Application of an Improved Micro-amount of Virion Enrichment Technique (MiVET) for the Detection of Avian Influenza A Virus in Spiked Chicken Meat Samples

Highly sensitive detection of pathogens is effective for screening meat during quarantine inspection and export. The “micro-amount of virion enrichment technique” (MiVET) was recently developed, which is a new method combining virus concentration with immunomagnetic beads and simple RNA extraction with sodium dodecyl benzenesulfonate (SDBS) for the specific and sensitive detection of avian influenza viruses (AIVs). AIV subtypes H3N2 and H4N2 were used to spike the surface of chicken breast meat samples. The modified MiVET protocol was tested by comparing it against three different homogenate preparation conditions, as well as in samples with added α-amylase and collagenase to digest inhibitors. The performance of the modified MiVET was evaluated by real-time RT-PCR assay targeting the matrix gene. Compared with conventional RNA extraction, the modified MiVET reproducibly concentrated AIVs in chicken meat samples with 100–1000-fold improvement by 60 s-hand homogenization. The 30 s- and 60 s-stomacher homogenizations resulted 100-fold and 10–100-fold improvement, respectively. The modified MiVET required < 60 min from homogenate preparation to final RNA elution. Further, use of the modified MiVET also decreased the rate of false-negative results. The modified MiVET is effective for the rapid and highly sensitive detection of AIVs in chicken meat samples, and can be applied to quarantine and export inspection at airports and seaports

ECCD Experiment Using an Upgraded ECH System on LHD

Electron cyclotron current drive (ECCD) is an attractive tool for controlling plasmas. In the large helical device (LHD), ECCD experiments have been performed by using an EC-wave power source, gyrotron, with a frequency of 84 GHz. The maximum driven current was ?9 kA with 100 kW injection power to plasma and 8 s duration of EC-wave pulse. These years, high-power and long-pulse 77 GHz gyrotrons were newly installed. An ECCD experiment with 775 kW injection power was performed. The 77 GHz waves of 8 s pulse duration sustained the plasmas. The EC-wave beam direction was scanned toroidally, keeping the beam direction aiming at the magnetic axis in X-mode polarization. In spite of the change in the EC-wave beam direction, plasma parameters such as the line-average electron density, the central electron temperature and the plasma stored energy were kept nearly the same values for the discharges, ?0.3 × 1019 m?3, ?3 keV and ?30 kJ, except for the plasma current. The plasma current showed a systematic change with the change in the beam direction for ECCD, and at an optimum direction with N// ? ?0.3, the plasma current reached its maximum, ?40 kA. Also, current drive efficiency normalized with density and power was improved by 50% compared with that at the former 84 GHz ECCD experiment

High Harmonic ECH Experiment for Extension of Heating Parameter Regime in LHD

High harmonic electron cyclotron resonance heating (ECH) can extend the plasma heating region to higher density and higher β compared to the normal heating scenario. In this study, the heating characteristics of the second-harmonic ordinary (O2) and third-harmonic extraordinary (X3) modes and the possible extension of heating regime are experimentally confirmed. At the same time, a comparative study using ray-tracing calculation was performed in the realistic three-dimensional configuration of the Large Helical Device. The O2 mode heating showed a 40% absorption rate even above the X2 mode cut-off density. The X3 mode heating using powerful 77 GHz gyrotrons demonstrated an increase of about 40% in the central electron temperature in the plasmas at β-value of about 1%. These results were quantitatively explained to some extent by ray-tracing calculations

Experimental Results for Electron Bernstein Wave Heating in the Large Helical Device

Electron cyclotron heating (ECH) using electron Bernstein waves (EBWs) was studied in the large helical device (LHD). Oblique launching of the slow extraordinary (SX-) mode from the high field side and oblique launching of the ordinary (O-) mode from the low field side were adopted to excite EBWs in the LHD by using electron cyclotron (EC) wave antennas installed apart from the plasma surface. Increases in the stored energy and electron temperature were observed for both cases of launching. These launching methods for ECH using EBWs (EBWH) is promising for high-density operation in future helical fusion devices instead of conventional ECH by normal electromagnetic modes

増強されたECHアンテナシステムを用いたLHDにおけるECCD適用性の向上

The power injection system for electron cyclotron heating (ECH) and electron cyclotron current drive (ECCD) was modified and upgraded. An outside horizontal port 2-O on the Large Helical Device (LHD) was furnished with two antenna systems for the EC-waves of the frequencies of 77 and 154 GHz, respectively. In addition to them, two new antenna systems for 77 and 154 GHz waves were installed in the 2-O port. Each antenna in the 2-O port has wide range of EC-wave beam direction control so that these are suitable for ECCD which requires toroidally oblique EC-wave beam injection. In the LHD 18th experimental campaign in 2014-2015, an ECCD experiment with second harmonic resonance condition, on-axis magnetic field of 1.375 T for 77 GHz waves, was performed in which some combination patterns of two 77 GHz ECCDs were applied. The discharges of dual co- and dual counter-ECCDs showed remarkable plasma currents of ∼±26 kA in both of the co- and counter-directions, by 6 s pulse duration and injection powers of 366 and 365 kW. The new antenna has nearly the same capability for ECCD with that of the existing antenna. The improvement in the flexibility of the ways of applying plural ECCDs will offer a highly useful tool for investigations on the phenomena concerning with the plasma current such as magnetohydro-dynamics

Development and application of a ray-tracing code integrating with 3D equilibrium mapping in LHD ECH experiments

