Metal-to-semiconductor transition in squashed armchair carbon nanotubes

We investigate electronic transport properties of the squashed armchair carbon nanotubes, using tight-binding molecular dynamics and Green's function method. We demonstrate a metal-to-semiconductor transistion while squashing the nanotubes and a general mechanism for such transistion. It is the distinction of the two sublattices in the nanotube that opens an energy gap near the Fermi energy. We show that the transition has to be achieved by a combined effect of breaking of mirror symmetry and bond formation between the flattened faces in the squashed nanotubes.Comment: 4 papges, 4 figures, to appear in Phys. Rev. Let

Application of TensorFlow to recognition of visualized results of fragment molecular orbital (FMO) calculations

We have applied Google's TensorFlow deep learning toolkit to recognize the visualized results of the fragment molecular orbital (FMO) calculations. Typical protein structures of alpha-helix and beta-sheet provide some characteristic patterns in the two-dimensional map of inter-fragment interaction energy termed as IFIE-map (Kurisaki et al., Biophys. Chem. 130 (2007) 1). A thousand of IFIE-map images with labels depending on the existences of alpha-helix and beta-sheet were prepared by employing 18 proteins and 3 non-protein systems and were subjected to training by TensorFlow. Finally, TensorFlow was fed with new data to test its ability to recognize the structural patterns. We found that the characteristic structures in test IFIE-map images were judged successfully. Thus the ability of pattern recognition of IFIE-map by TensorFlow was proven.Comment: 26 pages, 3 figures, 4 table

Copy number loss of (src homology 2 domain containing)-transforming protein 2 (SHC2) gene: discordant loss in monozygotic twins and frequent loss in patients with multiple system atrophy

<p>Abstract</p> <p>Background</p> <p>Multiple system atrophy (MSA) is a sporadic disease. Its pathogenesis may involve multiple genetic and nongenetic factors, but its etiology remains largely unknown. We hypothesized that the genome of a patient with MSA would demonstrate copy number variations (CNVs) in the genes or genomic regions of interest. To identify genomic alterations increasing the risk for MSA, we examined a pair of monozygotic (MZ) twins discordant for the MSA phenotype and 32 patients with MSA.</p> <p>Results</p> <p>By whole-genome CNV analysis using a combination of CNV beadchip and comparative genomic hybridization (CGH)-based CNV microarrays followed by region-targeting, high-density, custom-made oligonucleotide tiling microarray analysis, we identified disease-specific copy number loss of the (Src homology 2 domain containing)-transforming protein 2 (<it>SHC2</it>) gene in the distal 350-kb subtelomeric region of 19p13.3 in the affected MZ twin and 10 of the 31 patients with MSA but not in 2 independent control populations (<it>p </it>= 1.04 × 10^-8, odds ratio = 89.8, Pearson's chi-square test).</p> <p>Conclusions</p> <p>Copy number loss of <it>SHC2 </it>strongly indicates a causal link to MSA. CNV analysis of phenotypically discordant MZ twins is a powerful tool for identifying disease-predisposing loci. Our results would enable the identification of novel diagnostic measure, therapeutic targets and better understanding of the etiology of MSA.</p

Trimerization and genotype-phenotype correlation of COL4A5 mutants in Alport syndrome

INTRODUCTION: Alport syndrome is a hereditary glomerulonephritis that results from the disruption of collagen α345(IV) heterotrimerization caused by mutation in METHODS: We selected 9 α5(IV) missense mutants with typical glycine substitutions that clinically differed in disease progression. To quantify the trimerization of each mutant, split nanoluciferase-fused α3/α5 mutants and α4 were transfected into the cells, and intracellular and secreted heterotrimer were detected by luminescence using an assay that we developed previously. RESULTS: Trimer formation and secretion patterns tended to be similar to the wild type in most of the mutations that did not show proteinuria at a young age. On the other hand, trimer secretion was significantly reduced in all the mutations that showed proteinuria and early onset of renal failure. One of these mutants has low ability of intracellular trimer formation, and the others had the defect of low-level secretion. In addition, the mutant that is assumed to be nonpathogenic has similar trimer formation and secretion pattern as wild-type α5(IV). CONCLUSION: The result of cell-based α345(IV) heterotrimer formation assay was largely correlated with clinical genotype-phenotype. These trimerization assessments provide additional phenotypic considerations and may help to distinguish between pathogenic and nonpathogenic mutations

Extended x-ray absorption fine structure study on the cerium(IV)-induced DNA hydrolysis: Implication to the roles of 4f orbitals in the catalysis

At various Ce(IV)/DPP (DPP: diphenyl phosphate) molar ratios, the structure of Ce clusters in aqueous solutions was studied by extended x-ray absorption fine structure measurements. Although the Ce–Ce bond was strong in the absence of DPP, the corresponding signal was significantly reduced when the Ce(IV)/DPP molar ratio was 1. The result indicates the existence of a strong interaction between Ce(IV) ions and DPP, and suggests the formation of a Ce–DPP structure in solution. With an increase in the molar ratio, the signal of Ce–Ce bonds increased again, and exceeded that observed in the absence of DPP, suggesting the formation of a Ce–Ce–DPP structure. Ce(IV) ions in the complexes were found to have ~ 0.67 4f electrons. On the other hand, no measurable charge transfer was observed in the case of Ce(III) ions. These results demonstrate the role of the 4f orbital of Ce(IV) ions for its enormous activity for DNA hydrolysis

Geometrical structure effect on localization length of carbon nanotubes

The localization length and density of states of carbon nanotubes are evaluated within the tight-binding approximation. By comparison with the corresponding results for the square lattice tubes, it is found that the hexagonal structure affects strongly the behaviors of the density of states and localization lengths of carbon nanotubes.Comment: 7 pages, 4 figures, revised version to appear in Chin. Phys. Lett. The title is changed. Some arguments are adde

High energy electron observation by Polar Patrol Balloon flight in Antarctica

We accomplished a balloon observation of the high-energy cosmic-ray electrons in 10-1000GeV to reveal the origin and the acceleration mechanism. The observation was carried out for 13 days at an average altitude of 35km by the Polar Patrol Balloon (PPB) around Antarctica in January 2004. The detector is an imaging calorimeter composed of scintillating-fiber belts and plastic scintillation counters sandwiched between lead plates. The geometrical factor is about 600cm^2sr, and the total thickness of lead absorber is 9 radiation lengths. The performance of the detector has been confirmed by a test flight at the Sanriku Balloon Center and by an accelerator beam test using the CERN-SPS (Super Proton Synchrotron at CERN). The new telemetry system using the Iridium satellite, the power system supplied by solar panels and the automatic flight level control operated successfully during the flight. We collected 5.7×10^3 events over 100GeV, and selected the electron candidates by a preliminary data analysis of the shower images. We report here an outline of both detector and observation, and the first result of the electron energy spectrum over 100GeV obtained by an electronic counter