On the computational power of insertion-deletion systems

Gene insertion and deletion are basic phenomena found in DNA processing or RNA editing in molecular biology. The genetic mechanism and development based on these evolutionary transformations have been formulated as a formal system with two operations of insertion and deletion, called insertion-deletion systems (Kari and Thierrin, 1996; Kari et al., 1997).We investigate the generative power of insertion-deletion systems (InsDel systems), and show that the family INS ¹ ₁ DEL ¹ ₁ is equal to the family of recursively enumerable languages. This gives a positive answer to an open problem posed in Kari et al. (1997) where it was conjectured contrary. This revised version was published online in June 2006 with corrections to the Cover Date.     

Complete Mining of Frequent Patterns from Graphs: Mining Graph Data

Basket Analysis, which is a standard method for data mining, derives frequent itemsets from database. However, its mining ability is limited to transaction data consisting of items. In reality, there are many applications where data are described in a more structural way, e.g. chemical compounds and Web browsing history. There are a few approaches that can discover characteristic patterns from graph-structured data in the field of machine learning. However, almost all of them are not suitable for such applications that require a complete search for all frequent subgraph patterns in the data. In this paper, we propose a novel principle and its algorithm that derive the characteristic patterns which frequently appear in graph-structured data. Our algorithm can derive all frequent induced subgraphs from both directed and undirected graph structured data having loops (including self-loops) with labeled or unlabeled nodes and links. Its performance is evaluated through the applications to Web browsing pattern analysis and chemical carcinogenesis analysis.     

Shape from Shading with Interreflections Under a Proximal Light Source: Distortion-Free Copying of an Unfolded Book

We address the problem of recovering the 3D shape of an unfolded book surface from the shading information in a scanner image. This shape-from-shading problem in a real world environment is made difficult by a proximal, moving light source, interreflections, specular reflections, and a nonuniform albedo distribution. Taking all these factors into account, we formulate the problem as an iterative, non-linear optimization problem. Piecewise polynomial models of the 3D shape and albedo distribution are introduced to efficiently and stably compute the shape in practice. Finally, we propose a method to restore the distorted scanner image based on the reconstructed 3D shape. The image restoration experiments for real book surfaces demonstrate that much of the geometric and photometric distortions are removed by our method.     

Software system of the Earth Simulator

The Earth Simulator (ES) is a large scale, distributed memory, parallel computer system consisting of 640 processor nodes (PN) with shared memory vector multi-processors (64GFLOPS/PN, 5120 APs in total, AP: arithmetic processor). All the nodes are connected via a high speed (16GB/s) single-stage crossbar network called the Interconnection Network (IN).

The operating system for the Earth Simulator is based on SUPER-UX, the UNIX operating system for the SX series scientific supercomputers. In order to realize high-performance parallel processing on the highly parallel machine, the operating system is enhanced for scalability.

The Earth Simulator system is managed as a two-level cluster system called the Super Cluster System. In the Super Cluster System, the Earth Simulator system is divided into 40 clusters (16 PNs/cluster). A single controller called Super Cluster Control Station (SCCS) manages all these clusters. This management system provides Single System Image (SSI) operation, management and job control for the large scale multi-node system.

The Job Scheduler (JS) and NQS running on the SCCS control all jobs of the system. They schedule the resources such as processing nodes and files which have not usually been treated as scheduling resources. This allows efficient scheduling of large scale jobs.

The MPI library (MPI/ES) and the HPF compiler (HPF/ES) are available for distributed parallel programming on the Earth Simulator. MPI/ES conforms to the MPI 2.0 standard and is optimized to exploit the hardware features. HPF/ES conforms to the core part of HPF 2.0 and supports some features of the HPF 2.0 approved extensions and HPF/JA 1.0 extensions. HPF/ES suitably handles the 3-level parallelism of the Earth Simulator system, that is, vectorization, shared-memory parallelization, and distributed-memory parallelization. Moreover, HPF/ES extends the language to easily handle irregular problems.     

Application of an ultrahigh-resolution scanning electron microscope (UHS-T1) to biological specimens

In 1985 we developed an ultrahigh-resolution scanning electron microscope with a resolution of 0.5 nm. It is equipped with a field emission gun and an objective lens with a very short focal length. In this study we report a survey of some different preparation techniques and biological specimens using the new scanning electron microscope. Intracellular structures such as cell organelles were observed surprisingly sharper than those observed by ordinary scanning electron microscopes. However, at magnifications over 250,000 X, platinum particles could be discerned as scattered pebbles on the surface of all structures in coated materials. Using an uncoated but conductively stained specimen, we successfully observed ribosomes on a rough endoplasmic reticulum at a direct magnification of 1 million. In these images some protrusions were recognized on the ribosomes. Ferritin and immunoglobulin G were used as samples of biological macromolecules. These samples were observed without metal coating and conductive staining. The ferritin particles appeared as rounded bodies without any substructure on the surface and immunoglobulin G as complexes of three-unit bodies. In the latter the central body might correspond to the Fc fragment and two side ones to Fab fragments. We assume that ultrahigh-resolution scanning electron microscopy is an effective means for observation of the cell fine structures and biological macromolecules. It will open a new research field in biomedicine.     

