Prediction of peptide binding to major histocompatibility complex class II molecules through use of boosted fuzzy classifier with SWEEP operator method

To treat autoimmune diseases, it is important to identify which peptides bind to major histocompatibility complex (MHC) class II molecules (HLA-DRs). Predicting the peptides that bind to MHC class II molecules can effectively reduce the number of experiments required for identifying helper T cell epitopes. In our previous study, we applied fuzzy neural networks (FNNs) to solve this problem. However, an FNN requires a long calculation time and a large number of peptides; this means performing several experiments. In this study, we applied a boosted fuzzy classifier with the SWEEP operator method (BFCS) to solve this problem. For comparison, two other conventional modeling methods, namely, support vector machine and FNN combined with the SWEEP operator method (FNN-SWEEP) instead of using solely an FNN, were employed. Compared with FNN, FNN-SWEEP is extremely fast and has an almost identical prediction accuracy. The model constructed by BFCS showed an accuracy approximately 5%-10% higher than that constructed by FNN-SWEEP. In addition, BFCS was 30,000-120,000 times faster than FNN-SWEEP. This result suggests that BFCS has the potential to function as a new method of predicting peptides that bind to various protein receptors.     

Pretreatment of polyamide monofilament with hydrochloric acid improves sensitivity of three-dimensional microarray, Bio-Strand

A single-nucleotide-polymorphism-typing method using a novel three-dimensional DNA microarray, Bio-Strand, is promising because it is rapid, inexpensive and easily automated. It has been developed with the intent to overcome the drawbacks of conventional DNA microarrays, which use flat surfaces and impermeable materials such as glass slides; Bio-Strand as a novel DNA microarray, with its permeability, has a significantly improved stability compared with conventional DNA microarrays that use impermeable materials. In this study, we have developed a simple method of pretreating a polyamide monofilament to increase its surface area and to make it permeable, which makes Bio-Strand more sensitive and stable, allowing it to be adapted for clinical diagnostic applications. The fluorescence signal obtained with a nylon 6 monofilament pretreated under optimal conditions (hydrolysis by 5 M HCl/ethanol followed by washing with 50% ethanol and 100% ethanol) was significantly stronger than that obtained with an untreated monofilament.     

Use of dynamic electronic speckle pattern interferometry with the Hilbert transform method to investigate thermal expansion of a joint material

A dynamic electronic speckle pattern interferometry method is applied to investigate thermal expansion of a joint material (ceramic-stainless steel) as a practical industrial object. The speckle interference signal is considered in the temporal domain and the phase is analyzed by the Hilbert transform method. Errors caused by the bias and modulation variations over the phase values are first examined by numerical simulation. Two experiments are performed with in-plane and out-of-plane sensitive systems to study the 3D deformation field thoroughly. The deformation field showed clearly the difference between the thermal expansions of the stainless steel and ceramic. It was also revealed that the boundary of materials and its vicinity suffer very large thermal strain due to the significantly large difference in the linear coefficient of thermal expansions.     

Measurement of concrete strength using the emission intensity ratio between Ca(II) 396.8 nm and Ca(I) 422.6 nm in a Nd:YAG laser-induced plasma

An experiment to investigate the potential of a laser-induced plasma method for determining concrete compressive strength was conducted by focusing a Nd:YAG laser on concrete samples with different degrees of compressive strength. This technique was developed in light of the role of the shock wave in the generation of a laser-induced plasma. It was found that the speed of the shock front depends on the hardness of the sample. It was also found that a positive relationship exists between the speed of the shock front and the ionization rate of the ablated atoms. Hence, the ratio of the intensity between the Ca(II) 396.8 nm and Ca(I) 422.6 nm emission lines detected from the laser-induced plasma can be used to examine the hardness of the material. In fact, it was observed that the ratio changes with respect to the change in the concrete compressive strength. The findings also show that the ratio increases with time after the cement is mixed with water.     

