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Daisuke Fukushi,1 Keigo Murakami,2 Yuji Watanabe,3 Norihiko Sugimoto,4 Hirotsugu Uehara,4 Masafumi Seki5 1Division of Gastroenterology, Tohoku Medical and Pharmaceutical University Hospital, Sendai City, Miyagi, Japan; 2Division of Pathology, Tohoku Medical and Pharmaceutical University Hospital, Sendai City, Miyagi, Japan; 3Laboratory for Clinical Microbiology, Tohoku Medical and Pharmaceutical University Hospital, Sendai City, Miyagi, Japan; 4Fuso Pharmaceutical Industry, Osaka City, Osaka, Japan; 5Division of Infectious Diseases and Infection Control, Tohoku Medical and Pharmaceutical University Hospital, Sendai City, Miyagi, JapanCorrespondence: Masafumi Seki, Division of Infectious Diseases and Infection Control, Tohoku Medical and Pharmaceutical University, 1-15-1 Fukumuro, Miyagino-ku, Sendai City, Miyagi, 983-8536, Japan, Tel +81-22-983-1221, Fax +81-22-290-8959, Email m-seki@tohoku-mpu.ac.jp; seki@hosp.tohoku-mpu.ac.jpBackground: Detection of Mycobacterium avium complex (MAC) in tissue is essential for the diagnosis of MAC infections when the Mycobacterium is not isolated from sputum. However, detection of MAC in paraffin-embedded sections has not been established.Methods: We encountered two patients with suspected MAC infections after surgery: patient 1 had a pulmonary nodule that was initially suspected to be lung cancer and was excised under video-assisted thoracoscopic surgery (VATS). Patient 2, who was under treatment with steroids and anti-IL-6 inhibitors for rheumatoid arthritis, was suspected to have disseminated ileocecal cancer with metastasis to the lung and skin. In both cases, we postoperatively detected MAC genes in paraffin-embedded tissue sections using the novel mycobacterial nucleic acid identification test, ie tissue-direct polymerase chain reaction (tdPCR)-based nucleic acid lateral flow immunoassay (NALFIA). Both patients showed granulomatous lesions with hematoxylin-eosin staining, and mycobacteria by Ziehl–Neelsen staining in tissue sections from the lung and skin, respectively, although MAC were not isolated from the sections. MAC genes were finally detected by tdPCR-NALFIA in both cases.Conclusion: Although Ziehl–Neelsen staining and culture tests are the gold standard in identifying causative mycobacteria, the rapid results of tdPCR-NALFIA performed simultaneously with sputum and/or tissue culture may make it an important auxiliary diagnostic tool for identifying mycobacterial infection, leading to improvement in the management of MAC patients.Keywords: Mycobacterium avium complex, MAC, Ziehl–Neelsen staining, rapid diagnosis

Impacts of temperature assimilation on Venusian thermal tides are investigated by the observing system simulation experiments assuming Akatsuki Longwave Infrared Camera (LIR) observations. Synthetic temperature data are prepared by a Venusian general circulation model (VGCM) to test if LIR temperature data resolves a discrepancy in the structure of thermal tides between observations and the VGCM. They are assimilated at 70 km altitude with several combinations of frequency and horizontal region. The result shows that the three-dimensional structure of thermal tides is significantly improved not only in temperature but also in horizontal wind, even if observations are available only at a limited frequency of 6-hourly or on the dayside. The zonal–mean zonal wind and temperature fields are also modified at 60–80 km altitudes globally through the vertical momentum transport of thermal tides. It would be promising to assimilate Akatsuki LIR observations to produce realistic objective analysis of the Venus atmosphere.

Numerical simulation of Venus’ atmosphere is useful to understand the dynamics of the system. The Venus atmospheric data assimilation system “ALEDAS-V” (Sugimoto et al. 2017) based on the Venus atmospheric general circulation model “AFES-Venus” (Sugimoto et al. 2014) has been used to simulate Venus’ atmosphere and generated some key phenomena such as the super-rotation, baroclinic waves, and thermal tides. To further understand the dynamics of Venus’ atmosphere, Bred Vectors (BV) are computed with the AFES-Venus model. This method can identify different growing modes of the system and has been used to study the dynamics of the Earth (Toth and Kalnay 1993, 1997) and Martian atmospheres (Greybush et al. 2013). However, to our knowledge, there has been no similar study on Venus’ atmosphere. To conduct the breeding cycle, we first produced a five (Earth) year free run of the AFES-Venus model initialized from an idealized zonal wind profile. Next, the forecast states on January 01 and August 25 in the 5th Earth year are used as the initial conditions for the control run and the perturbed run, respectively. These two initial conditions have the same sub-solar positions. To emphasize the active dynamics, the BV norm is defined by the temperature norm from the 60 km to 80 km altitudes, weighted by pressure and latitude. For the breeding cycle, a rescaling norm and rescaling interval are specified. During the breeding cycle, at every rescaling interval (including the initial time), if the norm is bigger than the specified rescaling norm, the BV is rescaled to the rescaling norm. Different combinations of the parameters are tested. The BV amplitude generally remains stable throughout the whole year without significant seasonal variability (Figure 1), which is different from the Martian atmosphere. The growth rate of the BV amplitude can represent the characteristics of the instabilities. It is calculated by taking the natural logarithm of the ratio of the BV amplitude at the end of the time interval (before rescaling) to the amplitude at the beginning of the interval. It is then converted to the daily growth rate by dividing the ratio of the time interval to one day. When the rescaling norm is smaller or the rescaling interval is shorter, the average growth rate is higher (Figure 2). Further BV analysis will be conducted such as analyzing the BV structure by taking composite mean along the super-rotation and conducting BV breeding cycle without thermal tides. These results will be useful to understand the dynamics of the thermal tide, baroclinic waves, super-rotation, and other important features of Venus atmosphere. Figure 1. The bred vector amplitude (K2 ) time evolution from the experiments with different rescaling days (1, 2, 5, 10, 20) and the same rescaling norm (10 K2 ). Figure 2. The average daily growth rate of the bred vector amplitude (K2 ) for different combination of rescaling norm and rescaling days. The average is taken from February to December. Reference Greybush, S. J., E. Kalnay, M. J. Hoffman, and R. J. Wilson, 2013: Identifying Martian atmospheric instabilities and their physical origins using bred vectors. Q. J. R. Meteorol. Soc., 139, 639–653, https://doi.org/10.1002/qj.1990. Sugimoto, N., M. Takagi, and Y. Matsuda, 2014: Baroclinic instability in the Venus atmosphere simulated by GCM. J. Geophys. Res. Planets, 119, 1950–1968, https://doi.org/10.1002/2014JE004624. ——, A. Yamazaki, T. Kouyama, H. Kashimura, T. Enomoto, and M. Takagi, 2017: Development of an ensemble Kalman filter data assimilation system for the Venusian atmosphere. Sci. Rep., 7, 9321, https://doi.org/10.1038/s41598-017-09461-1. Toth, Z., and E. Kalnay, 1993: Ensemble Forecasting at NMC: The Generation of Perturbations. Bull. Am. Meteorol. Soc., 74, 2317–2330, https://doi.org/10.1175/1520-0477(1993)0742.0.CO;2. ——, and ——, 1997: Ensemble Forecasting at NCEP and the Breeding Method. Mon. Weather Rev., 125, 3297–3319, https://doi.org/10.1175/1520-0493(1997)1252.0.CO;2.

