Gene function prediction from synthetic lethality networks via ranking on demand.

MOTIVATION: Synthetic lethal interactions represent pairs of genes whose individual mutations are not lethal, while the double mutation of both genes does incur lethality. Several studies have shown a correlation between functional similarity of genes and their distances in networks based on synthetic lethal interactions. However, there is a lack of algorithms for predicting gene function from synthetic lethality interaction networks. RESULTS: In this article, we present a novel technique called kernelROD for gene function prediction from synthetic lethal interaction networks based on kernel machines. We apply our novel algorithm to Gene Ontology functional annotation prediction in yeast. Our experiments show that our method leads to improved gene function prediction compared with state-of-the-art competitors and that combining genetic and congruence networks leads to a further improvement in prediction accuracy.

Tubular graphite cones with single-crystal nanotips and their antioxygenic properties.

Tubular graphite cones (TGCs) with a single-crystal nanotip have been achieved by means of microwave plasma-assisted chemical vapor deposition using in-situ-evaporated Fe catalysts. The absence of the disorder-induced D band in Raman spectra revealed the single-crystalline feature of the nanotip. TGCs were found to stem from Fe catalytic carbon spherules on the order of 100 mum diameter, whose critical role in promoting both nucleation and plasma annealing in the formation of highly crystalline TGCs is discussed. The crystalline quality of such TGCs can be further verified by the investigation of their oxidative stability in air. All TGCs can survive up to 600 degrees C without any structural variations, and a few TGCs still survive with an anisotropic etched and stepped nanotip at temperatures up to 800 degrees C, much better than CNTs. Thus, TGCs with single crystalline nanotips are potential candidates for scanning probes in high-temperature oxygen-containing environments.

Tailoring the local interaction between graphene layers in graphite at the atomic scale and above using scanning tunneling microscopy.

With recent developments in carbon-based electronics, it is imperative to understand the interplay between the morphology and electronic structure in graphene and graphite. We demonstrate controlled and repeatable vertical displacement of the top graphene layer from the substrate mediated by the scanning tunneling microscopy (STM) tip-sample interaction, manifested at the atomic level as well as over superlattices spanning several tens of nanometers. Besides the full-displacement, we observed the first half-displacement of the surface graphene layer, confirming that a reduced coupling rather than a change in lateral layer stacking is responsible for the triangular/honeycomb atomic lattice transition phenomenon, clearing the controversy surrounding it. Furthermore, an atomic scale mechanical stress at a grain boundary in graphite, resulting in the localization of states near the Fermi energy, is revealed through voltage-dependent imaging. A method of producing graphene nanoribbons based on the manipulation capabilities of the STM is also implemented.

Fibre optic distributed sensor system for condition monitoring of synthetic ropes

Reliability of the measuring devices is very important problem. Optical fibre sensors are very efficient. The use of optical fibre sensors for monitoring the physical and chemical parameters has been expanding over resent years. These sensors are applied for monitoring the structural integrity of long, parallel lay synthetic ropes. Such ropes are corrosion free, however, their operational lifetime under cyclic load is not well understood and premature failure can occur due to slippage and breakage of yarns within the rope. The monitoring system has been proposed which is based on acoustic detection of yarn breakage. Monitoring the strain and temperature is performed using the array of fibre gratings distributed along the rope length.

Simple model of electronic density of states of graphite and its application to the investigation of superlattices

A model of graphite which is easy to comprehend and simple to implement for the simulation of scanning tunneling microscopy (STM) images is described. This model simulates the atomic density of graphite layers, which in turn correlates with the local density of states. The mechanism and construction of such a model is explained with all the necessary details which have not been explicitly reported before. This model is applied to the investigation of rippling fringes which have been experimentally observed on a superlattice, and it is found that the rippling fringes are not related to the superlattice itself. A superlattice with abnormal topmost layers interaction is simulated, and the result affirms the validity of the moiré rotation pattern assumption. The "odd-even" transition along the atomic rows of a superlattice is simulated, and the simulation result shows that when there is more than one rotated layer at the top, the "odd-even" transition will not be manifest. ©2005 The Japan Society of Applied Physics.