3,403 research outputs found

    Tau functions as Widom constants

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    We define a tau function for a generic Riemann-Hilbert problem posed on a union of non-intersecting smooth closed curves with jump matrices analytic in their neighborhood. The tau function depends on parameters of the jumps and is expressed as the Fredholm determinant of an integral operator with block integrable kernel constructed in terms of elementary parametrices. Its logarithmic derivatives with respect to parameters are given by contour integrals involving these parametrices and the solution of the Riemann-Hilbert problem. In the case of one circle, the tau function coincides with Widom's determinant arising in the asymptotics of block Toeplitz matrices. Our construction gives the Jimbo-Miwa-Ueno tau function for Riemann-Hilbert problems of isomonodromic origin (Painlev\'e VI, V, III, Garnier system, etc) and the Sato-Segal-Wilson tau function for integrable hierarchies such as Gelfand-Dickey and Drinfeld-Sokolov.Comment: 26 pages, 6 figure

    Traumatic Tricuspid Regurgitation Following Cardiac Massage

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    We report a 66-yr-old male patient who developed tricuspid regurgitation secondary to internal cardiac massage. After uneventful off-pump coronary artery bypass surgery, the subject experienced cardiac arrest in the intensive care unit. External cardiac massage was initiated and internal cardiac massage was performed eventually. A transesophageal echocardiography revealed avulsion of the anterior papillary muscle and chordae to the anterior leaflet after successful cardiopulmonary resuscitation. Emergency repair of the papillary muscle was performed under cardiopulmonary bypass

    REGNET: Mining context-specific human transcription networks using composite genomic information

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    Background: Genome-wide expression profiles reflect the transcriptional networks specific to the given cell context. However, most statistical models try to estimate the average connectivity of the networks from a collection of gene expression data, and are unable to characterize the context-specific transcriptional regulations. We propose an approach for mining context-specific transcription networks from a large collection of gene expression fold-change profiles and composite gene-set information.Results: Using a composite gene-set analysis method, we combine the information of transcription factor binding sites, Gene Ontology or pathway gene sets and gene expression fold-change profiles for a variety of cell conditions. We then collected all the significant patterns and constructed a database of context-specific transcription networks for human (REGNET). As a result, context-specific roles of transcription factors as well as their functional targets are readily explored. To validate the approach, nine predicted targets of E2F1 in HeLa cells were tested using chromatin immunoprecipitation assay. Among them, five (Gadd45b, Dusp6, Mll5, Bmp2 and E2f3) were successfully bound by E2F1. c-JUN and the EMT transcription networks were also validated from literature.Conclusions: REGNET is a useful tool for exploring the ternary relationships among the transcription factors, their functional targets and the corresponding cell conditions. It is able to provide useful clues for novel cell-specific transcriptional regulations. The REGNET database is available at http://mgrc.kribb.re.kr/regnet.open0

    EST sequencing and gene expression profiling in Scutellaria baicalensis

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    Scutellaria baicalensis is an important medicinal plant, but few genomic resources are available for this species, as well as for other non-model plants. One of the major new directions in genome research is to discover the full spectrum of genes transcribed from the whole genome. Here, we report extensive transcriptome data of the early growth stage of S. baicalensis. This transcriptome consensus sequence was constructed by de novo assembly of shotgun sequencing data, obtained using multiple next-generation DNA sequencing (NGS) platforms (Roche/454 GS_FLX+ and Illumina/Solexa HiSeq2000). We show that this new approach to obtain extensive mRNA is an efficient strategy for genome-wide transcriptome analysis. We obtained 1,226,938 and 161,417,646 reads using the GS_FLX and the Illumina/Solexa HiS-eq2000, respectively. De novo assembly of the high-quality GS_FLX and Illumina reads (95 % and 75 %) resulted in more than 82 Mb of mRNA consensus sequence, which we assembled into 51,188 contigs, with at least 500 bp per contig. Of these contigs, 39,581 contained known genes, as determined by BLASTX searches against non-redundant NCBI database. Of these, 20,498 different genes were expressed during the early growth stage of S. baicalensis. We have made the expressed sequences available on a public database. Our results demonstrate the utility of combining NGS technologies as a basis for the development of genomic tools in non-model, medicinal plant species. Knowledge of all described genes and quantitation of the expressed genes, including the transcription factors involved, will be useful in studies of the biology of S. baicalensis gene regulation

