Canonical treatment of two dimensional gravity as an anomalous gauge theory

The extended phase space method of Batalin, Fradkin and Vilkovisky is applied to formulate two dimensional gravity in a general class of gauges. A BRST formulation of the light-cone gauge is presented to reveal the relationship between the BRST symmetry and the origin of $SL(2,R)$ current algebra. From the same principle we derive the conformal gauge action suggested by David, Distler and Kawai.Comment: 11 pages, KANAZAWA-92-1

Effects of the geometrical configuration of air-water mixer on the size and distribution of micro-bubbles in aeration systems

The objective of this work is to present a novel geometrical configuration for microbubble generators (MBGs) to improve dissolved-oxygen levels in water. Among various methodologies from the literature, Orifice and Venturi tubes have been considered as baseline cases. Experimental data from the literature are used to verify a computational fluid dynamics (CFD) case developed for a better understanding of the dynamics of MBGs. As a result, the validated CFD setup has been implemented on a modified Venturi-type generator, where air is injected coaxially with respect to the tube axis, whereas a helicoid wall at variable pitch angle is used. Results show a reduction in the mean bubble diameter distribution from the baseline Venturi tubes, particularly, at low-speed inlet velocities. This is of interest, especially to decrease the energy requirement for most common water aeration systems

PoSSuM: a database of similar protein–ligand binding and putative pockets

Numerous potential ligand-binding sites are available today, along with hundreds of thousands of known binding sites observed in the PDB. Exhaustive similarity search for such vastly numerous binding site pairs is useful to predict protein functions and to enable rapid screening of target proteins for drug design. Existing databases of ligand-binding sites offer databases of limited scale. For example, SitesBase covers only ∼33 000 known binding sites. Inferring protein function and drug discovery purposes, however, demands a much more comprehensive database including known and putative-binding sites. Using a novel algorithm, we conducted a large-scale all-pairs similarity search for 1.8 million known and potential binding sites in the PDB, and discovered over 14 million similar pairs of binding sites. Here, we present the results as a relational database Pocket Similarity Search using Multiple-sketches (PoSSuM) including all the discovered pairs with annotations of various types. PoSSuM enables rapid exploration of similar binding sites among structures with different global folds as well as similar ones. Moreover, PoSSuM is useful for predicting the binding ligand for unbound structures, which provides important clues for characterizing protein structures with unclear functions. The PoSSuM database is freely available at http://possum.cbrc.jp/PoSSuM/

Agrobacterium-mediated transformation of kabocha squash (Cucurbita moschata Duch) induced by wounding with aluminum borate whiskers

An efficient genetic transformation method for kabocha squash (Cucurbita moschata Duch cv. Heiankogiku) was established by wounding cotyledonary node explants with aluminum borate whiskers prior to inoculation with Agrobacterium. Adventitious shoots were induced from only the proximal regions of the cotyledonary nodes and were most efficiently induced on Murashige–Skoog agar medium with 1 mg/L benzyladenine. Vortexing with 1% (w/v) aluminum borate whiskers significantly increased Agrobacterium infection efficiency in the proximal region of the explants. Transgenic plants were screened at the T0 generation by sGFP fluorescence, genomic PCR, and Southern blot analyses. These transgenic plants grew normally and T1 seeds were obtained. We confirmed stable integration of the transgene and its inheritance in T1 generation plants by sGFP fluorescence and genomic PCR analyses. The average transgenic efficiency for producing kabocha squashes with our method was about 2.7%, a value sufficient for practical use

Gauge Equivalence in Two--Dimensional Gravity

Two-dimensional quantum gravity is identified as a second-class system which we convert into a first-class system via the Batalin-Fradkin (BF) procedure. Using the extended phase space method, we then formulate the theory in most general class of gauges. The conformal gauge action suggested by David, Distler and Kawai is derived from a first principle. We find a local, light-cone gauge action whose Becchi-Rouet-Stora-Tyutin invariance implies Polyakov's curvature equation $\partial_{-}R=\partial_{-}^{3}g_{++}=0$, revealing the origin of the $SL(2,R)$ Kac-Moody symmetry. The BF degree of freedom turns out be dynamically active as the Liouville mode in the conformal gauge, while in the light-cone gauge the conformal degree of freedom plays that r{\^o}le. The inclusion of the cosmological constant term in both gauges and the harmonic gauge-fixing are also considered.Comment: 30 pages, KANAZAWA 93-

Transmission electron microscopic observations of nanobubbles and their capture of impurities in wastewater

Unique properties of micro- and nanobubbles (MNBs), such as a high adsorption of impurities on their surface, are difficult to verify because MNBs are too small to observe directly. We thus used a transmission electron microscope (TEM) with the freeze-fractured replica method to observe oxygen (O2) MNBs in solutions. MNBs in pure water and in 1% NaCl solutions were spherical or oval. Their size distribution estimated from TEM images close to that of the original solution is measured by light-scattered methods. When we applied this technique to the observation of O2 MNBs formed in the wastewater of a sewage plant, we found the characteristic features of spherical MNBs that adsorbed surrounding impurity particles on their surface

Improved accuracy of multiple ncRNA alignment by incorporating structural information into a MAFFT-based framework

