60 839) had complete records of RT-PCR test across 35 states and the Federal Capital Territory, 12 289 (30.0%) of whom were confirmed COVID-19 cases. Of those confirmed cases, 3467 (28.2%) had complete records of clinical outcome (alive or dead), 342 (9.9%) of which died. The overall CI and CF were 5.6 per 100 000 population and 2.8%, respectively. The highest proportion of COVID-19 cases and deaths were recorded in persons aged 31-40 years (25.5%) and 61-70 years (26.6%), respectively; and males accounted for a higher proportion of confirmed cases (65.8%) and deaths (79.0%). Sixty-six per cent of confirmed COVID-19 cases were asymptomatic at diagnosis. In conclusion, this paper has provided an insight into the early epidemiology of COVID-19 in Nigeria, which could be useful for contextualising public health planning.

Novel analysis technique for measuring edge density fluctuation profiles with reflectometry in the Large Helical Device.

A new method for measuring density fluctuation profiles near the edge of plasmas in the Large Helical Device (LHD) has been developed utilizing reflectometry combined with pellet-induced fast density scans. Reflectometer cutoff location was calculated by proportionally scaling the cutoff location calculated with fast far infrared laser interferometer (FIR) density profiles to match the slower time resolution results of the ray-tracing code LHD-GAUSS. Plasma velocity profile peaks generated with this reflectometer mapping were checked against velocity measurements made with charge exchange spectroscopy (CXS) and were found to agree within experimental uncertainty once diagnostic differences were accounted for. Measured density fluctuation profiles were found to peak strongly near the edge of the plasma, as is the case in most tokamaks. These measurements can be used in the future to inform inversion methods of phase contrast imaging (PCI) measurements. This result was confirmed with both a fixed frequency reflectometer and calibrated data from a multi-frequency comb reflectometer, and this method was applied successfully to a series of discharges. The full width at half maximum of the turbulence layer near the edge of the plasma was found to be only 1.5-3 cm on a series of LHD discharges, less than 5% of the normalized minor radius.

Two-dimensional wave-number spectral analysis techniques for phase contrast imaging turbulence imaging data on large helical device.

An analysis method for unfolding the spatially resolved wave-number spectrum and phase velocity from the 2D CO2 laser phase contrast imaging system on the large helical device is described. This is based on the magnetic shear technique which identifies propagation direction from 2D spatial Fourier analysis of images detected by a 6 × 8 detector array. Because the strongest modes have wave-number at the lower end of the instrumental k range, high resolution spectral techniques are necessary to clearly resolve the propagation direction and hence the spatial distribution of fluctuations along the probing laser beam. Multiple-spatial point cross-correlation averaging is applied before calculating the spatial power spectrum. Different methods are compared, and it is found that the maximum entropy method (MEM) gives best results. The possible generation of artifacts from the over-narrowing of spectra are investigated and found not to be a significant problem. The spatial resolution Δρ (normalized radius) around the peak wave-number, for conventional Fourier analysis, is ∼0.5, making physical interpretation difficult, while for MEM, Δρ ∼ 0.1.

Investigating fusion plasma instabilities in the Mega Amp Spherical Tokamak using mega electron volt proton emissions (invited).

The proton detector (PD) measures 3 MeV proton yield distributions from deuterium-deuterium fusion reactions within the Mega Amp Spherical Tokamak (MAST). The PD's compact four-channel system of collimated and individually oriented silicon detectors probes different regions of the plasma, detecting protons (with gyro radii large enough to be unconfined) leaving the plasma on curved trajectories during neutral beam injection. From first PD data obtained during plasma operation in 2013, proton production rates (up to several hundred kHz and 1 ms time resolution) during sawtooth events were compared to the corresponding MAST neutron camera data. Fitted proton emission profiles in the poloidal plane demonstrate the capabilities of this new system.

Coherence imaging of scrape-off-layer and divertor impurity flows in the Mega Amp Spherical Tokamak (invited).

A new coherence imaging Doppler spectroscopy diagnostic has been deployed on the UK's Mega Amp Spherical Tokamak for scrape-off-layer and divertor impurity flow measurements. The system has successfully obtained 2D images of C III, C II, and He II line-of-sight flows, in both the lower divertor and main scrape-off-layer. Flow imaging has been obtained at frame rates up to 1 kHz, with flow resolution of around 1 km/s and spatial resolution better than 1 cm, over a 40° field of view. C III data have been tomographically inverted to obtain poloidal profiles of the parallel impurity flow in the divertor under various conditions. In this paper we present the details of the instrument design, operation, calibration, and data analysis as well as a selection of flow imaging results which demonstrate the diagnostic's capabilities.

The MAST motional Stark effect diagnostic.

