A probabilistic simulator for population dynamics of quasispecies

We constructed a probabilistic simulator that allows all the events in population dynamics such as death, birth, mutation, and suppression/stimulation to be described by probabilistic rules. The simulator also facilitates a lattice used for expressing distribution and diversity (number of distinct strains) of quasispecies. The simulator is used to investigate the diversity threshold in HIV and T-cell interaction. This work was presented in part at the 13th International Symposium on Artificial Life and Robotics, Oita, Japan, January 31–February 2, 2008     

Virtual Fiber Configuration for Dynamic Lightpath Establishment in Large-scaled Optical Networks

Recently, progress has been made in the Generalized Multi-Protocol Label Switching (GMPLS) and Automatic Switched Optical Networks (ASON) standardizations. These technologies realize construction of large-scaled optical networks, interconnections among single-domain Wavelength Division Multiplexing (WDM) networks, and direct communication over multi-domain WDM networks. Meanwhile, it is known that the topology of the Internet exhibits the power-law attribute. Since the topology of the Internet, which is constructed by interconnecting ASs, exhibits the power-law, there is a possibility that large-scale WDM networks, which are constructed by interconnecting WDM networks, will also exhibit the power-law attribute. One of the structural properties of a topology that adheres to the power-law is that most nodes have just a few links, although some have a tremendous number of them. Another property is that the average distance between nodes is smaller than in a mesh-like network. A natural question is how such a structural property performs in WDM networks. In this paper, we first investigate the property of the power-law attribute of physical topologies for WDM networks. We compare the performance of WDM networks with mesh-like and power-law topologies, and show that links connected to high-degree nodes are bottlenecks in power-law topologies. To relax this, we introduce a concept of virtual fiber, which consists of two or more fibers, and propose its configuration method to utilize wavelength resources more effectively. We compare performances of power-law networks with and without our method by computer simulations. The results show that our method reduces the blocking probabilities by more than one order of magnitude.     

The integral experiment on beryllium with D-T neutrons for verification of tritium breeding

A clean benchmark experiment on beryllium was performed with D-T neutrons at the FNS facility of the Japan Atomic Energy Agency. The main objective was to verify the integral data related to the tritium production on lithium isotopes. Tritium production rates, as well as activation reaction rates were measured inside the beryllium assembly that was shaped as a pseudo-cylindrical slab with an area-equivalent diameter of 628 mm and a thickness of 355 mm. Experimental results were analyzed with a three-dimensional Monte Carlo transport code MCNP-4C and FENDL/MC-2.0, JENDL-3.2/3.3 neutron transport libraries. Evaluation of reaction rates was based on the cross section data taken from the JENDL Dosimetry File and ENDF B-VI data libraries. Analysis shows that all calculation combinations (transport and activation cross section libraries) used for evaluation of reaction rates give data that is agreeable with measured values within 10%.     

Characteristics and classification of high-current fault arcs on distribution systems

When a fault occurs on transmission or distribution systems due to lightning or overvoltage, often an arc discharge occurs at the fault point. The arc discharge, which is caused by a fault current, has a high current, high temperature, strong light emission, etc., thus it sometimes causes heavy damages to electric power equipment. The arc discharge is influenced by the conditions around the arcs, i.e., gas, insulation materials, gap length, weather, etc. Also, the arc voltage along the arc column indicates the characteristics of the arc. If the voltage waveforms of the arcs caused by the fault on transmission or distribution systems are classified, it is possible to find the location and the equipment where the fault occurred. In this paper, the arc voltage data in 6-kV class XLPE cables and 6-kV class overhead lines are analyzed and an artificial neural network method is applied to classify the arc voltage waveforms. The results obtained from the six artificial neural networks developed show that the artificial neural network method is effective for classification of arc voltage waveforms if adequate input parameters are selected.     

Distance metric learning for graph structured data

Machine Learning - Graphs are versatile tools for representing structured data. As a result, a variety of machine learning methods have been studied for graph data analysis. Although many such...     

Ion exchange of intercalation compounds from WOP2O7 and intercalation ofn-alkylamines

Ion exchange of Na _x WOP₂O₇ ·nH₂O (x 1.4) prepared from WOP₂O₇ was attempted, using alkaline and alkaline earth ions. The degree of exchange was observed to be >50% at 90° C except for Mg²⁺. The basal spacing of ion-exchanged materials for the hydrated phase were dependent on the number of water molecules in the interlayer spaces, while those for the dehydrated phase increased with the size of ions in the interlayer spaces. The network of water molecules linked by the hydrogen bond in the interlayer spaces seems to determine the basal spacing. By the ion-exchange reaction,n-alkylammonium ions were intercalated into the interlayer spaces of Na _x WOP₂O₇ ·nH₂O (x 1.4) and Sn _x H _y WOP₂O₇ ·nH₂O (2x +y 0.5). In spite of the difference in the charge density of the host layer, a similar arrangement of alkyl chains in the interlayer spaces resulted, and neutral amines were considered to be intercalated as well as ammonium ions. Direct reaction ofn-alkylamine with WOP₂O₇ produced an intercalation compound without reduction of tungsten. The arrangement of the amines in the interlayer spaces is similar to that supposed to the ion-exchanged derivatives when heated at 140° Cin vacuo.     

