Development of biomimetic catalytic oxidation methods and non-salt methods using transition metal-based acid and base ambiphilic catalysts

This review focuses on the development of ruthenium and flavin catalysts for environmentally benign oxidation reactions based on mimicking the functions of cytochrome P-450 and flavoenzymes, and low valent transition-metal catalysts that replace conventional acids and bases. Several new concepts and new types of catalytic reactions based on these concepts are described

Molecular basis for SMC rod formation and its dissolution upon DNA binding.

SMC condensin complexes are central modulators of chromosome superstructure in all branches of life. Their SMC subunits form a long intramolecular coiled coil, which connects a constitutive "hinge" dimerization domain with an ATP-regulated "head" dimerization module. Here, we address the structural arrangement of the long coiled coils in SMC complexes. We unequivocally show that prokaryotic Smc-ScpAB, eukaryotic condensin, and possibly also cohesin form rod-like structures, with their coiled coils being closely juxtaposed and accurately anchored to the hinge. Upon ATP-induced binding of DNA to the hinge, however, Smc switches to a more open configuration. Our data suggest that a long-distance structural transition is transmitted from the Smc head domains to regulate Smc-ScpAB's association with DNA. These findings uncover a conserved architectural theme in SMC complexes, provide a mechanistic basis for Smc's dynamic engagement with chromosomes, and offer a molecular explanation for defects in Cornelia de Lange syndrome

Subsidence and Nonunion after Anterior Cervical Interbody Fusion Using a Stand-Alone Polyetheretherketone (PEEK) Cage

Background: The purposes of the present study are to evaluate the subsidence and nonunion that occurred after anterior cervical discectomy and fusion using a stand-alone intervertebral cage and to analyze the risk factors for the complications.Methods: Thirty-eight patients (47 segments) who underwent anterior cervical fusion using a stand-alone polyetheretherketone (PEEK) cage and an autologous cancellous iliac bone graft from June 2003 to August 2008 were enrolled in this study. The anterior and posterior segmental heights and the distance from the anterior edge of the upper vertebra to the anterior margin of the cage were measured on the plain radiographs. Subsidence was defined as ≥ a 2 mm (minor) or 3 mm (major) decrease of the segmental height at the final follow-up compared to that measured at the immediate postoperative period. Nonunion was evaluated accordingto the instability being ≥ 2 mm in the interspinous distance on the flexion-extension lateral radiographs.Results: The anterior and posterior segmental heights decreased from the immediate postoperative period to the final follow-up at 1.33 ± 1.46 mm and 0.81 ± 1.27 mm, respectively. Subsidence ≥ 2 mm and 3 mm were observed in 12 segments (25.5%) and 7 segments (14.9%), respectively. Among the expected risk factors for subsidence, a smaller anteroposterior (AP) diameter (14 mm vs. 12 mm) of cages (p = 0.034; odds ratio [OR], 0.017) and larger intraoperative distraction (p = 0.041; OR, 3.988) had a significantlyhigher risk of subsidence. Intervertebral nonunion was observed in 7 segments (7/47, 14.9%). Compared with the union group, the nonunion group had a significantly higher ratio of two-level fusion to one-level fusions (p = 0.001).Conclusions: Anterior cervical fusion using a stand-alone cage with a large AP diameter while preventing anterior intraoperative over-distraction will be helpful to prevent the subsidence of cages. Two-level cervical fusion might require more careful attention for avoiding nonunion.Keywords: Anterior cervical fusion, PEEK cage, Subsidence, NonunionOAIID:oai:osos.snu.ac.kr:snu2011-01/102/0000004226/3SEQ:3PERF_CD:SNU2011-01EVAL_ITEM_CD:102USER_ID:0000004226EMP_ID:A076317DEPT_CD:801FILENAME:E031T_CiOS-2011_Yang_Subsidence and nonunion after anterior cervical.pdfDEPT_NM:의학과EMAIL:[email protected]_YN:NCONFIRM:

Owl Eyes: Spotting UI Display Issues via Visual Understanding

Graphical User Interface (GUI) provides a visual bridge between a software application and end users, through which they can interact with each other. With the development of technology and aesthetics, the visual effects of the GUI are more and more attracting. However, such GUI complexity posts a great challenge to the GUI implementation. According to our pilot study of crowdtesting bug reports, display issues such as text overlap, blurred screen, missing image always occur during GUI rendering on different devices due to the software or hardware compatibility. They negatively influence the app usability, resulting in poor user experience. To detect these issues, we propose a novel approach, OwlEye, based on deep learning for modelling visual information of the GUI screenshot. Therefore, OwlEye can detect GUIs with display issues and also locate the detailed region of the issue in the given GUI for guiding developers to fix the bug. We manually construct a large-scale labelled dataset with 4,470 GUI screenshots with UI display issues and develop a heuristics-based data augmentation method for boosting the performance of our OwlEye. The evaluation demonstrates that our OwlEye can achieve 85% precision and 84% recall in detecting UI display issues, and 90% accuracy in localizing these issues. We also evaluate OwlEye with popular Android apps on Google Play and F-droid, and successfully uncover 57 previously-undetected UI display issues with 26 of them being confirmed or fixed so far.Comment: Accepted to 35th IEEE/ACM International Conference on Automated Software Engineering (ASE 20

Clique-based data mining for related genes in a biomedical database

<p>Abstract</p> <p>Background</p> <p>Progress in the life sciences cannot be made without integrating biomedical knowledge on numerous genes in order to help formulate hypotheses on the genetic mechanisms behind various biological phenomena, including diseases. There is thus a strong need for a way to automatically and comprehensively search from biomedical databases for related genes, such as genes in the same families and genes encoding components of the same pathways. Here we address the extraction of related genes by searching for densely-connected subgraphs, which are modeled as cliques, in a biomedical relational graph.</p> <p>Results</p> <p>We constructed a graph whose nodes were gene or disease pages, and edges were the hyperlink connections between those pages in the Online Mendelian Inheritance in Man (OMIM) database. We obtained over 20,000 sets of related genes (called 'gene modules') by enumerating cliques computationally. The modules included genes in the same family, genes for proteins that form a complex, and genes for components of the same signaling pathway. The results of experiments using 'metabolic syndrome'-related gene modules show that the gene modules can be used to get a coherent holistic picture helpful for interpreting relations among genes.</p> <p>Conclusion</p> <p>We presented a data mining approach extracting related genes by enumerating cliques. The extracted gene sets provide a holistic picture useful for comprehending complex disease mechanisms.</p

Comparative Analysis of Viral Gene Expression Programs during Poxvirus Infection: A Transcriptional Map of the Vaccinia and Monkeypox Genomes

Poxviruses engage in a complex and intricate dialogue with host cells as part of their strategy for replication. However, relatively little molecular detail is available with which to understand the mechanisms behind this dialogue.We designed a specialized microarray that contains probes specific to all predicted ORFs in the Monkeypox Zaire (MPXV) and Vaccinia Western Reserve (VACV) genomes, as well as >18,000 human genes, and used this tool to characterize MPXV and VACV gene expression responses in vitro during the course of primary infection of human monocytes, primary human fibroblasts and HeLa cells. The two viral transcriptomes show distinct features of temporal regulation and species-specific gene expression, and provide an early foundation for understanding global gene expression responses during poxvirus infection.The results provide a temporal map of the transcriptome of each virus during infection, enabling us to compare viral gene expression across species, and classify expression patterns of previously uncharacterized ORFs