Observations of the Venus Climate Orbiter “Akatsuki” provide us with horizontal distributions of the horizontal winds derived from cloud tracking of the Ultraviolet Imager (UVI) and of temperature observed by the Longwave Infrared Camera (LIR). However, these observations are limited in altitude, local time (day or night side), and frequency. Then it is difficult to elucidate the general circulation of the Venus atmosphere, including various temporal and spatial scales, only from observations. In this study, we produced a Venus dataset (analysis) that has high temporal and spatial resolutions by assimilating horizontal winds derived by the Akatsuki observations. At the top of the cloud layer of Venus, there are planetary-scale atmospheric waves that are excited by the solar heating and move with the sun, called the thermal tides. In this presentation, we focused on thermal tides to verify the analysis. We use the Venus atmospheric data assimilation system “ALEDAS-V" (Sugimoto et al., 2017) [1] for assimilation and the Venus atmospheric general circulation model “AFES-Venus" (Sugimoto et al., 2014) [2] for ensemble forecasts. AFES-Venus is a full nonlinear dynamical GCM on the assumption of hydrostatic balance, designed for the Venus atmosphere. ALEDAS-V uses the Local Ensemble Transform Kalman Filter, and is the first data assimilation system for the Venus atmosphere. We assimilated the cloud top (~70km) zonal and meridional winds obtained by tracking morphology, using Akatsuki UVI data (Horinouchi et al., 2021) [3] from September 1st to December 31st, 2018. The assimilation data (analysis) from October 1st to November 30th, 2018, is analyzed, because the root-mean-square-deviations (RMSD) from FR (free run; the case without data assimilation) are stable. Figures (a) and (d) show the observed zonal and meridional winds, respectively. The zonal wind has a local minimum near 11 LT (local time) around the equator (Figure a). The meridional wind is the weakest at the equator and increases with latitude, and the amplitude is maximum around noon (Figure d) in the local time direction. Note that these winds obtained from observations exist only the dayside equatorward of 50° latitudes (Figure a and d). Figures (b) and (e) show the deviations from the zonal means of zonal and meridional winds at an altitude of 70 km in the FR, respectively. For zonal wind, diurnal (zonal wavenumber 1) and semidiurnal (zonal wavenumber 2) tides are dominant at latitudes poleward and equatorward of 30, respectively (Figure b). The zonal wind deviation has a local minimum at 14-15LT, which is ~ 2 hours behind the observation (Figures a and b). The meridional wind deviation is polar and equatorial on the dayside and nightside, respectively (Figure e), and this distribution is consistent with Akatsuki's observation (Figure d). Figures (c) and (f) show the zonal and meridional winds as a result of assimilation, respectively. The zonal wind in the equatorial region have a local minimum near 11 LT. The assimilation improved the semidiurnal tide closer to the observations (Figures a and c). The meridional wind is not so different from FR. This is probably because FR was originally very similar to observations (Figures d and f). These results are consistent with a previous study by Sugimoto et al. (2019) [4]. In addition, while the observed winds exist only on the dayside, the results of assimilation show that the horizontal winds field is modified significantly even on the nightside. It is suggested that spatially limited data assimilation can improve the general circulation of GCM. In the future work, we are planning to release the assimilation dataset as the “objective analysis data” of Venus for the first time in the world. [1] Sugimoto, N., et al. Development of an ensemble Kalman filter data assimilation system for the Venusian atmosphere. Scientific Reports 7(1), 9321 (2017). [2] Sugimoto, N., et al. Baroclinic instability in the Venus atmosphere simulated by GCM. J. Geophys. Res. Planets 119, 1950–1968 (2014). [3] Horinouchi, T., et al. Venus Climate Orbiter Akatsuki Cloud Motion Vector Data Set v1.0, JAXA Data Archives and Transmission System (2021). [4] Sugimoto, N., et al. Impact of data assimilation on thermal tides in the case of Venus Express wind observation. Geophys. Res. Lett. 46, 4573–4580 (2019).