    Transcription Factor Sp1 Is Involved in Expressional Regulation of Coxsackie and Adenovirus Receptor in Cancer Cells

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    Coxsackie and adenovirus receptor (CAR) was first known as a virus receptor. Recently, it is also known to have tumor suppressive activity such as inhibition of cell proliferation, migration, and invasion. It is important to understand how CAR expression can be regulated in cancers. Based on an existence of putative Sp1 binding site within CAR promoter, we investigated whether indeed Sp1 is involved in the regulation of CAR expression. We observed that deletion or mutation of Sp1 binding motif (−503/−498) prominently impaired the Sp1 binding affinity and activity of CAR promoter. Histone deacetylase inhibitor (TSA) treatment enhanced recruitment of Sp1 to the CAR promoter in ChIP assay. Meanwhile, Sp1 binding inhibitor suppressed the recruitment. Exogenous expression of wild-type Sp1 increased CAR expression in CAR-negative cells; meanwhile, dominant negative Sp1 decreased the CAR expression in CAR-positive cells. These results indicate that Sp1 is involved in regulation of CAR expression

    Prediction of males’ physical work capacity in various simulated altitudes using an incremental cycle ergometer exercise test at sea level

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    Standard approach to predict the decrease in physical fitness that will occur following a transition to a higher altitude is unavailable. Therefore, the study aimed to design simple mathematical models to predict submaximal exercise performance in various altitude environments, using a simple physical work capacity test conducted at sea level involving >200 subjects. After splitting the subjects’ data in a ratio of 7:3, we used 70% of the data for regression model development and employed 30% for cross-validation testing. All subjects performed submaximal exercise tests using a cycle ergometer at artificial altitudes of 2000 m, 3000 m, 4000 m, 5000 m, and at sea level. We applied simple regression analysis to create a predictive model with the statistical significance set at the level of <5%. There were 233 subjects involved in this study. The coefficient of determination of our regression model was 40–58%, and the standard error of estimation was 14.96–17.27 watts. The cross-validation of our regression model was 8–10%. Among the regression models developed, the one applied to an artificial altitude of 5000 m was 17%, and the regression model applied to an artificial altitude below 4000 m had no issues in generalization since the cross-validation was less than 10%. However, the regression model applied to an artificial altitude of 5000 m had a cross-validity of 17%; therefore, it should be used with caution

    Development of multistage 10-m shuttle run test for VO2max estimation in healthy adults

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    Background and objective: The disadvantage of the traditional 20-m multistage shuttle run test (MST) is that it requires a long space for measurements and does not include various age groups to develop the test. Therefore, we developed a new MST to improve the spatial limitation by reducing the measurement to a 10-m distance and to resolve the bias via uniform distributions of gender and age. Material and methods: Study subjects included 120 healthy adults (60 males and 60 females) aged 20 to 50 years. All subjects performed a graded maximal exercise test (GXT) and a 10-m MST at five-day intervals. We developed a regression model using 70% of the subject’s data and performed a cross-validation test using 30% of the data. Results: The male regression model’s coefficient of determination (R2) was 58.8%, and the standard error of estimation (SEE) was 4.17 mL/kg/min. The female regression model’s R2 was 69.2%, and the SEE was 3.39 mL/kg/min. The 10-m MST showed a high correlation with GXT on the VO2max (males: 0.816; females: 0.821). In the cross-validation test for the developed regression models, the male’s SEE was 4.38 mL/kg/min, and the female’s SEE was 4.56 mL/kg/min. Conclusion: Thus, the 10-m MST is an accurate and valid method for estimating the VO2max. Therefore, the 10-m MST developed by us can be used when the existing 20-m MST cannot be used due to spatial limitations and can be applied to both men and women in their 20s and 50s
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