Scalability of hybrid programming for a CFD code on the Earth Simulator

The Earth Simulator (ES) is an SMP cluster system. There are two types of parallel programming models available on the ES. One is a flat programming model, in which a parallel program is implemented by MPI interfaces only, both within an SMP node and among nodes. The other is a hybrid programming model, in which a parallel program is written by using thread programming within an SMP node and MPI programming among nodes simultaneously. It is generally known that it is difficult to obtain the same high level of performance using the hybrid programming model as can be achieved with the flat programming model.

In this paper, we have evaluated scalability of the code for direct numerical simulation of the Navier–Stokes equations on the ES. The hybrid programming model achieves the sustained performance of 346.9 Gflop/s, while the flat programming model achieves 296.4 Gflop/s with 16 PNs of the ES for a DNS problem size of 256³. For small scale problems, however, the hybrid programming model is not as efficient because of microtasking overhead. It is shown that there is an advantage for the hybrid programming model on the ES for the larger size problems.     

Fast Algorithms to Enumerate All Common Intervals of Two Permutations

Given two permutations of n elements, a pair of intervals of these permutations consisting of the same set of elements is called a common interval . Some genetic algorithms based on such common intervals have been proposed for sequencing problems and have exhibited good prospects. In this paper we propose three types of fast algorithms to enumerate all common intervals: (i) a simple O(n ² ) time algorithm (LHP), whose expected running time becomes O(n) for two randomly generated permutations, (ii) a practically fast O(n ² ) time algorithm (MNG) using the reverse Monge property, and (iii) an O(n+K) time algorithm (RC), where K is the number of common intervals. It will also be shown that the expected number of common intervals for two random permutations is O(1) . This result gives a reason for the phenomenon that the expected time complexity O(n) of the algorithm LHP is independent of K . Among the proposed algorithms, RC is most desirable from the theoretical point of view; however, it is quite complicated compared with LHP and MNG. Therefore, it is possible that RC is slower than the other two algorithms in some cases. For this reason, computational experiments for various types of problems with up to n=10 ⁶ are conducted. The results indicate that (i) LHP and MNG are much faster than RC for two randomly generated permutations, and (ii) MNG is rather slower than LHP for random inputs; however, there are cases in which LHP requires Ω(n ² ) time, but MNG runs in o(n ² ) time and is faster than both LHP and RC. Received December 21, 1996; revised June 2, 1998.     

Development of Sensor and Control Systems of a Wearable Robot to Walk on a Step

The goal of our study is to develop a system for walking on a step using a wearable robot. Our system consists of (1) sensing of a step from the movement of the walker, (2) detection of the foot placement state related to the step, and (3) generation of gait patterns of climbing and stepping down for the step. In the generation of gait patterns for the step, toe trajectories are generated according to the height of the step to avoid collision of the swinging leg with the step. The hip trajectory is generated by an optimization technique that minimizes the sum of the joint angular jerk of the robot subject to constraints on the hip position and the velocity at toe liftoff. Each joint angle trajectory is calculated from the generated trajectories by means of inverse kinematic equations. We investigated the feasibility of the proposed sensor and control systems for two steps with different heights.     

Thermophysical properties of (U,Y)O2

We prepared polycrystalline pellets of (U,Y)O₂, containing YO_1.5 up to 11 mol.%. We performed indentation tests on the pellets, and evaluated the Young’s modulus and hardness. We measured the heat capacity and the thermal diffusivity, and evaluated the thermal conductivity. We succeeded in evaluating the effect of Y content on the thermophysical properties of (U,Y)O₂. We revealed that the Young’s modulus, hardness, and thermal conductivity of (U,Y)O₂ decreased with increasing the Y content.     

Metastatic Voyage of Ovarian Cancer Cells in Ascites with the Assistance of Various Cellular Components

Epithelial ovarian cancer (EOC) is the most lethal gynecologic malignancy and has a unique metastatic route using ascites, known as the transcoelomic root. However, studies on ascites and contained cellular components have not yet been sufficiently clarified. In this review, we focus on the significance of accumulating ascites, contained EOC cells in the form of spheroids, and interaction with non-malignant host cells. To become resistant against anoikis, EOC cells form spheroids in ascites, where epithelial-to-mesenchymal transition stimulated by transforming growth factor-β can be a key pathway. As spheroids form, EOC cells are also gaining the ability to attach and invade the peritoneum to induce intraperitoneal metastasis, as well as resistance to conventional chemotherapy. Recently, accumulating evidence suggests that EOC spheroids in ascites are composed of not only cancer cells, but also non-malignant cells existing with higher abundance than EOC cells in ascites, including macrophages, mesothelial cells, and lymphocytes. Moreover, hetero-cellular spheroids are demonstrated to form more aggregated spheroids and have higher adhesion ability for the mesothelial layer. To improve the poor prognosis, we need to elucidate the mechanisms of spheroid formation and interactions with non-malignant cells in ascites that are a unique tumor microenvironment for EOC.     

