Large-scale electronic-structure theory and nanoscale defects formed in cleavage process of silicon

Several methods are constructed for large-scale electronic structure calculations. Test calculations are carried out with up to 10^7 atoms. As an application, cleavage process of silicon is investigated by molecular dynamics simulation with 10-nm-scale systems. As well as the elementary formation process of the (111)-(2 x 1) surface, we obtain nanoscale defects, that is, step formation and bending of cleavage path into favorite (experimentally observed) planes. These results are consistent to experiments. Moreover, the simulation result predicts an explicit step structure on the cleaved surface, which shows a bias-dependent STM image.Comment: 4 page 4 figures. A PDF file with better graphics is available at http://fujimac.t.u-tokyo.ac.jp/lses

Betti numbers for numerical semigroup rings

We survey results related to the magnitude of the Betti numbers of numerical semigroup rings and of their tangent cones.Comment: 22 pages; v2: updated references. To appear in Multigraded Algebra and Applications (V. Ene, E. Miller Eds.

Observation and electric current control of a local spin in a single-molecule magnet

In molecular spintronics, the spin state of a molecule may be switched on and off by changing the molecular structure. Here, we switch on and off the molecular spin of a double-decker bis(phthalocyaninato)terbium(III) complex (TbPc2) adsorbed on an Au(111) surface by applying an electric current via a scanning tunnelling microscope. The dI/dV curve of the tunnelling current recorded onto a TbPc2 molecule shows a Kondo peak, the origin of which is an unpaired spin of a π-orbital of a phthalocyaninato (Pc) ligand. By applying controlled current pulses, we could rotate the upper Pc ligand in TbPc2, leading to the disappearance and reappearance of the Kondo resonance. The rotation shifts the molecular frontier-orbital energies, quenching the π-electron spin. Reversible switching between two stable ligand orientations by applying a current pulse should make it possible to code information at the single-molecule level

SEAS: A System for SEED-Based Pathway Enrichment Analysis

Pathway enrichment analysis represents a key technique for analyzing high-throughput omic data, and it can help to link individual genes or proteins found to be differentially expressed under specific conditions to well-understood biological pathways. We present here a computational tool, SEAS, for pathway enrichment analysis over a given set of genes in a specified organism against the pathways (or subsystems) in the SEED database, a popular pathway database for bacteria. SEAS maps a given set of genes of a bacterium to pathway genes covered by SEED through gene ID and/or orthology mapping, and then calculates the statistical significance of the enrichment of each relevant SEED pathway by the mapped genes. Our evaluation of SEAS indicates that the program provides highly reliable pathway mapping results and identifies more organism-specific pathways than similar existing programs. SEAS is publicly released under the GPL license agreement and freely available at http://csbl.bmb.uga.edu/~xizeng/research/seas/

Overexpression of EVE1, a novel ubiquitin family protein, arrests inflorescence stem development in Arabidopsis

In Arabidopsis, inflorescence stem formation is a critical process in phase transition from the vegetative to the reproductive state. Although inflorescence stem development has been reported to depend on the expression of a variety of genes during floral induction and repression, little is known about the molecular mechanisms involved in the control of inflorescence stem formation. By activation T-DNA tagging mutagenesis of Arabidopsis, a dominant gain-of-function mutation, eve1-D (eternally vegetative phase1-Dominant), which has lost the ability to form an inflorescence stem, was isolated. The eve1-D mutation exhibited a dome-shaped primary shoot apical meristem (SAM) in the early vegetative stage, similar to that seen in the wild-type SAM. However, the SAM in the eve1-D mutation failed to transition into an inflorescence meristem (IM) and eventually reached senescence without ever leaving the vegetative phase. The eve1-D mutation also displayed pleiotropic phenotypes, including lobed and wavy rosette leaves, short petioles, and an increased number of rosette leaves. Genetic analysis indicated that the genomic location of the EVE1 gene in Arabidopsis thaliana corresponded to a bacterial artificial chromosome (BAC) F4C21 from chromosome IV at ∼17cM which encoded a novel ubiquitin family protein (At4g03350), consisting of a single exon. The EVE1 protein is composed of 263 amino acids, contains a 52 amino acid ubiquitin domain, and has no glycine residue related to ubiquitin activity at the C-terminus. The eve1-D mutation provides a way to study the regulatory mechanisms that control phase transition from the vegetative to the reproductive state

A Novel RNA-Recognition-Motif Protein Is Required for Premeiotic G1/S-Phase Transition in Rice (Oryza sativa L.)

The molecular mechanism for meiotic entry remains largely elusive in flowering plants. Only Arabidopsis SWI1/DYAD and maize AM1, both of which are the coiled-coil protein, are known to be required for the initiation of plant meiosis. The mechanism underlying the synchrony of male meiosis, characteristic to flowering plants, has also been unclear in the plant kingdom. In other eukaryotes, RNA-recognition-motif (RRM) proteins are known to play essential roles in germ-cell development and meiosis progression. Rice MEL2 protein discovered in this study shows partial similarity with human proline-rich RRM protein, deleted in Azoospermia-Associated Protein1 (DAZAP1), though MEL2 also possesses ankyrin repeats and a RING finger motif. Expression analyses of several cell-cycle markers revealed that, in mel2 mutant anthers, most germ cells failed to enter premeiotic S-phase and meiosis, and a part escaped from the defect and underwent meiosis with a significant delay or continued mitotic cycles. Immunofluorescent detection revealed that T7 peptide-tagged MEL2 localized at cytoplasmic perinuclear region of germ cells during premeiotic interphase in transgenic rice plants. This study is the first report of the plant RRM protein, which is required for regulating the premeiotic G1/S-phase transition of male and female germ cells and also establishing synchrony of male meiosis. This study will contribute to elucidation of similarities and diversities in reproduction system between plants and other species

Experiences with surgical treatment of ventricle septal defect as a post infarction complication

<p>Abstract</p> <p>Background</p> <p>Complications of acute myocardial infarction (AMI) with mechanical defects are associated with poor prognosis. Surgical intervention is indicated for a majority of these patients. The goal of surgical intervention is to improve the systolic cardiac function and to achieve a hemodynamic stability. In this present study we reviewed the outcome of patients with post infarction ventricular septal defect (PVSD) who underwent cardiac surgery.</p> <p>Methods</p> <p>We analysed retrospectively the hospital records of 41 patients, whose ages range from 48 to 81, and underwent a surgical treatment between 1990 and 2005 because of PVSD.</p> <p>Results</p> <p>In 22 patients concomitant coronary artery bypass grafting (CAGB) was performed. In 15 patients a residual shunt was found, this required re-op in seven of them. The time interval from infarct to rupture was 8.7 days and from rupture to surgery was 23.1 days. Hospital mortality in PVSD group was 32%. The mortality of urgent repair within 3 days of intractable cardiogenic shock was 100%. The mortality of patients with an anterior VSD and a posterior VSD was 29.6% vs 42.8%, respectively. All patients who underwent the surgical repair later than day 36 survived.</p> <p>Conclusion</p> <p>Surgical intervention is indicated for a majority of patients with mechanical complications. Cardiogenic shock remains the most important factor that affects the early results. The surgical repair of PVSD should be performed 4–5 weeks after AMI. To improve surgical outcome and hemodynamics the choice of surgical technique and surgical timing as well as preoperative management should be tailored for each patient individually.</p