A motional Stark effect (MSE) diagnostic is now installed and operating routinely on the MAST spherical tokamak, with 35 radial channels, spatial resolution of ∼2.5 cm, and time resolution of ∼1 ms at angular noise levels of ∼0.5°. Conventional (albeit very narrow) interference filters isolate π or σ polarized emission. Avalanche photodiode detectors with digital phase-sensitive detection measure the harmonics of a pair of photoelastic modulators operating at 20 and 23 kHz, and thus the polarization state. The π component is observed to be significantly stronger than σ, in reasonably good agreement with atomic physics calculations, and as a result, almost all channels are now operated on π. Trials with a wide filter that admits the entire Stark pattern (relying on the net polarization of the emission) have demonstrated performance almost as good as the conventional channels. MSE-constrained equilibrium reconstructions can readily be produced between pulses.

Two-dimensional phase contrast imaging for local turbulence measurements in large helical device (invited).

Two-dimensional phase contrast imaging (2D) installed on the large helical device (LHD) is a unique diagnostic for local turbulence measurements. A 10.6 microm infrared CO(2) laser and 6x8 channel HgCdTe 2D detector are used. The length of the scattering volume is larger than plasma size. However, the asymmetry of turbulence structure with respect to the magnetic field and magnetic shear make local turbulence measurements possible. From a 2D image of the integrated fluctuations, the spatial cross-correlation function was estimated using time domain correlation analysis, then, the integrated 2D k-spectrum is obtained using maximum entropy method. The 2D k-spectrum is converted from Cartesian coordinates to cylindrical coordinates. Finally, the angle in cylindrical coordinate is converted to flux surface labels. The fluctuation profile over almost the entire plasma diameter can be obtained at a single moment. The measurable k-region can be varied by adjusting the detection optics. Presently, k=0.1-1.0 mm(-1) can be measured which is expected region of ion temperature gradient modes and trapped electron mode in LHD. The spatial resolution is 10%-50% of the minor radius.

Detection of high k turbulence using two dimensional phase contrast imaging on LHD.

High k turbulence, up to 30 cm(-1), can be measured using the two dimensional CO2 laser phase contrast imaging system on LHD. Recent hardware improvements and experimental results are presented. Precise control over the lens positions in the detection system is necessary because of the short depth of focus for high k modes. Remote controllable motors to move optical elements were installed, which, combined with measurements of the response to ultrasound injection, allowed experimental verification and shot-to-shot adjustment of the object plane. Strong high k signals are observed within the first 100-200 ms after the initial electron cyclotron heating (ECH) breakdown, in agreement with gyrotron scattering. During later times in the discharge, the entire k spectrum shifts to lower values (although the total amplitude does not change significantly), and the weaker high k signals are obscured by leakage of low k components at low frequency, and detector noise, at high frequency.

Use of chromosomal integron arrays as a phylogenetic typing system for Vibrio cholerae pandemic strains.

Approximately 200 serogroups of Vibrio cholerae exist, with only two, O1 and O139, responsible for epidemic and pandemic cholera. Strains from these serogroups have evolved from a common progenitor, with lateral gene transfer largely driving their emergence. These strains are so closely related that separation using single- or multi-locus phylogeny has proven difficult. V. cholerae strains contain a genetic system called the integron that is located in the chromosome and that can integrate and excise DNA elements called mobile gene cassettes (MGCs) by site-specific recombination. Large arrays of MGCs are found in V. cholerae strains. For instance, the O1 El Tor strain N16961 contains 179 MGCs. Since integron arrays are dynamic through recombination and excision of MGCs, it was hypothesized that the MGC composition in a given V. cholerae pandemic strain would be useful as a phylogenetic typing system. To address this, a PCR-based method was used to rapidly characterize the MGC composition of V. cholerae arrays. The results showed that the MGC composition of pandemic V. cholerae cassette arrays is relatively conserved, providing further evidence that these strains have evolved from a common progenitor. Comparison of MGC composition between the V. cholerae pandemic strains was also able to resolve the evolution of O139 from a subgroup of O1 El Tor. This level of differentiation of closely related V. cholerae isolates was more sensitive than conventional single-gene phylogeny or multi-locus sequence analysis. Using this method, novel MGCs from an O1 classical strain and an Argentinian O139 isolate were also identified, and a major deletion in the MGC array in all pandemic O139 strains and a subset of O1 El Tor strains was identified. Analysis of sequenced V. cholerae integron arrays showed that their evolution can proceed by rearrangements and deletions/insertions of large portions of MGCs in addition to the insertion or excision of single MGCs.

Association between the endothelin-1 gene Lys198Asn polymorphism blood pressure and plasma endothelin-1 levels in normal and pre-eclamptic pregnancy.

