MolBioLib: A C++11 Framework for Rapid Development and Deployment of Bioinformatics Tasks

Summary: We developed MolBioLib to address the need for adaptable next-generation sequencing analysis tools. The result is a compact, portable and extensively tested C++11 software framework and set of applications tailored to the demands of next-generation sequencing data and applicable to many other applications. MolBioLib is designed to work with common file formats and data types used both in genomic analysis and general data analysis. A central relational-database-like Table class is a flexible and powerful object to intuitively represent and work with a wide variety of tabular datasets, ranging from alignment data to annotations. MolBioLib has been used to identify causative single-nucleotide polymorphisms in whole genome sequencing, detect balanced chromosomal rearrangements and compute enrichment of messenger RNAs (mRNAs) on microtubules, typically requiring applications of under 200 lines of code. MolBioLib includes programs to perform a wide variety of analysis tasks, such as computing read coverage, annotating genomic intervals and novel peak calling with a wavelet algorithm. Although MolBioLib was designed primarily for bioinformatics purposes, much of its functionality is applicable to a wide range of problems. Complete documentation and an extensive automated test suite are provided

All-in/all-out magnetic domains: X-ray diffraction imaging and magnetic field control

Long-range non-collinear all-in/all-out magnetic order has been directly observed for the first time in real space in the pyrochlore Cd$_2$Os$_2$O$_7$ using resonant magnetic microdiffraction at the Os L$_3$ edge. Two different antiferromagnetic domains related by time-reversal symmetry could be distinguished and have been mapped within the same single crystal. The two types of domains are akin to magnetic twins and were expected - yet unobserved so far - in the all-in/all-out model. Even though the magnetic domains are antiferromagnetic, we show that their distribution can be controlled using a magnetic field-cooling procedure.Comment: Main text: 11 pages, 4 figures ; Supplementary materials: 9 pages, 5 figure

Epitaxially stabilized iridium spinel oxide without cations in the tetrahedral site

Single-crystalline thin film of an iridium dioxide polymorph Ir2O4 has been fabricated by the pulsed laser deposition of LixIr2O4 precursor and the subsequent Li-deintercalation using soft chemistry. Ir2O4 crystallizes in a spinel (AB2O4) without A cations in the tetrahedral site, which is isostructural to lambda-MnO2. Ir ions form a pyrochlore sublattice, which is known to give rise to a strong geometrical frustration. This Ir spinel was found to be a narrow gap insulator, in remarkable contrast to the metallic ground state of rutile-type IrO2. We argue that an interplay of strong spin-orbit coupling and a Coulomb repulsion gives rise to an insulating ground state as in a layered perovskite Sr2IrO4.Comment: 9 pages, 3 figure

8.5 カエル卵無細胞系における細胞周期制御

カエル卵無細胞系における細胞周期制御大隅圭太［東京工業大学大学院生命理工学研究科］＊所属は当時のものを記

Classical and Quantum Correlations of Scalar Field in the Inflationary Universe

We investigate classical and quantum correlations of a quantum field in the inflationary universe using a particle detector model. By considering the entanglement and correlations between two comoving detectors interacting with a scalar field, we find that the entanglement between the detectors becomes zero after their physical separation exceeds the Hubble horizon. Furthermore, the quantum discord, which is defined as the quantum part of total correlation, approaches zero on super horizon scale. These behaviors support appearance of classical nature of the quantum fluctuation generated during the inflationary era.Comment: 21 pages, accepted for publication in Phys. Rev.