Planetary-scale 4-day Kelvin-type waves at the cloud top of the Venus atmosphere have been reported from the 1980s, and their significance for atmospheric dynamics has been pointed out. However, these waves have not been reproduced in Venus atmospheric general circulation models (VGCMs). Recently, horizontal winds associated with the planetary-scale waves at the cloud top have been obtained from cloud images taken by cameras onboard Venus orbiters, which could enable us to clarify the structure and roles of Kelvin-type waves. In order to examine this possibility, our team carried out an idealized observing system simulation experiment (OSSE) with a data assimilation system which we developed. The wind velocity data provided by a CCSR/NIES (Center for Climate System Research/National Institute for Environmental Studies) VGCM where equatorial Kelvin-type waves were assumed below the cloud bottom was used as idealized observations. Results show that 4-day planetary-scale Kelvin-type waves are successfully reproduced if the wind velocity between 15&deg, S and 15&deg, N latitudes is assimilated every 6 h at 70 km altitude. It is strongly suggested that the Kelvin-type waves could be reproduced and investigated by the data assimilation with the horizontal wind data derived from Akatsuki ultraviolet images. The present results also contribute to planning future missions for understanding planetary atmospheres.

Distributions of temperature and static stability in the Venus atmosphere consistent with recent radio occultation measurements are reproduced using a general circulation model. A low-stability layer is maintained at low- and mid-latitudes at 50–60 km altitude and is sandwiched by high- and moderate-stability layers extending above 60 and below 50 km, respectively. In the polar region, the low-stability layer is located at 46–63 km altitude and the relatively low-stability layer is also found at 40–46 km altitude. To investigate how these thermal structures form, we examine the dynamical effects of the atmospheric motions on the static stability below 65 km altitude. The results show that the heat transport due to the mean meridional circulation is important at low-latitudes. At mid- and high-latitudes, meanwhile, the baroclinic Rossby-type wave plays an important role in maintaining the thermal structure. In addition, appreciable equatorward heat transport is found to maintain the deep and low-stability layer in the polar region, which might be induced by the interaction between the baroclinic Rossby-type wave in the low-stability layer and the trapped Rossby-type wave below it.

著者人数: 13名, Accepted: 2018-11-28, 資料番号: SA1180242000

Abstract Structure of the planetary scale wave, which has been studied for over decades since its discovery in 1980s, is yet to be shrouded in mystery. To clarify this, images by cameras would definitely be necessary. Our team has been assimilating data with AFES LETKF Data Assimilation System for Venus (ALEDAS-V): the first data assimilation system for the Venusian atmosphere, as a pre-experiment before executing the mission. Results show that you can successfully reproduce 4-day planetary scale wave when assimilating data of wind velocity of latitude S15°- N15° every 6 hours at an altitude of 70 km. This discovery will contribute not only to a mission to observe wind velocity of Venus, but also to proposal regarding missions for further understanding of atmospheric structure on other planets, in the future. Introduction The planetary scale wave, which is considered as 4-day “equatorial Kelvin wave” is existing at the cloud top in the equatorial region on the Venus atmosphere [1,2]. The equatorial Kelvin wave is pointed out to have a possibility of contributing to generation and maintenance of what is called “Super Rotation”: the wind circulating Venus 60 times faster than the speed of Venusian rotation [3]. However, the equatorial Kelvin wave has not been simulated in any Venusian atmospheric General Circulation Model (VGCM) in the world. We have so far developed AFES-Venus; Atmospheric GCM for the Earth Simulator for Venus, and ALEDAS-V; AFES LETKF Data Assimilation System for Venus, using LETKF; Local Ensemble Transform Kalman Filter, for the first time in the world [4,5]. In this study, we made an observation data regarding the speed of wind, by varying conditions such as altitude, latitudinal range, and frequency of observations, assuming observations with various wavelength cameras. We created the idealized observation data from CCSR/NIES Venus AGCM [6], in which the equatorial Kelvin wave is reproduced at ~70 km by 5.5-day wave forcing from the lowest level (~30 km). Experimental setting AFES-Venus solves dry 3-D Primitive equation on sphere. The physical parameters are based on Venus. The latitude-longitude grids (128 times 64) with 60 vertical layers are used. Solar heating is based on Tomasko (1980) and Crisp (1989), and radiative process is simplified by Newtonian cooling. The simulation starts from zonal wind assuming super rotation and spin up for 4 Earth years. ALEDAS-V uses the LETKF [7] to produce an improved estimate (called analysis) by combining observations and short time ensemble forecasts of AFES-Venus. The number of ensemble members is 31. Assimilation cycle is 6 hourly interval. Observation period and error are set to 1 month and 3 m/s, respectively. We first assimilated the wave observation at several altitudes and different frequency, however, the 4-day wave was not perfectly reproduced. Therefore, we conducted sensitivity experiments of observational domain at an altitude of 70 km, where the wave was mostly reproduced. In this experiment, observation with ultraviolet wavelength camera on Akatsuki for example, is assumed to be used for observations. Results We have been conducting various cases of experiments, though, we will show the results partially here. Figure 1: Longitude-time cross sections of wind at the equator at 70 km (deviations from time averages) (a): free-run-forecast, where data is not assimilated (b): horizontal winds data assimilated in latitudes of S15°- N15°, every 6 hours at 70 km Figure.1 shows Longitude-time cross section of deviation of zonal wind from its time average at the equator at altitude of 70 km. Black arrows refers 4-day waves, and it is approximately 4-days from bottom-left to upper-right of the arrow. In spite of the vague expression in (a), 4-day wave is apparent in (b). The 4-day wave was reproduced by data assimilation. Figure 2: Time variations of temperature (color) and horizontal winds (vector) at 70 km. Horizontal winds data is assimilated in latitudes of S15°- N15°, every 6 hours at 70 km. Figure. 2 is time variations of temperature and horizontal winds at an altitude of 70 km. In this figure, high-pass filter with 10-day running mean subtracted is drawn. The black lines in the images characterize borders between contrasting vectors. The locations of two lines in Day 1 and Day 5 are almost the same, respectively. Therefore, it is explicit that 4-day wave is successfully reproduced. Our team also conducted several other experiments and analyzed their results. By drawing latitude-longitude cross section of averaged zonal wind and temperature, we found that the velocity of wind at 65 km – 70 km at S45°- N45° is contrasting by assimilating different latitudenal range data. In another experiment, where we drew time-altitude cross section of wind at the equator, we confirmed that 4-day wave was apparent only when assimilating data. Finally, we investigated latitudinal dependency and observation frequential dependency with root-mean-square-deviation. From these, we learned that there is a strong jet in mid-latitude and also reinforced our hypothesis of the best observation latitude. Summary and Conclusions We sought the reproduction of 4-day wave in Venus atmosphere by assimilating data of an idealized observation with ALEDAS-V. And we discovered that under the following conditions, we can expect to reproduce 4-day wave successfully, using ultraviolet wavelength cameras. First, the altitude of assimilating data would be better to set at 70 km. Also, the most potential frequency for data assimilation would be once in 6 hours, with latitude between S15°- N15°. Our research has an important roll as pre-investigation before executing an actual mission, thus we will carry on a further research to contribute solving the enigma of Venus. Acknowledgements This study was conducted under the joint research project of the Earth Simulator Center and supported by the Japan Science and Technology Agency. References [1] A.D. Del Genio and W.B. Rossow, Icarus, 1982 [2] A.D. Del Genio and W.B. Rossow, J. Atmos. Sci., 1990 [3] M. Yamamoto et al., J. Atmos. Sci., 1997 [4] H. Ando et al., Nature Communications, 2016 [5] N. Sugimoto et al., Scientific Reports, 2017 [6] M. Yamamoto et al., Icarus, 2012 [7] T. Miyoshi and S. Yamane, Mon. Wea. Rev., 2007

