Exact Algorithms for B-Bandwidth Problem with Restricted B

The B-BANDWIDTH problem is a decision problem whether the bandwidth of a given graph is smaller than B, and it is NP-complete even if the graph is a small graph class of trees. Cygan and Pilipczuk proposed exponential time and space algorithms for B-BANDWIDTH with n/3 ≤ B where n is the number of vertices. In this paper, we propose two algorithms for the B-BANDWIDTH problem with n/4 ≤ B < n/3. These algorithms are extension of Cygan and Pilipczuk algorithms with restricted B. One of the algorithms takes O∗(4.5n) time and O∗(1.5n) space when n/4 ≤ B < n / 2 log2 1.5, and the other takes O∗(4.77n) time and O∗(1.59n) space when n / 2 log2 1.5 ≤ B < n/3. Our algorithms are fastest O∗(2n) space algorithms for n/4 ≤B < n/3.The 17th Korea-Japan Joint Workshop on Algorithms and Computation, July 13-15, 2014, Okinawa, Japa

FACILE AND SENSITIVE HPLC-UV METHOD FOR DETERMINATION OF NINTEDANIB IN RAT PLASMA

Objective: In this study, a facile and sensitive high-performance liquid chromatographic method for determination of nintedanib in rat plasma was developed and validated.Methods: After plasma protein was precipitated by addition of acetonitrile, the supernatant underwent centrifugation. An aliquot was then injected into a high-performance liquid chromatographic system with a Mightysil RP-18 GP II ODS column (250 × 3.0 mm, length by inner diameter, 5-μm particle size) maintained at 50 °C. A mobile phase mixture of 20 mmol phosphate buffer (pH 3.0) and acetonitrile (7:3, v/v) was used at a flow rate of 0.6 mL/min, with UV detection at a wavelength of 390 nm for isocratic separation and detection of nintedanib, its main metabolite (BIBF1202), and p-nitrophenol as an internal standard.Results: The quantitative range of nintedanib concentration in this method was 12.5–400 ng/ml, and the calibration curves were linear. The intra-and inter-day accuracy values (relative errors) were in the range of −3.65%–4.00% and −3.65%–3.64%, respectively. The intra-and inter-day precision values (relative standard deviations) were&lt;5.9% and 8.36%, respectively. The method was successfully applied to a pharmacokinetic analysis of nintedanib in rats after intravenous administration.Conclusion: In this study, a rapid, sensitive, and simple HPLC-UV method for the quantitation of nintedanib in rat plasma was developed and validated. The method was shown to be accurate and precise and was successfully applied to a pharmacokinetic study

Negative thermal expansion of water in hydrophobic nanospaces

The density and intermolecular structure of water in carbon micropores (w = 1.36 nm) are investigated by small-angle X-ray scattering (SAXS) and X-ray diffraction (XRD) measurements between 20 K and 298 K. The SAXS results suggest that the density of the water in the micropores increased with increasing temperature over a wide temperature range (20-277 K). The density changed by 10%, which is comparable to the density change of 7% between bulk ice (I(c)) at 20 K and water at 277 K. The results of XRD at low temperatures (less than 200 K) show that the water forms the cubic ice (I(c)) structure, although its peak shape and radial distribution functions changed continuously to those of a liquid-like structure with increasing temperature. The SAXS and XRD results both showed that the water in the hydrophobic nanospaces had no phase transition point. The continuous structural change from ice I(c) to liquid with increasing temperature suggests that water shows negative thermal expansion over a wide temperature range in hydrophobic nanospaces. The combination of XRD and SAXS measurements makes it possible to describe confined systems in nanospaces with intermolecular structure and density of adsorbed molecular assemblies.ArticlePHYSICAL CHEMISTRY CHEMICAL PHYSICS. 14(2):981-986 (2012)journal articl

Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones

The human genome sequence defines our inherent biological potential; the realization of the biology encoded therein requires knowledge of the function of each gene. Currently, our knowledge in this area is still limited. Several lines of investigation have been used to elucidate the structure and function of the genes in the human genome. Even so, gene prediction remains a difficult task, as the varieties of transcripts of a gene may vary to a great extent. We thus performed an exhaustive integrative characterization of 41,118 full-length cDNAs that capture the gene transcripts as complete functional cassettes, providing an unequivocal report of structural and functional diversity at the gene level. Our international collaboration has validated 21,037 human gene candidates by analysis of high-quality full-length cDNA clones through curation using unified criteria. This led to the identification of 5,155 new gene candidates. It also manifested the most reliable way to control the quality of the cDNA clones. We have developed a human gene database, called the H-Invitational Database (H-InvDB; http://www.h-invitational.jp/). It provides the following: integrative annotation of human genes, description of gene structures, details of novel alternative splicing isoforms, non-protein-coding RNAs, functional domains, subcellular localizations, metabolic pathways, predictions of protein three-dimensional structure, mapping of known single nucleotide polymorphisms (SNPs), identification of polymorphic microsatellite repeats within human genes, and comparative results with mouse full-length cDNAs. The H-InvDB analysis has shown that up to 4% of the human genome sequence (National Center for Biotechnology Information build 34 assembly) may contain misassembled or missing regions. We found that 6.5% of the human gene candidates (1,377 loci) did not have a good protein-coding open reading frame, of which 296 loci are strong candidates for non-protein-coding RNA genes. In addition, among 72,027 uniquely mapped SNPs and insertions/deletions localized within human genes, 13,215 nonsynonymous SNPs, 315 nonsense SNPs, and 452 indels occurred in coding regions. Together with 25 polymorphic microsatellite repeats present in coding regions, they may alter protein structure, causing phenotypic effects or resulting in disease. The H-InvDB platform represents a substantial contribution to resources needed for the exploration of human biology and pathology