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Search Results: 1 - 10 of 254 matches for " Masamichi Ishizaka "
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Protein complex prediction via verifying and reconstructing the topology of domain-domain interactions
Yosuke Ozawa, Rintaro Saito, Shigeo Fujimori, Hisashi Kashima, Masamichi Ishizaka, Hiroshi Yanagawa, Etsuko Miyamoto-Sato, Masaru Tomita
BMC Bioinformatics , 2010, DOI: 10.1186/1471-2105-11-350
Abstract: Here, we introduce a combinatorial approach for prediction of protein complexes focusing not only on determining member proteins in complexes but also on the DDI/PPI organization of the complexes. Our method analyzes complex candidates predicted by the existing methods. It searches for optimal combinations of domain-domain interactions in the candidates based on an assumption that the proteins in a candidate can form a true protein complex if each of the domains is used by a single protein interaction. This optimization problem was mathematically formulated and solved using binary integer linear programming. By using publicly available sets of yeast protein-protein interactions and domain-domain interactions, we succeeded in extracting protein complex candidates with an accuracy that is twice the average accuracy of the existing methods, MCL, MCODE, or clustering coefficient. Although the configuring parameters for each algorithm resulted in slightly improved precisions, our method always showed better precision for most values of the parameters.Our combinatorial approach can provide better accuracy for prediction of protein complexes and also enables to identify both direct PPIs and DDIs that mediate them in complexes.Recently developed high-throughput methods such as yeast two-hybrid or mass spectrometry to obtain protein-protein interactions (PPIs) have provided a global view of the interaction network [1-5]. As a PPI network grows, it becomes increasingly important to detect functional modules for understanding cellular organization and its dynamics [6]. Protein complexes are clusters of multiple proteins, and they often play a crucial part in basal cellular mechanism. Therefore, computational methods to predict protein complexes are becoming important.There are four steps in characterizing a protein complex [7]. The first step is to identify its member proteins. The second step is to determine its topology by identifying pairs of proteins which have direct inte
Clusters and pivots for evaluating a large numberof alternatives in AHP
Ishizaka, Alessio;
Pesquisa Operacional , 2012, DOI: 10.1590/S0101-74382012005000002
Abstract: ahp has been successful in many cases but it has a major limitation: a larger number of alternatives requires a high number of judgements in the comparison matrices. in order to reduce this problem,we present a method with clusters and pivots. this method also helps with a further four problems of the analytic hierarchy process. it enlarges the comparison scale, facilitates the construction of a consistent or near consistent matrix, eliminates the problem of the choice of the priorities derivation method and allows the use of incomparable alternatives.
Directable Needle Guide: Efficacy for Image-Guided Percutaneous Interventions
Hiroshi Ishizaka
ISRN Radiology , 2013, DOI: 10.5402/2013/516941
Abstract: Diagnostic and therapeutic image-guided percutaneous interventions have become increasingly important in the clinical management of various conditions. Though precise needle placement via a safe route is essential for successful percutaneous interventions, it is often difficult in cases of deeply situated, small lesions. The present paper describes the efficacy of the directable needle guide (DNG), which allows manipulation of the direction of a fine needle within organs. The DNG was used in patients for needle biopsy of hepatic ( ) and splenic ( ) lesions and for percutaneous ethanol injection therapy for liver tumors ( ) under sonographic or computed tomography guidance. The DNG enabled the direction of a 21- or 22-gauge needle to be successfully changed during needle advancement in all cases, allowing adjustment of the location of the needle tip or needle access root to avoid vessels, the gallbladder, and the lungs. We conclude that DNG increases the safety and ease of percutaneous interventions. 1. Introduction Image-guided percutaneous interventions with a fine needle are used for various clinical purposes, including biopsies, antitumor therapy with ethanol injection, laser thermal ablation, gene-technology implants, and nerve blocks [1–4]. Though precise needle placement passing through a safe root is essential for percutaneous interventions, it is often difficult due to needle deflection and patients’ respiratory or postural variations during the procedure and also because of intervening vital structures on the root. When a thin beveled needle is inserted into any organ, the tip of the needle has a tendency to curve toward the side when advancing, due to its flexibility. However, when a beveled needle is inserted with a twisting motion, it advances in a straight path. This phenomenon was applied to create a directable needle guide (DNG) that could be used to steer a needle within organs. The present paper describes the utility of the DNG in our clinical experience. 2. Subjects and Methods The DNG was used in patients undergoing both needle biopsy of hepatic ( ) or splenic ( ) lesions and percutaneous ethanol injection therapy for liver tumors ( ). Sonography and computed tomography (CT) images were used for imaging guidance in 43 and 17 lesions, respectively. The DNG (0.018 inches in diameter; 250?mm long) with a flattened segment (0.010 inches in thickness) on the distal portion of the beveled side of the tip (Leadway, Hakko, Tokyo, Japan, a prototype not commercially available at present) (Figures 1(a) and 1(b)) was used to direct the needle
Modes of Retrotransposition of Long Interspersed Element-1 by Environmental Factors
Yukihito Ishizaka
Frontiers in Microbiology , 2012, DOI: 10.3389/fmicb.2012.00191
Abstract: Approximately 42% of the human genome is composed of endogenous retroelements, and the major retroelement component, long interspersed element-1 (L1), comprises ~17% of the total genome. A single human cell has more than 5 × 105 copies of L1, 80~100 copies of which are competent for retrotransposition (RTP). Notably, L1 can induce RTP of other retroelements, such as Alu and SVA, and is believed to function as a driving force of evolution. Although L1-RTP during early embryogenesis has been highlighted in the literature, recent observations revealed that L1-RTP also occurs in somatic cells. However, little is known about how environmental factors induce L1-RTP. Here, we summarize our current understanding of the mechanism of L1-RTP in somatic cells. We have focused on the mode of L1-RTP that is dependent on the basic helix–loop–helix/per–arnt–sim (bHLH/PAS) family of transcription factors. Along with the proposed function of bHLH/PAS proteins in environmental adaptation, we discuss the functional linking of L1-RTP and bHLH/PAS proteins for environmental adaptation and evolution.