Feasibility of radio occultation measurement (RO) among small satellites is investigated by observing system simulation experiment (OSSE) of the Venus data assimilation system in two test cases introducing real orbits. One observes cold collar in polar region. The other observes thermal tides in equatorial region. The reproducibility of the cold collar or thermal tides is investigated by several types of orbits. Results suggests that the cold collar is successfully reproduced with two or three satellites. In addition, zonal wind can be improved by temperature assimilation of the thermal tides with two satellites. Therefore, RO among small satellites would be promising to reproduce global phenomena in the Venus atmosphere. 1. Introduction Venus atmosphere has a global, thick cloud cover at about 48–70 km altitude. Therefore, it is very difficult to observe under the cloud by the images. One of the most useful methods to obtain vertical temperature profiles is RO. For Earth, daily observations have been performed by GNSS (Global Navigation Satellite System). However, Venus has been observed only between one satellite, e.g., Venus Express or Akatsuki [1], and Earth. For multiple satellites, by transmitting and receiving radio waves between them, more observations, multiple points and better time resolution, could be obtained. In the previous study, we have shown that RO among small satellites can reproduce the cold collar with fixed observational points [2]. In order to check feasibility, however, we have to consider realistic orbits of flying multiple satellites around Venus. So far, we have developed Venus atmospheric general circulation model (AGCM) named AFES-Venus (AGCM for the Earth Simulator for Venus) [3]. Recently, using the local ensemble transform Kalman filter (LETKF) [4], we have succeeded in developing the AFES LETKF data assimilation system for Venus (ALEDAS-V) [5]. In this study, we performed OSSE assuming RO among small satellites in two test cases with real orbits targeting the cold collar and thermal tides. 2. Experimental setting AFES-Venus solves dry 3-D Primitive equation on sphere. The physical parameters are based on Venus. The latitude-longitude grids (128 times 64) with 60 vertical layers are used. The simulation starts from idealized super rotation and spin up for 4 Earth years. Reproduced zonal wind is in good agreement with observations [6]. ALEDAS-V uses the LETKF [4] to produce an improved estimate (called analysis) by combining observations and short time ensemble forecasts of AFES-Venus. The number of ensemble members is 31. Assimilation cycle is 6 hourly interval. Observational errors and inflation are set to 3.0 K and 10%, respectively. Details are described in [2, 5]. Two experiments are conducted; one is evaluated by the cold collar (experiment 1), and the other is evaluated by the thermal tides (experiment 2). Idealized temperature observations at 40-90 km are prepared by the GCMs assuming RO among small satellites. Experiment 1 uses data from IPSL VGCM because the cold collar is more realistically reproduced [7]. Note that temperature bias between IPSL VGCM and AFES-Venus is corrected. Experiment 2 uses data from AFES-Venus itself but experimental settings are different. Observation points are based on real orbits; Experiment 1 covers polar region and experiment 2 does equatorial region. They are assimilated to AFES-Venus by ALEDAS-V and results are compared with frf (free run forecast). The reproducibility of the cold collar or thermal tides is investigated by several orbits. 3. Results Figure 1 shows the temperature distributions at 30-90°N at ~66 km in experiment 1. Four situations are considered: (a) frf and (b,c,d) has different orbits. p1, p2 and p3 indicate each pair of satellites. Cold collar is most clearly reproduced for (d) in which all 3 satellites proceed RO. Figure 1: Temperature distributions at ~66 km (at 30-90°N seen from the north pole): (a) frf, (b) 1 pair of satellites (p1), (c) 2 pairs (p1 and p3), and (d) 3 pairs (p1, p2 and p3). Figure 2 shows latitude-height cross sections of zonal wind (contour) and difference of zonal wind between frf and the Qt8 cases (color) in which the solar heating is reduced to 80% compared with that used in frf. The 4 types of orbits are considered. The zonal wind above the cloud top (~80 km) is significantly decelerated in (d). It is suggested that temperature observations of the thermal tides can improve zonal wind. Figure 2: Latitude-height cross sections of zonal wind (contour) and difference of zonal wind between frf and the Qt8 cases (color). 4 types of orbits are shown: a2 (a), b1 (b), b2 (c), and c2 (d). c2 has most observations, following b2, b1 and a2. Summary and Conclusions In the present study, we have checked feasibility of the Venus future mission of RO among small satellites by introducing real orbits. In experiment 1, the cold collar is reproduced with 2 or 3 satellites observing polar region. In experiment 2, zonal wind is improved by the temperature observations of the thermal tides in equatorial region. Results suggest that RO with two or three small satellites would be promising to reproduce global phenomena. Furthermore, it is also suggested that this kind of observing system simulation experiment would be very useful to design future missions. Acknowledgements This study and supported by the Japan Science and Technology Agency (JST). References [1] Ando, H. et al.: Thermal structure of Venus atmosphere from sub-cloud region to the mesosphere observed by radio occultation, Scientific Rep., 2020. [2] Sugimoto, N. et al.: Observing system simulation experiment for radio occultation measurements of the Venus atmosphere among small satellites, Journal of JSCE A2: Applied Mechanics, 2019. [3] Sugimoto, N. et al.: Baroclinic instability in the Venus atmosphere simulated by GCM, J. Geophys. Res., Planets, 2014. [4] Miyoshi, T. and S. Yamane: Local ensemble transform Kalman filtering with an AGCM at a T159/L48 resolution. Mon. Wea. Rev. 135, 2007. [5] Sugimoto, N. et al.: Development of an ensemble Kalman filter data assimilation system for the Venusian atmosphere, Scientific Rep., 2017. [6] Sugimoto, N. et al.: Waves in a Venus general circulation model, Geophys. Res. Lett., 2014. [7] Garate-Lopez, I and S. Lebonnois: Latitudinal variation of clouds’ structure responsible for Venus’ cold collar, Icarus, 2018.