OBJECTIVE: This study examined the frequency of the Lys198Asn polymorphism in the endothelin-1 (ET-1) gene in women with pre-eclampsia and normal pregnancy; and its contribution to levels of plasma ET-1 and blood pressure. DESIGN AND METHODS: This was a retrospective study examining the frequency of the ET-1 Lys198Asn polymorphism in 72 proteinuric pre-eclamptics and 81 normal pregnant women. Height, weight, blood pressure and plasma ET-1 were measured antenatally and at 6 weeks post-partum. Using specific mutagenic primers, the frequency of the G/G (normal), G/T heterozygote and T/T (mutant) genotypes of the Lys198Asn polymorphism were examined. RESULTS: The polymorphism was not associated with pre-eclampsia. However, in the combined pregnant groups after correction for BMI and group, a significant effect of the T-allele (T/T,G/T) on systolic blood pressure was found (121 +/- 1.5 mmHg compared with 116 +/- 1.3 mmHg in the G/G homozygotes). A significant interaction was found between the T-allele and pregnancy in determining systolic blood pressure, so that the effect was no longer seen post-partum. Pregnant women with the T/T genotype had significantly elevated plasma ET-1 levels 5.8 pg/ml [confidence interval (CI) 3.7-9.1] compared with 3.1 pg/ml (CI 2.6-3.8) in the G/T heterozygotes and 3.6 pg/ml (CI 3.0-4.1) in the normal G/G homozygotes. CONCLUSION: The Lys198Asn polymorphism does not directly contribute to the incidence of pre-eclampsia. However, the association of the T-allele with raised blood pressure and the T/T genotype with increased plasma ET-1 levels suggest that this polymorphism may interact with other genes or environmental factors to sensitize pregnant women to develop pre-eclampsia.

Effects of lipoproteins from pre-eclamptic women on umbilical endothelial cell 6-oxo-prostaglandin f1alpha and endothelin 1 synthesis, and nitric oxide synthase 3 mRNA expression.

In order to evaluate whether lipid abnormalities may contribute to endothelial dysfunction in pre-eclampsia, the present study examined the in vitro effects of very-low-density lipoprotein (VLDL), low-density lipoprotein (LDL) and high-density lipoprotein (HDL), isolated from women with pre-eclampsia and matched controls, on the endothelial synthesis of 6-oxo-prostaglandin F(1alpha) (6-oxo-PGF(1alpha); a metabolite of prostacyclin) and endothelin 1, and on the expression of nitric oxide synthase 3 (NOS3) mRNA. VLDL, LDL and HDL cholesterol were isolated from 20 pre-eclamptic and 20 age- and gestation-matched normal pregnant women. The lipoproteins (50 microgram/ml) and lipoprotein-free control plasma were incubated for 1, 3 and 6 h at 37 degrees C with a human umbilical endothelial cell line. The synthesis of 6-oxo-PGF(1alpha) and endothelin 1, and NOS3 mRNA expression, were measured at each time point. VLDL from pre-eclamptic women stimulated endothelial cell 6-oxo-PGF(1alpha) synthesis to a lesser extent than that from normal pregnant women (P<0.05). LDL from women with pre-eclampsia also stimulated 6-oxo-PGF(1alpha) synthesis to a lesser extent than LDL from normal pregnant women, but the effect was less sustained. The effect of HDL from women with pre-eclampsia on 6-oxo-PGF(1alpha) synthesis was similar to that of HDL from normal pregnant women. The pre-incubation levels of lipid peroxides in VLDL and LDL were not different between the normal pregnant and pre-eclamptic women, and cannot account for the decrease in 6-oxo-PGF(1alpha) synthesis. VLDL, LDL and HDL from women with pre-eclampsia did not affect endothelial cell synthesis of endothelin 1 or expression of NOS3 mRNA differently from lipoproteins from normal pregnant women. This study suggests that VLDL, and to a lesser extent LDL, from women with pre-eclampsia could potentially contribute to the reduced systemic 6-oxo-PGF(1alpha) synthesis observed in the pre-eclamptic syndrome.

Is proteinuric pre-eclampsia a different disease in primigravida and multigravida?