Hydroxyapatite crystal growth on calcium hydroxyapatite ceramics

Calcium hydroxyapatite (Ca-HAP) ceramics containing tricalcium phosphate (TCP) were soaked in three solutions: phosphate buffer, tris buffer, and simulated body fluid (SBF). Petal-like crystals of Ca-HAP were deposited on the Ca-HAP ceramics when (i) Ca-HAP ceramics contained -TCP, (ii) the soaking solution contained phosphate ion and (iii) the pH of soaking solution was higher than 7.3. These conditions facilitate the presence of HPO ₄ ^2– and Ca²⁺ ions, the latter from dissolution of -TCP. A well-defined X-ray diffraction pattern for the deposited Ca-HAP crystals indicates preferred growth of {002} planes. Slower crystal growth of Ca-HAP was found for SBF (pH=7.5) than in the phosphate buffer, due possibly to the lower phosphate ion content in SBF.     

Stromal CCL5 Promotes Breast Cancer Progression by Interacting with CCR3 in Tumor Cells

Chemokines secreted from stromal cells have important roles for interactions with carcinoma cells and regulating tumor progression. C-C motif chemokine ligand (CCL) 5 is expressed in various types of stromal cells and associated with tumor progression, interacting with C-C chemokine receptor (CCR) 1, 3 and 5 expressed in tumor cells. However, the expression on CCL5 and its receptors have so far not been well-examined in human breast carcinoma tissues. We therefore immunolocalized CCL5, as well as CCR1, 3 and 5, in 111 human breast carcinoma tissues and correlated them with clinicopathological characteristics. Stromal CCL5 immunoreactivity was significantly correlated with the aggressive phenotype of breast carcinomas. Importantly, this tendency was observed especially in the CCR3-positive group. Furthermore, the risk of recurrence was significantly higher in the patients with breast carcinomas positive for CCL5 and CCR3 but negative for CCR1 and CCR5, as compared with other patients. In summary, the CCL5-CCR3 axis might contribute to a worse prognosis in breast cancer patients, and these findings will contribute to a better understanding of the significance of the CCL5/CCRs axis in breast carcinoma microenvironment.     

Thermodynamic Regularities in Perovskite and K2NiF4 Compounds

It has been found that the enthalpy of formation of perovskite compounds, Δ_fH° (ABO₃, B = transition metais), from binary oxides can be well characterized in terms the tolerance factor, t≡(r_A+ r_o)√2 (r_B+ r_o), where r_A and r_B are the radii of A-site ions with 12-coordination and B-site ions with 6-coordination, respectively, and Δ_fH°=−168 + 270(1 − t) kJ·mol⁻¹ for A^IB^VO₃, Δ_fH°=−125 + 1000(1 − t) kJ·mol⁻¹ for A^IIB^IVO₃, and Δ_fH°=− 90 + 720(1 − t) kJ·mol⁻¹ for A^IIIB^IIIO₃. Although the thermodynamic data of K₂NiF₄ compounds are not extensive, a similar regularity can be found when use is made of the radii of A-site ions with 9-coordination for the K₂NiF₄ compounds. These correlations will be quite useful in predicting.     

A Modified Nonparametric Prewhitened Covariance Estimator

Abstract. This paper proposes a fully modified version of the spectral matrix estimator (and the long‐run variance estimator as a special case) proposed originally by Xiao and Linton [Journal of Time Series Analysis (2002) Vol. 23, pp. 215–250], and derives its asymptotic results. A striking feature of the modified spectral matrix estimator is to achieve the convergence rate of O(T ^?8/9) in the mean squared error (MSE), which is usually achieved under the fourth‐order spectral window. However, this estimator does not sacrifice the positive definiteness of the resulting estimate for the rate improvement; it is Hermitian and positive definite in finite samples by construction. The faster convergence rate is established by a multiplicative bias correction of the crude spectral estimator under the second‐order spectral window. The approximations to some sensible definitions of the MSE of the estimator and the bandwidths that minimize the asymptotic MSEs are also derived. Monte Carlo results indicate that for a wide variety of processes the modified spectral matrix estimator reduces the bias without inflating the variance and thus improves the MSE, compared with the crude, bias‐uncorrected estimator.