Gravity waves play essential roles in the terrestrial atmosphere because they propagate far from source regions and transport momentum and energy globally. Gravity waves are also observed in the Venus atmosphere, but their characteristics have been poorly understood. Here we demonstrate activities of small-scale gravity waves using a high-resolution Venus general circulation model with less than 20 and 0.25 km in the horizontal and vertical grid intervals, respectively. We find spontaneous gravity wave radiation from nearly balanced flows. In the upper cloud layer (~70 km), the thermal tides in the super-rotation are primary sources of small-scale gravity waves in the low-latitudes. Baroclinic/barotropic waves are also essential sources in the mid- and high-latitudes. The small-scale gravity waves affect the three-dimensional structure of the super-rotation and contribute to material mixing through their breaking processes. They propagate vertically and transport momentum globally, which decelerates the super-rotation in the upper cloud layer (~70 km) and accelerates it above ~80 km., Gravity waves are observed in Venus atmosphere, but their characteristics are not well-known. Here, the authors show spontaneous generation of gravity waves from the thermal tides in the Venus atmosphere as small-scale gravity waves are resolved in high-resolution general circulation model.

We present distributions of the zonal-mean temperature and static stability in the Venusian atmosphere obtained from Venus Express and Akatsuki radio occultation profiles penetrating down to an altitude of 40 km. At latitudes equatorward of 75°, static stability derived from the observed temperature profiles is consistent with previous in-situ measurements in that there is a low-stability layer at altitudes of 50–58 km and highly and moderately stratified layers above 58 km and below 50 km, respectively. Meanwhile, at latitudes poleward of 75°, a low-stability layer extends down to 42 km, which has been unreported in analyses of previous measurements. The deep low-stability layer in the polar region cannot be explained by vertical convection in the middle/lower cloud layer, and the present result thus introduces new constraints on the dynamics of the sub-cloud atmosphere. The Venusian atmosphere is in striking contrast to the Earth’s troposphere, which generally has a deeper low-stability layer at low latitudes than at mid- and high latitudes.

This study proposes that secondary eyewall formation (SEF) of tropical cyclones (TCs) can be attributed to an instability of flow in the free atmosphere coupled with Ekman pumping. Unstable solutions of a 1.5-layer shallow-water system are obtained under fast–wind speed conditions in the free atmosphere. The instability condition derived in the linear model indicates the importance of the ratio of angular velocity to vorticity, and the condition is more likely to be satisfied when the ratio is large and its radial gradient is positive. Thus, fast angular velocity, low absolute vertical vorticity, small negative radial gradient of angular velocity, and large negative gradient of vertical vorticity are favorable. Eigenvalue analyses are performed over a wide range of parameters using a vorticity profile with an infinitesimal secondary maximum. The growth rate increases with vorticity outside the radius of maximum wind (RMW), the radius of the secondary vorticity maximum, its magnitude, and the Rossby number defined by maximum tangential velocity, the RMW, and the Coriolis parameter. Furthermore, the growth rate is positive only between 2 and 7 times the RMW, and it is negative close to or far outside the RMW. These features are consistent with previous studies on SEF. A dimensionless quantity obtained from the unstable condition in the linear theory is applied to SEF events simulated by two different full-physics numerical models; increases several hours before a secondary peak of tangential velocity forms, suggesting that the initial process of SEF can be attributed to the proposed mechanism.