Binegativity and geometry of entangled states in two qubits
Satoshi Ishizaka
Physics , 2003, DOI: 10.1103/PhysRevA.69.020301
Abstract: We prove that the binegativity is always positive for any two-qubit state. As a result, as suggested by the previous works, the asymptotic relative entropy of entanglement in two qubits does not exceed the Rains bound, and the PPT-entanglement cost for any two-qubit state is determined to be the logarithmic negativity of the state. Further, the proof reveals some geometrical characteristics of the entangled states, and shows that the partial transposition can give another separable approximation of the entangled state in two qubits.
Bound entanglement provides convertibility of pure entangled states
Satoshi Ishizaka
Physics , 2004, DOI: 10.1103/PhysRevLett.93.190501
Abstract: I show that two distant parties can transform pure entangled states to arbitrary pure states by stochastic local operations and classical communication (SLOCC) at the single copy level, if they share bound entangled states. This is the effect of bound entanglement since this entanglement processing is impossible by SLOCC alone. Similar effect of bound entanglement occurs in three qubits where two incomparable entangled states of GHZ and W can be inter-converted. In general multipartite settings composed by $N$ distant parties, all $N$-partite pure entangled states are inter-convertible by SLOCC with the assistance of bound entangled states with positive partial transpose.
Analytical formula connecting entangled state and the closest disentangled state
Satoshi Ishizaka
Physics , 2003, DOI: 10.1103/PhysRevA.67.060301
Abstract: The separable state closest to a given entangled state in the relative entropy measure is called the closest disentangled state. We provide an analytical formula connecting the entangled state and the closest disentangled state in two qubits. Using this formula, when any disentangled state ($\sigma$) located at the entangle-disentangle boundary is given, entangled states to which $\sigma$ is closest can be obtained analytically. Further, this formula naturally defines the direction normal to the boundary surface. The direction is uniquely determined by $\sigma$ in almost all cases.
Quantum channel locally interacting with environment
Satoshi Ishizaka
Physics , 2000, DOI: 10.1103/PhysRevA.63.034301
Abstract: The quantum channel subject to local interaction with two-level environment is studied. The two-level environment is regarded as a quantum bit (qubit) as well as a pair of particles owned by Alice and Bob. The amount of entanglement initially shared by Alice and Bob is distributed among these three qubits due to the interaction. In this model, we show that the singlet fraction of the decohered quantum channel is uniquely determined by the distributed entanglement. When the decohered quantum channel is used under the standard teleportation scheme, the optimal teleportation fidelity is well understood by considering the remaining entanglement between environment and transmitted state.
Dilemma that cannot be resolved by biased quantum coin flipping
Satoshi Ishizaka
Physics , 2007, DOI: 10.1103/PhysRevLett.100.070501
Abstract: We show that a biased quantum coin flip (QCF) cannot provide the performance of a black-boxed biased coin flip, if it satisfies some fidelity conditions. Although such a QCF satisfies the security conditions of a biased coin flip, it does not realize the ideal functionality, and therefore, does not fulfill the demands for universally composable security. Moreover, through a comparison within a small restricted bias range, we show that an arbitrary QCF is distinguishable from a black-boxed coin flip unless it is unbiased on both sides of parties against insensitive cheating. We also point out the difficulty in developing cheat-sensitive quantum bit commitment in terms of the uncomposability of a QCF.
Strong monotonicity in mixed-state entanglement manipulation
Satoshi Ishizaka
Physics , 2006, DOI: 10.1103/PhysRevA.73.062308
Abstract: A strong entanglement monotone, which never increases under local operations and classical communications (LOCC), restricts quantum entanglement manipulation more strongly than the usual monotone since the usual one does not increase on average under LOCC. We propose new strong monotones in mixed-state entanglement manipulation under LOCC. These are related to the decomposability and 1-positivity of an operator constructed from a quantum state, and reveal geometrical characteristics of entangled states. These are lower bounded by the negativity or generalized robustness of entanglement.
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