<p>Abstract</p> <p>Background</p> <p>Structural alignment of RNAs is becoming important, since the discovery of functional non-coding RNAs (ncRNAs). Recent studies, mainly based on various approximations of the Sankoff algorithm, have resulted in considerable improvement in the accuracy of pairwise structural alignment. In contrast, for the cases with more than two sequences, the practical merit of structural alignment remains unclear as compared to traditional sequence-based methods, although the importance of multiple structural alignment is widely recognized.</p> <p>Results</p> <p>We took a different approach from a straightforward extension of the Sankoff algorithm to the multiple alignments from the viewpoints of accuracy and time complexity. As a new option of the MAFFT alignment program, we developed a multiple RNA alignment framework, X-INS-i, which builds a multiple alignment with an iterative method incorporating structural information through two components: (1) pairwise structural alignments by an external pairwise alignment method such as SCARNA or LaRA and (2) a new objective function, Four-way Consistency, derived from the base-pairing probability of every sub-aligned group at every multiple alignment stage.</p> <p>Conclusion</p> <p>The BRAliBASE benchmark showed that X-INS-i outperforms other methods currently available in the sum-of-pairs score (SPS) criterion. As a basis for predicting common secondary structure, the accuracy of the present method is comparable to or rather higher than those of the current leading methods such as RNA Sampler. The X-INS-i framework can be used for building a multiple RNA alignment from any combination of algorithms for pairwise RNA alignment and base-pairing probability. The source code is available at the webpage found in the Availability and requirements section.</p

An efficient genetic algorithm for structural RNA pairwise alignment and its application to non-coding RNA discovery in yeast

<p>Abstract</p> <p>Background</p> <p>Aligning RNA sequences with low sequence identity has been a challenging problem since such a computation essentially needs an algorithm with high complexities for taking structural conservation into account. Although many sophisticated algorithms for the purpose have been proposed to date, further improvement in efficiency is necessary to accelerate its large-scale applications including non-coding RNA (ncRNA) discovery.</p> <p>Results</p> <p>We developed a new genetic algorithm, Cofolga2, for simultaneously computing pairwise RNA sequence alignment and consensus folding, and benchmarked it using BRAliBase 2.1. The benchmark results showed that our new algorithm is accurate and efficient in both time and memory usage. Then, combining with the originally trained SVM, we applied the new algorithm to novel ncRNA discovery where we compared <it>S. cerevisiae </it>genome with six related genomes in a pairwise manner. By focusing our search to the relatively short regions (50 bp to 2,000 bp) sandwiched by conserved sequences, we successfully predict 714 intergenic and 1,311 sense or antisense ncRNA candidates, which were found in the pairwise alignments with stable consensus secondary structure and low sequence identity (≤ 50%). By comparing with the previous predictions, we found that > 92% of the candidates is novel candidates. The estimated rate of false positives in the predicted candidates is 51%. Twenty-five percent of the intergenic candidates has supports for expression in cell, i.e. their genomic positions overlap those of the experimentally determined transcripts in literature. By manual inspection of the results, moreover, we obtained four multiple alignments with low sequence identity which reveal consensus structures shared by three species/sequences.</p> <p>Conclusion</p> <p>The present method gives an efficient tool complementary to sequence-alignment-based ncRNA finders.</p

Phase III randomized trial of sunitinib versus capecitabine in patients with previously treated HER2-negative advanced breast cancer

This multicenter, randomized, open-label phase III trial (planned enrollment: 700 patients) was conducted to test the hypothesis that single-agent sunitinib improves progression-free survival (PFS) compared with capecitabine as treatment for advanced breast cancer (ABC). Patients with HER2-negative ABC that recurred after anthracycline and taxane therapy were randomized (1:1) to sunitinib 37.5 mg/day or capecitabine 1,250 mg/m2 (1,000 mg/m2 in patients >65 years) BID on days 1–14 q3w. The independent data-monitoring committee (DMC) determined during the first interim analysis (238 patients randomized to sunitinib, 244 to capecitabine) that the trial be terminated due to futility in reaching the primary endpoint. No statistical evidence supported the hypothesis that sunitinib improved PFS compared with capecitabine (one-sided P = 0.999). The data indicated that PFS was shorter with sunitinib than capecitabine (median 2.8 vs. 4.2 months, respectively; HR, 1.47; 95% CI, 1.16–1.87; two-sided P = 0.002). Median overall survival (15.3 vs. 24.6 months; HR, 1.17; two-sided P = 0.350) and objective response rates (11 vs. 16%; odds ratio, 0.65; P = 0.109) were numerically inferior with sunitinib versus capecitabine. While no new or unexpected safety findings were reported, sunitinib treatment was associated with higher frequencies and greater severities of many common adverse events (AEs) compared with capecitabine, resulting in more temporary discontinuations due to AEs with sunitinib (66 vs. 51%). The relative dose intensity was lower with sunitinib than capecitabine (73 vs. 95%). Based on these efficacy and safety results, sunitinib should not be used as monotherapy for patients with ABC

Psychological resilience in sport performers: a review of stressors and protective factors

Psychological resilience is important in sport because athletes must utilize and optimize a range of mental qualities to withstand the pressures that they experience. In this paper, we discuss psychological resilience in sport performers via a review of the stressors athletes encounter and the protective factors that help them withstand these demands. It is hoped that synthesizing what is known in these areas will help researchers gain a deeper profundity of resilience in sport, and also provide a rigorous and robust foundation for the development of a sport-specific measure of resilience. With these points in mind, we divided the narrative into two main sections. In the first section, we review the different types of stressors encountered by sport performers under three main categories: competitive, organizational, and personal. Based on our recent research examining psychological resilience in Olympics champions (Fletcher & Sarkar, 2012), in the second section we discuss the five main families of psychological factors (viz. positive personality, motivation, confidence, focus, perceived social support) that protect the best athletes from the potential negative effect of stressors. It is anticipated that this review will help sport psychology researchers examine the interplay between stressors and protective factors which will, in turn, focus the analytical lens on the processes underlying psychological resilience in athletes