Vertical temperature profiles at 40–75 km around 80° N in the Venus polar vortex are retrieved over 13 Earth days almost continuously from radio occultation measurements (VeRa) in the Venus Express mission. They show periodical variations with a dominant period of ∼3.1 Earth days. These fluctuations are confined in an altitude range of 45–65 km with a local minimum at ∼58 km altitude, where the static stability abruptly increases with height. The phase of the temperature fluctuations is almost reversed at the 58 km level, and varies little above and below this altitude. A numerical simulation of a Venusian atmospheric general circulation model (GCM) shows that the axi-asymmetric temperature disturbance with zonal wavenumber-1 is predominant at 50–75 km levels in the model atmosphere. The vertical structure of the reproduced disturbance agrees quite well with that retrieved by the radio occultation measurement: amplitude of the temperature fluctuation has a local minimum and its phase is reversed at the altitude (65 km in the model) where the static stability rapidly changes as in the observations. Above and below this altitude, the phase is almost constant in the vertical direction. The relationship among the temperature, horizontal winds and geopotential height associated with the simulated disturbance suggests that the axi-asymmetric temperature disturbance observed in the Venus polar region can be interpreted as neutral barotropic Rossby waves related to barotropic instability in the polar region.

International audience; A new simulation of Venus atmospheric circulation obtained with the LMD Venus GCM is described and the simulated wave activity is analysed. Agreement with observed features of the temperature structure, static stability and zonal wind field is good, such as the presence of a cold polar collar, diurnal and semi-diurnal tides. At the resolution used (96 longitudes × 96 latitudes), a fully developed superrotation is obtained both when the simulation is initialised from rest and from an atmosphere already in superrotation, though winds are still weak below the clouds (roughly half the observed values). The atmospheric waves play a crucial role in the angular momentum budget of the Venus’s atmospheric circulation. In the upper cloud, the vertical angular momentum is transported by the diurnal and semi-diurnal tides. Above the cloud base (approximately 1 bar), equatorward transport of angular momentum is done by polar barotropic and mid- to high-latitude baroclinic waves present in the cloud region, with frequencies between 5 and 20 cycles per Venus day (periods between 6 and 23 Earth days). In the middle cloud, just above the convective layer, a Kelvin type wave (period around 7.3 Ed) is present at the equator, as well as a low-latitude Rossby-gravity type wave (period around 16 Ed). Below the clouds, large-scale mid- to high-latitude gravity waves develop and play a significant role in the angular momentum balance.

Cyclone–anticyclone asymmetry in spontaneous gravity wave radiation from a co-rotating vortex pair is investigated in an $f$-plane shallow water system. The far field of gravity waves is derived analytically by analogy with the theory of aeroacoustic sound wave radiation (Lighthill theory). In the derived form, the Earth’s rotation affects not only the propagation of gravity waves but also their source. While the results correspond to the theory of vortex sound in the limit of $f\rightarrow 0$, there is an asymmetry in gravity wave radiation between cyclone pairs and anticyclone pairs for finite values of $f$. Anticyclone pairs radiate gravity waves more intensely than cyclone pairs due to the effect of the Earth’s rotation. In addition, there is a local maximum of intensity of gravity waves from anticyclone pairs at an intermediate $f$. To verify the analytical solution, a numerical simulation is also performed with a newly developed spectral method in an unbounded domain. The novelty of this method is the absence of wave reflection at the boundary due to a conformal mapping and a pseudo-hyperviscosity that acts like a sponge layer in the far field of waves. The numerical results are in excellent agreement with the analytical results even for finite values of $f$ for both cyclone pairs and anticyclone pairs.

The renormalization group equations (RGEs) describing spontaneous inertia–gravity wave (GW) radiation from part of a balanced flow through a quasi resonance that were derived in a companion paper by Yasuda et al. are validated through numerical simulations of the vortex dipole using the Japan Meteorological Agency nonhydrostatic model (JMA-NHM). The RGEs are integrated for two vortical flow fields: the first is the initial condition that does not contain GWs used for the JMA-NHM simulations, and the second is the simulated thirtieth-day field by the JMA-NHM. The theoretically obtained GW distributions in both RGE integrations are consistent with the numerical simulations using the JMA-NHM. This result supports the validity of the RGE theory. GW radiation in the dipole is physically interpreted either as the mountain-wave-like mechanism proposed by McIntyre or as the velocity-variation mechanism proposed by Viúdez. The shear of the large-scale flow likely determines which mechanism is dominant. In addition, the distribution of GW momentum fluxes is examined based on the JMA-NHM simulation data. The GWs propagating upward from the jet have negative momentum fluxes, while those propagating downward have positive ones. The magnitude of momentum fluxes is approximately proportional to the sixth power of the Rossby number between 0.15 and 0.4.

The size and mass of Venus is similar to those of the Earth; however, its atmospheric dynamics are considerably different and they are poorly understood due to limited observations and computational difficulties. Here, we developed a data assimilation system based on the local ensemble transform Kalman filter (LETKF) for a Venusian Atmospheric GCM for the Earth Simulator (VAFES), to make full use of the observational data. To examine the validity of the system, two datasets were assimilated separately into the VAFES forecasts forced with solar heating that excludes the diurnal component Qz; one was created from a VAFES run forced with solar heating that includes the diurnal component Qt, whereas the other was based on observations made by the Venus Monitoring Camera (VMC) onboard the Venus Express. The VAFES-LETKF system rapidly reduced the errors between the analysis and forecasts. In addition, the VAFES-LETKF system successfully reproduced the thermal tide excited by the diurnal component of solar heating, even though the second datasets only included horizontal winds at a single altitude on the dayside with a long interval of approximately one Earth day. This advanced system could be useful in the analysis of future datasets from the Venus Climate Orbiter ‘Akatsuki’.