Elimination of Voids at Interface of <Emphasis Type="Italic">β</Emphasis>-SiC Films and Si Substrate by Laser CVD

Void-free β-SiC films were deposited on Si(001) substrates by laser chemical vapor deposition using hexamethyldisilane (HMDS) as the precursor. The effect of the time of introducing HMDS, i e, the substrate temperature when HMDS introduced (T_in), on the preferred orientation, surface microstructure and void was investigated. The orientation of the deposited SiC films changed from <001> to random to <111> with increasing T_in. The surface showed a layer-by-layer microstructure with voids above T_in ? 773 K, and then transformed into mosaic structure without voids at T_in= 298 K. The mechanism of the elimination of voids was discussed. At T_in =298 K, Si surface can be covered by an ultrathin SiC film, which inhibits the out-diffusion of Si atoms from substrate and prohibites the formation of the voids.     

Advanced HSLA Steels for Automotive Use

Characteristic HSLA steels for automotive use are introduced in which both of precipitation and microstructure is controlled to obtain suitable mechanical properties.For outer panels such as fender,the combination of low yield strength,high tensile strength and deep-drawability were realized by controlling the distribution of NbC and precipitation free zone.The other steel,developed for chassis parts such as lower arm,utilizes extremely fine interphase precipitation to obtain high yield strength and excellent hole expansionability.Both steels have contributed to the reduction of weight in car body.     

Lysophosphatidylinositol Induced Morphological Changes and Stress Fiber Formation through the GPR55-RhoA-ROCK Pathway

We previously reported that lysophosphatidylinositol (LPI) functions as an endogenous agonist of GPR55, a novel cannabinoid receptor. However, the physiological roles of LPI-GPR55 have not yet been elucidated in detail. In the present study, we found that LPI induced morphological changes in GPR55-expressing HEK293 cells. LPI induced the cell rounding of GPR55-expressing HEK293 cells but not of empty-vector-transfected cells. LPI also induced the activation of small GTP-binding protein RhoA and increased stress fiber formation in GPR55-expressing HEK293 cells. The inhibition of RhoA and Rho kinase ROCK by the C3 exoenzyme and the ROCK inhibitor reduced LPI-induced cell rounding and stress fiber formation. These results clearly indicated that the LPI-induced morphological changes and the assembly of the cytoskeletons were mediated through the GPR55-RhoA-ROCK pathway.     

A Gedunin-Type Limonoid, 7-Deacetoxy-7-Oxogedunin,from Andiroba (Carapa guianensis Aublet) Reduced Intracellular Triglyceride Content and Enhanced Autophagy in HepG2 Cells

The seed oil of Carapa guianensis Aublet (Andiroba) has been used in folk medicine for its insect-repelling, anti-inflammatory, and anti-malarial activities. This study aimed to examine the triglyceride (TG) reducing effects of C. guianensis-derived limonoids or other commercially available limonoids in human hepatoblastoma HepG2 cells and evaluate the expression of lipid metabolism or autophagy-related proteins by treatment with 7-deacetoxy-7-oxogedunin (DAOG; 1), a principal limonoid of C. guianensis. The gedunin-type limonoids, such as DAOG (% of control at 20 μM: 70.9 ± 0.9%), gedunin (2, 74.0 ± 1.1%), epoxyazadiradione (4, 73.4 ± 2.0%), 17β-hydroxyazadiradione (5, 79.9 ± 0.6%), 7-deacetoxy-7α-hydroxygedunin (6, 61.0 ± 1.2%), andirolide H (7, 87.4 ± 2.2%), and 6α-hydroxygedunin (8, 84.5 ± 1.1%), were observed to reduce the TG content at lower concentrations than berberine chloride (BBR, a positive control, 84.1 ± 0.3% at 30 μM) in HepG2 cells pretreated with high glucose and oleic acid. Andirobin-, obacunol-, nimbin-, and salannin-type limonoids showed no effect on the intracellular TG content in HepG2 cells. The TG-reducing effect of DAOG was attenuated by the concomitant use of compound C (dorsomorphin), an AMPK inhibitor. Further investigation on the detailed mechanism of action of DAOG at non-cytotoxic concentrations revealed that the expressions of autophagy-related proteins, LC3 and p62, were upregulated by treatment with DAOG. These findings suggested that gedunin-type limonoids from Andiroba could ameliorate fatty liver, and that the action of DAOG in particular is mediated by autophagy.