Tokyo Institute of Technology

About: Tokyo Institute of Technology is a education organization based out in Tokyo, Tôkyô, Japan. It is known for research contribution in the topics: Catalysis & Thin film. The organization has 46775 authors who have published 101656 publications receiving 2357893 citations. The organization is also known as: Tokyo Tech & Tokodai.

Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer

Abstract: Association studies have linked microbiome alterations with many human diseases. However, they have not always reported consistent results, thereby necessitating cross-study comparisons. Here, a meta-analysis of eight geographically and technically diverse fecal shotgun metagenomic studies of colorectal cancer (CRC, n = 768), which was controlled for several confounders, identified a core set of 29 species significantly enriched in CRC metagenomes (false discovery rate (FDR) < 1 × 10−5). CRC signatures derived from single studies maintained their accuracy in other studies. By training on multiple studies, we improved detection accuracy and disease specificity for CRC. Functional analysis of CRC metagenomes revealed enriched protein and mucin catabolism genes and depleted carbohydrate degradation genes. Moreover, we inferred elevated production of secondary bile acids from CRC metagenomes, suggesting a metabolic link between cancer-associated gut microbes and a fat- and meat-rich diet. Through extensive validations, this meta-analysis firmly establishes globally generalizable, predictive taxonomic and functional microbiome CRC signatures as a basis for future diagnostics. Cross-study analysis defines fecal microbial species associated with colorectal cancer.

Observation of zigzag and armchair edges of graphite using scanning tunneling microscopy and spectroscopy

Abstract: The presence of structure-dependent edge states of graphite is revealed by both ambient and ultrahigh-vacuum (UHV) scanning tunneling microscopy and scanning tunneling spectroscopy observations. On a hydrogenated zigzag (armchair) edge, bright spots are (are not) observed together with a $(\sqrt{3}\ifmmode\times\else\texttimes\fi{}\sqrt{3})R30\ifmmode^\circ\else\textdegree\fi{}$ superlattice near the Fermi level (${V}_{S}\ensuremath{\sim}\ensuremath{-}30\phantom{\rule{0.3em}{0ex}}\mathrm{mV}$ for a peak of the local density of states) under UHV, demonstrating that a zigzag edge is responsible for the edge states, although there is no appreciable difference between as-prepared zigzag and armchair edges in air. Even in the hydrogenated armchair edge, however, bright spots are observed at defect points, at which partial zigzag edges are created in the armchair edge.

Q-Chem 2.0: a high-performance ab initio electronic structure program package

Abstract: Q-Chem 2.0 is a new release of an electronic structure programpackage, capable of performing first principles calculations on the ground andexcited states of molecules using both density functional theory and wavefunction-based methods. A review of the technical features contained withinQ-Chem 2.0 is presented. This article contains brief descriptive discussions of thekey physical features of all new algorithms and theoretical models, together withsample calculations that illustrate their performance. c 2000 John Wiley S electronic structure; density functional theory;computer program; computational chemistry Introduction A reader glancing casually at this article mightsuspect on the basis of its title that it is a thinlydisguised piece of marketing for a program pack-age. This is not the case. Rather, it is an attemptto document the key methodologies and algorithmsof our electronic structure program package, Q-Chem 2.0, in a complete and scientifically accurateway, with full references to the original literature.This is important for two principal reasons. First,while the use of electronic structure programs isburgeoning, many users of such programs do nothave much feel for the underlying algorithms thatmake large-scale calculations routine even on suchreadily available hardware as personal computers.Therefore, a link between the program package andthe original literature that is written at the level ofan introductory overview can be a useful bridge.Second, while citations of large-scale commercialprograms in published applications are tradition-ally part of the conditions of use of such codes, they