Poxvirus virions: their surface ultrastructure and interaction with the surface membrane of host cells

Virions of vaccinia and orf viruses were examined by ultrahigh-resolution scanning electron microscopy using a non-coating method. Intracellular mature particles of vaccinia virus appeared to be covered with a net and ultrastructurally their surface consists of many fine ridges and globules, while the surfaces of orf virus mature particles recovered from infected cells consist of spirally running protrusions. The ridge-like structures of vaccinia virus were presumed to correspond to surface tubules shown by negative staining of this virus, while the spiral protrusions of orf virus were presumed to correspond to spiral threads having a criss-cross appearance by the same staining. Using scanning electron microscopy in which the samples were prepared by the conventional method, we observed: (i) many virions, i.e. one or two hundreds, or occasionally more reaching about one thousand particles, of the IHD strain of vaccinia virus, (ii) many or a moderate number of virions, i.e. about one hundred or fewer particles, of the 58 strain of cowpox virus and (iii) rather few virions, i.e. several tens or fewer particles, of the Iwate strain of orf virus on the free surface of each cell infected with these viruses. It must be noted that the number of virions detected considerably differed in respective cells examined. Virus budding was frequently observed at the cell surface of monolayer cells infected with vaccinia virus but it was never detected with cowpox or orf virus, indicating a difference in the mechanism of virus release between vaccinia and the other two viruses. When whole cells infected with vaccinia virus were examined by a combination of high-voltage and scanning electron microscopies, virions on the cell surface and those inside the cells were clearly differentiated. All virions on the cell surface had an envelope, and some of the envelopes had a slack and/or one or more bulges.     

Correlations of leucocyte migration activating factor with interleukin-1 alpha, interleukin-1 beta and tumor necrosis factor-alpha in drug allergy

The pathogenic mechanism of drug allergy was investigated by determining leucocyte migration activating factor (LMAF), interleukin-1 alpha (IL 1 alpha) and 1 beta (IL-1 beta), and tumor necrosis factor-alpha (TNF-alpha) levels in 13 patients with suspected hypersensitivity to drugs, following with the relevant agents. LMAF was detected in 10 out of 11 patients in the absence of serum and in 8 out of 9 patients in the presence of serum by means of the leucocyte migration inhibition test (LMIT). The drug-stimulated group had a significantly higher level of IL-1 alpha production than a non-stimulated group, both without serum (p < 0.05) and with serum (p < 0.05), among patients positive for LMAF. Moreover, the LMAF-positive group had a significantly higher level of IL-1 alpha production than the LMIT-negative group, both without serum (p < 0.05) and with serum (p < 0.05). In contrast, the level of IL-1 beta production showed no significant difference, either without or with serum, between drug-stimulated and non-drug-stimulated patients who were positive for LMAF. The production of TNF-alpha in the LMAF-positive group was significantly greater in drug-stimulated patients than in non-drug-stimulated patients, but only in the presence of serum (p < 0.05). However, the level of TNF-alpha production showed no significant difference, either without or with serum, between the LMAF-positive group and the control group. Our findings suggest that IL-1 alpha may be prominently involved in the production of LMAF in allergic reactions to drugs and that the production of TNF-alpha may be enhanced in the presence of serum.     

Determination of internal state variables and constitutive modeling for Type 316 stainless steel

The purpose of this study is to develop an approach for unified constitutive modeling based on experimentally determined back stress and overstress. Back stress and overstress were experimentally determined for Type 316 stainless steel at 600°C, by analyzing the unloading curve for the stress-strain response of cyclic strain tests. The result has indicated that the cyclic strain hardening behavior is mainly caused by hardening in the back stress. A phenomenological unified constitutive model in which the back stress and drag stress are taken as the internal state variables is proposed, and has been shown that this model is able to simulate the cyclic inelastic behavior.     

Budding of fowlpox and pigeonpox viruses at the surface of infected cells

Chick embryo fibroblasts and chorioallantoic membranes infected with fowlpox virus (FWPV) or pigeonpox virus (PPV) were examined by transmission and scanning electron microscopy. Immature virus particles were observed in finely granular areas, i.e. virus factories, of the cytoplasm. These particles had various forms depending on their stages of development. Many tubular structures were also seen in these regions. Mature virus particles with ellipsoidal or brick-shaped forms enclosing electron-dense cores were detected throughout the cytoplasm. Notably, there was a high frequency of virus budding at the cell surface, but only occasional virus wrapping in the cytoplasm. Another remarkable feature of the infected cells was accumulation of many virions just beneath the plasma membrane, indicating that this phenomenon is closely related to virus budding. Based on the observed frequency of budding, this mechanism seems to be the predominant way for FWPV and PPV to exit the cell.