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.

Turbulence Transition in Magnetically Confined Hydrogen and Deuterium Plasmas.

In this study, we discovered a turbulence transition in a large helical device. The turbulence level and turbulence-driven energy transport decrease to a specific transition density and increase above it. The ruling turbulences below and above the transition density were ion-temperature gradient (ITG) and resistive-interchange (RI) turbulences, consistent with the predictions of gyrokinetic theory and two-fluid MHD model, respectively. Isotope experiments on hydrogen (H) and deuterium (D) clarified the role of transitions. In the ITG regime, turbulence levels and energy transport were comparable in the H and D plasmas. In contrast, in the RI regime, they were clearly suppressed in the D plasma. The results provide crucial knowledge for understanding isotope effects and future optimization of stellarator and heliotron devices.

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.

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.

New millimeter-wave diagnostics to locally probe internal density and magnetic field fluctuations in National Spherical Torus Experiment-Upgrade (invited).

A set of new millimeter-wave diagnostics will deliver unique measurement capabilities for National Spherical Torus Experiment-Upgrade to address a variety of plasma instabilities believed to be important in determining thermal and particle transport, such as micro-tearing, global Alfvén eigenmodes, kinetic ballooning, trapped electron, and electron temperature gradient modes. These diagnostics include a new integrated intermediate-k Doppler backscattering (DBS) and cross-polarization scattering (CPS) system (four channels, 82.5-87 GHz) to measure density and magnetic fluctuations, respectively. The system can access reasonably large normalized wavenumbers kθρs ranging from ≤0.5 to 15 (where ion sound gyroradius ρs = 1 cm and kθ is the binormal density turbulence wavenumber). The system addresses the challenges for making useful DBS/CPS measurements with a remote control of launch polarization (X- or O-mode), probed wavenumber, polarization match of the launch beam with the edge magnetic field pitch angle, and beam steering of the launched beam for wave-vector alignment. In addition, a low-k DBS system consisting of eight fixed frequencies (34-52 GHz) and four tunable frequencies (55-75 GHz) for low-k density turbulence and fast ion physics will be located at a nearby port location. The combined systems cover the near LCFS and pedestal regions (34-52 GHz), the pedestal or mid-radius (50-75 GHz), and core plasmas (82.5-87 GHz).

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.

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.

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.

Metabolism of androstenedione by placental microsomes in pregnancy hypertension.

The metabolism of [19-3H3]androstenedione by human placental microsomes was studied in vitro by radiometric analysis which distinguishes between 19-hydroxylation and elimination of the C-19 carbon. The ratio of the metabolic products tritiated water/tritiated formic acid is significantly greater for microsomes from patients with pregnancy hypertension when compared with normotensive pregnant women. This indicates that aromatization (2-hydroxylation) is deficient in pregnancy hypertension.

Subspecialisation in obstetrics and gynaecology--whither (or wither) the generalist.

In 1987, Council of the Royal Australian College of Obstetricians and Gynaecologists (RACOG) established its subspecialisation committee who identified subspecialty groups. It was the belief of the subspecialty committee that specialty training was necessary if haphazard evolution of the subspecialties and fragmentation within the discipline of obstetrics and gynaecology was to be avoided. The major issues of such training are manpower considerations and the time committed to the subspecialty, its effect on research and whether the generalist obstetrician and gynaecologist has been disadvantaged by such an initiative. Research initiatives must not suffer and the subspecialist should be prominent in the respective fields informing colleagues of important clinical and research advances. Undoubtedly the workload of the generalist will be eroded but their importance in the practice of obstetrics and gynaecology must be strengthened. The generalist should be encouraged to assist in the management of the patient in association with the subspecialist and referral should be on a tertiary basis. The limits of subspecialisation must be clearly defined and the availability and distribution of subspecialists determined. The numbers should be carefully monitored and training and accreditation and certification of subspecialists should remain within a central body such as the RACOG.

The treatment of hypertension in pregnancy.

Hypertensive disease in pregnancy remains a major cause of maternal and perinatal morbidity and mortality. Control of maternal hypertension with antihypertensive therapy improves maternal and foetal outcome. If the blood pressure is elevated in early pregnancy, complications are more likely to occur to both mother and foetus, and the outcome may not be favourable. In labour the threat of severe pre-eclampsia or eclampsia is a constant hazard.

Prolonged labour.

Although prolonged labour may be a decreasing obstetrical problem, the importance of its implications should not be overlooked. This article discusses the causes of arrested labour, its complications and their management.

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.

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.

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.