Baroclinic instability in the super-rotation of Venus is investigated by a newly developed atmospheric general circulation model. First, we adopt an idealized super-rotation, i.e., solid-body rotating flow in a weakly stratified layer at cloud level, as an initial basic state in a nominal case. With the evolution of time, baroclinic instability occurs in a weakly stratified layer with large vertical shear of the basic zonal flow. Horizontal wind associated with the baroclinic instability modes is of a few m s−1. The initial structure of the unstable modes is similar to those obtained in previous linear stability analyses. However, it is modified by nonlinear interactions in the later stage, reaching a quasi-steady state. Meridional transport of momentum and heat by these unstable modes accelerates the super-rotation by ~ 0.05 m s−1 day−1 at midlatitudes. Furthermore, the dependence of baroclinic instability on the basic state, i.e., the meridional profiles of zonal flow and the vertical profiles of static stability, are subsequently investigated. For the super-rotation with midlatitude jets at cloud level, the modes are modified from baroclinic to barotropic in the later stage. Typically, their horizontal wind is of O(10) m s−1. Their amplitude is maintained by energy conversion from zonal-mean available potential energy associated with the baroclinic basic state. In the case where static stability is smaller than that in the nominal case, the baroclinic modes transfer angular momentum from midlatitude to the equator near a 70 km level and accelerate the super-rotation by more than 10 m s−1 in the equatorial region.

Accepted: 2013-10-08, 資料番号: SA1004601000

International audience; Spontaneous generation of inertia-gravity waves from balanced flows is investigated in idealized simulations of dipoles. Long integrations are performed for dipoles with different Rossby numbers (Ro) to identify the backreaction of the waves. Emission of waves is detected only for large enough Ro (>0.15), and it then leads to a slow decay of the dipole's kinetic energy. A major finding is that this decay is well captured by the simulations, although positions of the waves appear still sensitive to the resolution, and their maximum vertical velocity increases linearly with resolution. The interpretation is that the emission process is well resolved and fairly insensitive to resolution, while the propagation and dissipation at small scales remains sensitive to resolution. The implication is that the simulations yield an estimate of the leakage of energy from balanced motions to gravity waves, providing a useful estimate of a poorly constrained flux in the ocean's energy budget.

Unlike the polar vortices observed in the Earth, Mars and Titan atmospheres, the observed Venus polar vortex is warmer than the midlatitudes at cloud-top levels (∼65 km). This warm polar vortex is zonally surrounded by a cold latitude band located at ∼60° latitude, which is a unique feature called ‘cold collar' in the Venus atmosphere. Although these structures have been observed in numerous previous observations, the formation mechanism is still unknown. Here we perform numerical simulations of the Venus atmospheric circulation using a general circulation model, and succeed in reproducing these puzzling features in close agreement with the observations. The cold collar and warm polar region are attributed to the residual mean meridional circulation enhanced by the thermal tide. The present results strongly suggest that the thermal tide is crucial for the structure of the Venus upper polar atmosphere at and above cloud levels., Unlike some planets, the Venusian polar vortex is warmer than the mid-latitudes at cloud-top level, but the mechanism behind this is unknown. Here, the authors use a general circulation model and suggest the cold collar and warm polar regions are due to residual mean meridional circulation intensified by thermal tides.

Cytolethal distending toxins (CDTs), which block eukaryotic cell proliferation by acting as inhibitory cyclomodulins, are produced by diverse groups of Gram-negative bacteria. Active CDT is composed of three polypeptides—CdtA, CdtB, and CdtC—encoded by the genes cdtA , cdtB , and cdtC , respectively. We developed a PCR-restriction fragment length polymorphism assay for the detection and differentiation of five alleles of cdtB (Cdt-I through Cdt-V) in Escherichia coli and used the assay to investigate the prevalence and characteristic of CDT-producing E. coli in children with diarrhea (A. Hinenoya et al., Microbiol. Immunol. 53:206–215, 2009). In these assays, two untypable cdtB genes were detected and the organisms harboring the cdtB gene were identified as Providencia alcalifaciens (strains AH-31 and AS-1). Nucleotide sequence analysis of the cdt gene cluster revealed that the cdtA , cdtB , and cdtC genes of P. alcalifaciens are of 750, 810, and 549 bp, respectively. To understand the possible horizontal transfer of the cdt genes among closely related species, the presence of cdt genes was screened in various Providencia spp. by colony hybridization assay, and the cdt gene cluster was found in only limited strains of P. alcalifaciens . Genome walking revealed that the cdt gene cluster of P. alcalifaciens is located adjacent to a putative transposase gene, suggesting the locus might be horizontally transferable. Interestingly, the CDT of P. alcalifaciens (PaCDT) showed some homology with the CDT of Shigella boydii . Whereas filter-sterilized lysates of strains AH-31 and AS-1 showed distention of CHO but not of HeLa cells, E. coli CDT-I exhibited distention of both cells. This activity of PaCDT was confirmed by generating recombinant PaCDT protein, which could also be neutralized by rabbit anti-PaCdtB antibody. Furthermore, recombinant PaCDT was found to induce G 2 /M cell cycle arrest and phosphorylation of host histone H2AX, a sensitive marker of DNA double-strand breaks. To our knowledge, this is the first report showing that certain clinical P. alcalifaciens strains could produce variants of the CDTs compared.