The central electron temperature has successfully reached up to 7.5 keV in large helical device(LHD) plasmas with a central high-ion temperature of 5 keV and a central electron density of1.3×1019 m−3. This result was obtained by heating with a newly-installed 154 GHz gyrotronand also the optimisation of injection geometry in electron cyclotron heating (ECH). Theoptimisation was carried out by using the ray-tracing code ‘LHDGauss’, which was upgradedto include the rapid post-processing three-dimensional (3D) equilibrium mapping obtainedfrom experiments. For ray-tracing calculations, LHDGauss can automatically read the relevantdata registered in the LHD database after a discharge, such as ECH injection settings (e.g.Gaussian beam parameters, target positions, polarisation and ECH power) and Thomsonscattering diagnostic data along with the 3D equilibrium mapping data. The equilibrium mapof the electron density and temperature profiles are then extrapolated into the region outsidethe last closed flux surface. Mode purity, or the ratio between the ordinary mode and theextraordinary mode, is obtained by calculating the 1D full-wave equation along the directionof the rays from the antenna to the absorption target point. Using the virtual magnetic fluxsurfaces, the effects of the modelled density profiles and the magnetic shear at the peripheralregion with a given polarisation are taken into account. Power deposition profiles calculatedfor each Thomson scattering measurement timing are registered in the LHD database. Theadjustment of the injection settings for the desired deposition profile from the feedbackprovided on a shot-by-shot basis resulted in an effective experimental procedure

Stable sustainment of plasmas with electron internal transport barrier by ECH in the LHD

The long pulse experiments in the Large Helical Device has made progress in sustainment of improved confinement states. It was found that steady-state sustainment of the plasmas with improved confinement at the core region, that is, electron internal transport barrier (e-ITB), was achieved with no significant difficulty. Sustainment of a plasma having e-ITB with the line average electron density ne_ave of 1.1 × 1019 m−3 and the central electron temperature Te0 of ∼3.5 keV for longer than 5 min only with 340 kW ECH power was successfully demonstrated

Progress of long pulse discharges by ECH in LHD

Using ion cyclotron heating and electron cyclotron heating (ECH), or solo ECH, trials of steady state plasma sustainment have been conducted in the superconducting helical/stellarator, large helical device (LHD) (Ida K et al 2015 Nucl. Fusion 55 104018). In recent years, the ECH system has been upgraded by applying newly developed 77 and 154 GHz gyrotrons. A new gas fueling system applied to the steady state operations in the LHD realized precise feedback control of the line average electron density even when the wall condition varied during long pulse discharges. Owing to these improvements in the ECH and the gas fueling systems, a stable 39 min discharge with a line average electron density ne_ave of 1.1  ×  1019 m−3, a central electron temperature Te0 of over 2.5 keV, and a central ion temperature Ti0 of 1.0 keV was successfully performed with ~350 kW EC-waves. The parameters are much improved from the previous 65 min discharge with ne_ave of 0.15  ×  1019 m−3 and Te0 of 1.7 keV, and the 30 min discharge with ne_ave of 0.7  ×  1019 m−3 and Te0 of 1.7 keV

Extension of operational regime in high-temperature plasmas and effect of ECRH on ion thermal transport in the LHD

A simultaneous high ion temperature (Ti) and high electron temperature (Te) regime was successfully extended due to an optimized heating scenario in the LHD. Such high-temperature plasmas were realized by the simultaneous formation of an electron internal transport barrier (ITB) and an ion ITB by the combination of high power NBI and ECRH. Although the ion thermal confinement was degraded in the plasma core with an increase of Te/Ti by the on-axis ECRH, it was found that the ion thermal confinement was improved at the plasma edge. The normalized ion thermal diffusivity ${{\chi}_{\text{i}}}/T_{\text{i}}^{1.5}$ at the plasma edge was reduced by 70%. The improvement of the ion thermal confinement at the edge led to an increase in Ti in the entire plasma region, even though the core transport was degraded

The whole blood transcriptional regulation landscape in 465 COVID-19 infected samples from Japan COVID-19 Task Force

「コロナ制圧タスクフォース」COVID-19患者由来の血液細胞における遺伝子発現の網羅的解析 --重症度に応じた遺伝子発現の変化には、ヒトゲノム配列の個人差が影響する--. 京都大学プレスリリース. 2022-08-23.Coronavirus disease 2019 (COVID-19) is a recently-emerged infectious disease that has caused millions of deaths, where comprehensive understanding of disease mechanisms is still unestablished. In particular, studies of gene expression dynamics and regulation landscape in COVID-19 infected individuals are limited. Here, we report on a thorough analysis of whole blood RNA-seq data from 465 genotyped samples from the Japan COVID-19 Task Force, including 359 severe and 106 non-severe COVID-19 cases. We discover 1169 putative causal expression quantitative trait loci (eQTLs) including 34 possible colocalizations with biobank fine-mapping results of hematopoietic traits in a Japanese population, 1549 putative causal splice QTLs (sQTLs; e.g. two independent sQTLs at TOR1AIP1), as well as biologically interpretable trans-eQTL examples (e.g., REST and STING1), all fine-mapped at single variant resolution. We perform differential gene expression analysis to elucidate 198 genes with increased expression in severe COVID-19 cases and enriched for innate immune-related functions. Finally, we evaluate the limited but non-zero effect of COVID-19 phenotype on eQTL discovery, and highlight the presence of COVID-19 severity-interaction eQTLs (ieQTLs; e.g., CLEC4C and MYBL2). Our study provides a comprehensive catalog of whole blood regulatory variants in Japanese, as well as a reference for transcriptional landscapes in response to COVID-19 infection