The effects of amino-acid mutations on specific interactions between urokinase-type plasminogen activator and its receptor: Ab initio molecular orbital calculations

During cancer invasion, the binding of urokinase-type plasminogen activator (uPA) to its receptor (uPAR) on the surface of a cancer cell is considered a trigger for invasion. Here, we present a stable structure of the solvated complex formed between uPA and uPAR (uPA-uPAR) and investigate the specific interactions between uPA and uPAR by ab initio fragment molecular orbital (FMO) calculations. The result indicates that the electrostatic interactions between the charged amino acid residues existing in both uPA and uPAR make a large contribution to the binding between uPA and uPAR. In particular, Lys23, Lys46, Lys98 and Lys61 of uPA are found to have strong attractive interactions with uPAR. To elucidate the effect of these residues on the interactions between uPA and uPAR, we substituted each of them with the uncharged amino acid Leu and investigated the interactions between the mutated uPA and wild-type uPAR. The interaction energies indicate that Lys46 and Lys98, which bind uPA to the rim of the central ligand-binding cavity of uPAR, make greater contributions to the binding between uPA and uPAR than Lys23, which is positioned at the bottom of the ligand-binding cavity of uPAR. The effect of hydrating water molecules located between uPA and uPAR is also investigated to be significant for the specific interactions between uPA and uPAR. These results are expected to be informative for developing new peptide antagonists that block the binding of uPA to uPAR.     

A control method with pheromone information for a transport system

Since the control methods of a transport system between processing machines are specialized for each layout of the system, it is difficult to design prompt schedules and control logic for new complicated systems, especially in cases of machine faults or restructuring the system to modify the layout. In this article, we describe a multiagent transport control system which utilizes pheromone information. Each element of the system acts as an agent and estimates the appropriate path and time to drive out the products using information obtained by communication with other elements as well as pheromone information deposited on the tracks of the products.     

Peroxiredoxin 2 as a chemotherapy responsiveness biomarker candidate in osteosarcoma revealed by proteomics

Purpose : We aimed to identify novel chemotherapy responsiveness biomarkers for osteosarcoma (OS) by investigating the global protein expression profile of 12 biopsy samples from OS patients. Experimental design : Six patients were classified as good responders and six as poor responders, according to the Huvos grading system. The protein expression profiles obtained by 2‐D DIGE consisted of 2250 protein spots. Results : Among them, we identified 55 protein spots whose intensity was significantly different (Bonferroni adjusted p‐value<0.01) between the two patient groups. Mass spectrometric protein identification demonstrated that the 55 spots corresponded to 38 distinct gene products including peroxiredoxin 2 (PRDX 2). Use of a specific antibody against PRDX 2 confirmed the differential expression of PRDX 2 between good and poor responders, while PRDX 2 levels as measured by Western blotting correlated highly with their corresponding 2‐D DIGE values. The predictive value of PRDX 2 expression was further confirmed by examining an additional four OS cases using Western blotting. Conclusions and clinical relevance : These results establish PRDX 2 as a candidate for chemotherapy responsiveness marker in OS. Measuring PRDX 2 in biopsy samples before treatment may contribute to more effective management of OS.     

Control of three-link underactuated manipulators using a switching method of fuzzy energy regions

In general, manipulators used for industry and in academic laboratories have actuators to drive each joint. On the other hand, underactuated manipulators handled by our research have some passive or free joints without actuators and brakes. We recently developed a switching method of fuzzy energy regions to control such manipulators. In such a method, it is necessary to design parameters related to energy regions and the gains of some partly stable controllers based on the computed torque method. Here, the switching method is applied for a three-link underactuated manipulator. We optimize such design parameters related to fuzzy energy regions by a genetic algorithm. The effectiveness of the present method is illustrated with some simulations. This work was presented in part at the 12th International Symposium on Artificial Life and Robotics, Oita, Japan, January 25–27, 2007     

Theory of ion mobility in liquid3He

An ion interacting with quasiparticles in liquid³He is treated theoretically by summing most divergent terms in perturbation series of the self-energy of the ion and the vertex part. The ion Green's function is renormalized by a factorZ(T), and the vertex part byZ(T) ^?1, where \({\text{Z(T)}} = {\text{(T/T}}_F {\text{)}}^{{\text{2V}}_{{\text{0}}^{\rho ^{\text{2}} } }^{\text{2}} } \) , forT ₀?T?T _F. Here,T ₀=(m/M)T _F, withm the³He mass andM the ion mass, and \({\text{V}}_{0^\rho } \) is the strength of the interaction. The factor explains the weak temperature dependence of the mobility around the minimum atT ₀; we also discuss its effect on the behavior of the mobility in³He-B nearT _c.     

Long-term availability prediction for groups of volunteer resources

Volunteer computing uses the free resources in Internet and Intranet environments for large-scale computation and storage. Currently, 70 applications use over 12 PetaFLOPS of computing power from such platforms. However, these platforms are currently limited to embarrassingly parallel applications. In an effort to broaden the set of applications that can leverage volunteer computing, we focus on the problem of predicting if a group of resources will be continuously available for a relatively long time period. Ensuring the collective availability of volunteer resources is challenging due to their inherent volatility and autonomy. Collective availability is important for enabling parallel applications and workflows on volunteer computing platforms. We evaluate our predictive methods using real availability traces gathered from hundreds of thousands of hosts from the SETI@home volunteer computing project. We show our prediction methods can guarantee reliably the availability of collections of volunteer resources. We show that this is particularly useful for service deployments over volunteer computing environments.     

Magnetic Correlation in BETS2(Cl2TCNQ)

We carried out⁷⁷Se NMR measurements on BETS₂(Cl₂TCNQ) under pressure in order to investigate the magnetic properties of the insulating state which appears above 0.6 GPa. The relaxation rate 1/T₁ at 0.7 GPa shows small peak-like anomaly at 20 K, indicating a spin density wave transition as observed in BETS₂(Br₂TCNQ).     

Plasma etching of high-k and metal gate materials

Etching characteristics of high-k dielectric materials (HfO₂) and metal electrode materials (Pt, TaN) have been studied in high-density chlorine-containing plasmas at pressures around 10 mTorr. The etching of HfO₂ was performed in BCl₃ without rf biasing, giving an etch rate of about 5 nm/min with a high selectivity of >10 over Si and SiO₂. The etching of Pt and TaN was performed in Ar/O₂ with high rf biasing and in Ar/Cl₂ with low rf biasing, respectively, giving a Pt etch rate of about several tens nm/min and a TaN etch rate of about 200 nm/min with a high selectivity of >8 over HfO₂ and SiO₂. The etched profiles were outwardly tapered for Pt, owing to the redeposition of etch or sputter products on feature sidewalls, while the TaN profiles were almost anisotropic, probably owing to the ion-enhanced etching that occurred.     

Quantum Bit-commitment for small storage based on quantum one-way permutations

We propose a quantum bit-commitment scheme based on quantum one-way permutations with the unconditionally binding and computationally concealing property. Our scheme reduces exponentially the number of bits which the receiver needs to store until, the opening phase compared with the classical counterpart. Keisuke Tanaka, Ph.D.: He is Assistant Professor of Department of Mathematical and Computing Sciences at Tokyo Institute of Technology. He received his B.S. from Yamanashi University in 1992 and his M.S. and Ph.D. from Japan Advanced Institute of Science and Technology in 1994 and 1997, respectively. For each degree, he majored in computer science. Before joining Tokyo Institute of Technology, he was Research Engineer at NTT Information Sharing Platform Laboratories. His research interests are cryptography, quantum computation, circuit complexity, and the design and analysis of algorithms.