The effect of the earth’s rotation on spontaneous inertial gravity wave radiation from an unsteady rotational flow is investigated numerically using a shallow water system on a rotating sphere, changing three parameters, the Rossby number (1 ≤ Ro ≤ 30), the Froude number 0.1 ≤ Fr ≤ 0.7), and the latitudinal positions of the jet (11.25°N ≤θ0 ≤ 78.75 °N). The spectral-like three-point combined compact difference (sp-CCD) scheme is used for numerical calculation to estimate the amplitude of gravity waves with high accuracy and resolution similar to the spherical harmonics model. The jet, which is initially balanced but evolves with time because of barotropic instability, is maintained by relaxation forcing. The time variations of nearly balanced rotational flows continuously radiate gravity waves. While the amount of gravity wave flux for large Ro (≥ 10) in all positions of the jet is almost constant, that for relatively small Ro (< 10) depends considerably on the positions of the jet and the observational latitude. First, there is almost no gravity wave radiation from the jet positioned at a high latitude. Second, even when gravity waves are radiated from the jet positioned at low latitude, they rarely propagate toward a higher latitude. To discuss the results, the source of gravity waves is introduced as an analogy to the aeroacoustic sound wave radiation theory (Lighthill theory) with an f-plane approximation at the position of the jet. Spectral analysis of the sources reasonably explains the waves. Because the effect of the earth’s rotation varies with the latitude, gravity waves are radiated only from an unsteady source with higher frequency than the inertial cut-off frequency at the position of the jet. In a similar way, gravity waves that propagate toward high latitudes should have a higher frequency than the inertial cut-off frequency at that latitude.

In this study, we have evaluated our recently developed polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) assay for the molecular subtyping of Shiga toxin-producing Escherichia coli (STEC). A total of 200 STEC strains including O157 (n=100), O26 (n=50), O111 (n=10), and non-O26/O111/O157 (n=40) serogroups isolated during 2005-2006 in Japan, which were identified to be clonally different by pulsed-field gel electrophoresis (PFGE) were further analyzed by the PCR-RFLP assay in comparison to PFGE. Ninety-five of O157, 48 of O26, five of O111 and 19 of non-O26/O111/O157 STEC strains yielded one to three amplicons ranging from 6.0 to 15.5 kb in size by the specific primer set targeting region V which is located in the upstream of stx genes. These strains were classified into 41 (O157), 8 (O26), 4 (O111) and 17 (non-O26/O111/O157) groups based on the RFLP patterns obtained by subsequent restriction digestion, respectively. Although the discriminatory power of PCR-RFLP assay was somewhat less than that of PFGE, it is more convenient for molecular subtyping of STEC strains especially for O157, the most important serogroup implicated in human diseases, as well as to identify the outbreak-associated isolates because of its simplicity, rapidity, ease and good reproducibility.

The use of natural compounds as inhibitory agents for virulence factor production is a new approach to overcome increased antimicrobial resistance in pathogenic bacteria. In this study, we examined whether red chilli (Capsicum annuum) contains any such compound(s) that can repress the cholera toxin (CT) production in Vibrio cholerae. We found that the methanol extract of red chilli could inhibit CT production in recently emerged V. cholerae O1 El Tor variant strains without affecting their viability. Interestingly, capsaicin, a well-studied active component of red chilli, also drastically inhibited CT production in V. cholerae strains belonging to various serogroups including variants. Real-time quantitative reverse transcription-PCR assay revealed that capsaicin effectively repressed the transcription of ctxA, tcpA and toxT genes, but not of toxR and toxS genes. On the contrary, capsaicin significantly enhanced the transcription of the hns gene, the product of which is known to regulate negatively the transcription of ctxAB, tcpA and toxT genes. These results suggest that capsaicin might act as a potent repressor for CT production possibly by enhancing the transcription of hns.

Shiga toxin-producing Escherichia coli (STEC) isolated from Japan were investigated for the distribution of virulence genes. A total of 232 STEC strains including 171 from cattle and 61 from human were examined for the occurrence of genes responsible for bacterial adhesions to intestine, e.g., eae (intimin, E. coli attaching and effacing), saa (STEC autoagglutinating adhesin), iha (irgA homologue adhesin), efa1 (E. coli factor for adherence), lpfA(O113) (long polar fimbriae), and ehaA (EHEC autotransporter) by colony hybridization assay. Similarly, the presence of toxigenic cdt (cytolethal distending toxin), and subAB (subtilase cytotoxin) genes were also checked. Among cattle isolates, 170, 163, 161, 155, 112 and 84 were positive for lpfA(O113) (99%), ehaA (95%), iha (94%), saa (91%), subAB (65%), and cdt-V (49%), respectively, while 2 were positive for eae (1.2%) and efa1 (1.2%) each. In case of human isolates, 60, 59, 58 and 58 were positive for ehaA (98%), iha (97%), efa1 (95%), and eae (95%), respectively, while 11, 2, 2, and 1 were positive for lpfA(O113) (18%), saa (3.3%), cdt-V (3.3%), and subAB (1.6%), respectively. Therefore, in human STEC isolates efa1 and eae whereas in cattle isolates saa, lpfA(O113), cdt-V and subAB were prevalent. These data indicate differential occurrence of some pathogenic genes in human and cattle originated STEC strains in Japan.

We propose the use of a high-speed spherical self-organizing map (HSS-SOM) to visualize climate variability as a complementary alternative to empirical orthogonal function (EOF) analysis. EOF analysis, which is the same as principal component analysis, is often used in the fields of meteorology and climatology to extract leading climate variability patterns, its production of linear mapping with only a low contribution rate may preclude producing any meaningful results. Due to computational limitations, however, conventional self-organizing maps are difficult to apply to huge climate datasets. The development of HSS-SOMs with dynamically growing neurons has helped reduce computational time. After demonstrating validity of our HSS-SOM using observational climate data and HSS-SOM effectiveness as a complementary alternative to the EOF, we extract dominant atmospheric circulation patterns from huge amounts of climate data in the general circulation model, in which both present climatology and future climate are simulated. These patterns correspond to those obtained in previous studies, indicating the HSS-SOM's usefulness in climate research.

Using culture-independent technology, PCR-RFLP were used to identify and type STEC in the stool of a patient with HUS. Fecal PCR-RFLP patterns were identical to those of the STEC O157:H7 isolated from the patient.