This study aimed to identify if the clinical features of proteinuric pre-eclampsia or the biochemical markers of endothelial dysfunction associated with this syndrome are altered according to parity in a direction that would suggest a different pathophysiology. Groups of 27 primigravid and 35 multigravid women with pre-eclampsia (defined as blood pressure >140/90 mmHg and 2+ proteinuria) were studied ante-partum, and at 6 weeks and 6 months post-partum. Clinical markers of severity of pre-eclampsia, including blood pressure, markers of renal, hepatic and coagulatory function, and biochemical markers of endothelial dysfunction were measured. Fetal outcome was assessed by birthweight and birthweight percentile. Ante-partum systolic blood pressure was 10 mmHg higher in the primigravida, and this difference was independent of age and anti-hypertensive medication. Analysis of systolic blood pressure before and after delivery showed the primigravid women to have elevated systolic blood pressure over the whole time period (P<0.01). The primigravid women had more severe hepatic dysfunction, with elevated aspartate aminotransferase levels, but plasma creatinine, proteinuria, platelet counts and haematocrit were similar, indicating that renal and coagulatory function and plasma volume were affected to the same extent in the two groups and were independent of parity. Birthweight was similar in the two groups, and the percentage of infants weighing less than the 10th centile for gestation was also similar. Biochemical markers of endothelial dysfunction, assessed by measuring the urinary prostacyclin metabolite 2, 3-dinor-6-oxo-prostaglandin F(1alpha) and plasma endothelin 1, did not differ according to parity. There were no differences in a number of other biochemical markers of pre-eclampsia, including plasma albumin, uric acid, triacylglycerol, and total, low-density lipoprotein and high-density lipoprotein cholesterol. Basophil, monocyte and lymphocyte counts were elevated before delivery in primigravid women with pre-eclampsia. The differences in lymphocyte counts persisted post-partum. Further studies are required to clarify the role, if any, of monocytes, basophils and lymphocytes in the pathophysiology of pre-eclampsia. In conclusion, the elevated systolic blood pressure and raised aspartate aminotransferase levels observed in primigravida suggest a more severe form of pre-eclampsia. The lack of differences in birthweight and other biochemical and endothelial markers of severity of pre-eclampsia do not suggest a different pathophysiology; however, the persistently higher white cell counts in the primigravid pre-eclamptics are of interest, and might reflect differences in immune responses in the two groups. We suggest that studies of the pathophysiology of pre-eclampsia should include multigravida, as long as there is adequate post-partum follow-up to exclude underlying disease.

Neutrophil CD11B expression and neutrophil activation in pre-eclampsia.

1. Neutrophil activation was examined in 22 women with pre-eclampsia and 22 age- and gestation-matched control subjects using whole-blood flow cytometry to assess basal and platelet-activating factor stimulated CD11b and CD18. 2. Basal neutrophil CD11b expression was significantly increased in women with pre-eclampsia compared with normal pregnancy before delivery. A similar non-significant trend for CD18 was also observed. 3. Before delivery, neutrophil CD11b expression increased in a dose-dependent fashion after platelet-activating factor stimulation, with the differences between the groups maintained. A similar dose-dependent increase in CD18 expression was observed after platelet-activating factor. 4. There were no between-group differences in expression of either CD11b or CD18 at either 6 weeks or 6 months post partum, either before or after platelet-activating factor stimulation. 5. Neutrophil CD11b was positively correlated with plasma uric acid (r = 0.44, P = 0.04) in women with pre-eclampsia, suggesting that the extent of neutrophil activation correlates with disease severity. 6. An increase in basal neutrophil CD11b expression in women with pre-eclampsia is likely to be an index of neutrophil activation in vivo. Neutrophil release of free radicals and proteases may then help perpetuate a vicious cycle of endothelial and vascular dysfunction in the placental and systemic circulations. The cause of this activation is not known but could involve platelet activation, increased production of endothelin-1 or release of cytokines. Further studies will be required to elucidate the consequences of neutrophil activation in pre-eclampsia.

Plasma and urinary 8-iso-prostane as an indicator of lipid peroxidation in pre-eclampsia and normal pregnancy.

1. This study was designed to seek evidence for excessive lipid peroxidation in pre-eclamptic women using 8-iso-prostane as a novel bioactive marker of lipid peroxidation in vivo. Plasma free, total and urinary 8-iso-prostane were measured in 20 women with proteinuric pre-eclampsia, and compared with 18 age- and gestation-matched pregnant control subjects, before delivery and at 6 weeks post-partum. 2. Plasma free 8-iso-prostane was significantly elevated in the pre-eclamptic women compared with control subjects before delivery, and fell to control levels post-partum. Conversely, levels in women with normal pregnancy rose post-partum. 3. Total plasma 8-iso-prostane levels were not significantly elevated in pre-eclamptic women compared with control subjects during pregnancy, but fell significantly in the pre-eclamptic women post-partum, suggesting that they had relatively higher levels compared with their non-pregnant state. 4. Urinary 8-iso-prostane excretion was significantly lower in the pre-eclamptic women compared with control subjects during pregnancy, suggesting that renal clearance of 8-iso-prostane is impaired in pre-eclampsia. 5. Increased levels of plasma free 8-iso-prostane in pre-eclampsia could be due to an increase in lipid peroxidation, an increase in phospholipase A2 activity or a reduction in renal clearance of 8-iso-prostane, or a combination of all three. The potent direct and indirect vasoconstrictor actions of 8-iso-prostane may contribute to the pathogenesis of pre-eclampsia.