Development of a quantitative real-time PCR method to enumerate total bacterial counts in ready-to-eat fruits and vegetables

A newly developed real-time PCR assay rapidly quantifies the total bacterial numbers in contaminated ready-to-eat vegetables and fruits compared with the standard plate count method. Primers targeting the rpoB gene, which encodes for the beta subunit of the bacterial RNA polymerase and which is common to most bacterial species, was used instead of the 16S rRNA gene, which has multiple copies and varies among bacterial species. A primer pair specific for rpoB was confirmed to amplify rpoB in a wide range of bacterial species after we assessed 49 strains isolated from five kinds of fruits and vegetables. We purchased fruits and vegetables from retail shops and enumerated the bacteria associated with them by use of real-time PCR and compared this to the number found by the culture method. We found a high correlation between the threshold PCR cycle number when compared with the plate count culture number. The real-time PCR assay developed in this study can enumerate the dominant bacterial species in ready-to-eat fruits and vegetables.     

Ultramultiple roundtrips of surface acoustic wave on sphere realizing innovation of gas sensors

A thin beam of wave usually diverges due to diffraction, which is a limitation of any device using such waves. However, a surface acoustic wave (SAW) on a sphere with an appropriate aperture does not diverge but is naturally collimated, realizing ultramultiple roundtrips along an equator of the sphere. This effect is caused by the balance between diffraction and focusing on a spherical surface, and it enables realization of high-performance ball SAW sensors. The advantage of ball SAW is most fully appreciated when applied to a very thin sensitive film for which the multiple-roundtrip enhances the sensitivity, but the attenuation loss is not very large. It is exemplified in a hydrogen gas sensor that realizes a wide sensing range of 10 ppm to 100% for the first time, and realizes relatively fast response time of 20 s without heating the sensitive film.     

Index characterization of differential–algebraic equations in hybrid analysis for circuit simulation

Modern modeling approaches in circuit simulation naturally lead to differential–algebraic equations (DAEs). The index of a DAE is a measure of the degree of numerical difficulty. In general, the higher the index, the more difficult it is to solve the DAE. The modified nodal analysis (MNA) is known to yield a DAE with index at most two in a wide class of nonlinear time‐varying electric circuits. In this paper, we consider a broader class of analysis method called the hybrid analysis. For linear time‐invariant RLC circuits, we prove that the index of the DAE arising from the hybrid analysis is at most one, and give a structural characterization for the index of a DAE in the hybrid analysis. This yields an efficient algorithm for finding an optimal hybrid analysis in which the index of the DAE to be solved attains zero. Finally, for linear time‐invariant electric circuits that may contain dependent sources, we prove that the optimal hybrid analysis by no means results in a higher index DAE than MNA. Copyright © 2008 John Wiley & Sons, Ltd.     

Study on absorption/desorption characteristics of a metal hydride tank for boil-off gas from liquid hydrogen

We have been performing research on the Totalized Hydrogen Energy Utilization System (THEUS) which has applications to commercial buildings and a planned added function of supplying energy to stations for hydrogen and electric vehicles. In that case we will utilize liquid hydrogen transported from a hydrogen station and all Boil-Off Gas (BOG) will be recovered in THEUS’s metal hydride tanks. It is known that BOG is chiefly composed of para-hydrogen, which has different thermo-physical properties from normal hydrogen. It has been reported that some metal hydride alloys work as a catalyst to accelerate the para-ortho conversion and the conversion proceeds relatively fast in the case of La–Ni₅. The conversion is considered to be an endothermic reaction. A misch metal (Mm)-Ni₅ metal hydride alloy, which contained La and Ni, was used in our THEUS metal hydride tank. To examine the effect of the para-ortho conversion on the THEUS operation, we investigated the absorption/desorption characteristics of the metal hydride tank with BOG. We confirmed that the effect of the heat of conversion was very small and BOG could be treated as normal hydrogen for practical application.