Image-based Automated Chemical Database Annotation with Ensemble of Machine-Vision Classifiers

This paper presents an image-based annotation strategy for automated annotation of chemical databases. The proposed strategy is based on the use of a machine vision-based classifier for extracting a 2D chemical structure diagram in research articles and converting them into standard chemical file formats, a virtual Chemical Expert" system for screening the converted structures based on the level of estimated conversion accuracy, and a fragment-based measure for calculation intermolecular similarity. In particular, in order to overcome limited accuracies of individual machine-vision classifier, inspired by ensemble methods in machine learning, it is attempted to use of the ensemble of machine-vision classifiers. For annotation, calculated chemical similarity between the converted structures and entries in a virtual small molecule database is used to establish the links. Annotation test to link 121 journal articles to entries in PubChem database demonstrates that ensemble approach increases the coverage of annotation, while keeping the annotation quality (e.g., recall and precision rates) comparable to using a single machine-vision classifier.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/87266/4/Saitou55.pd

Force Dependence of RF MEMS Switch Contact Heating

Contact-type RF MEMS switches have demonstrated low on-state resistance, high off-state impedance, and very large bandwidth; however, their power handling capability is low due to failure caused by contact heating. This paper examines contact heating by measuring V-I curves for contacts in gold switches. Multiphysics modeling allows extraction of contact temperature. Contacts are found to soften and self-anneal at a temperature of about 100¡C, corresponding to a contact voltage of about 80 mV. Larger contact force induces a larger decrease in contact resistance during softening, suppressing contact heating. The data provide a better understanding of micro-scale contact physics, leading to design for switches for improved power-handling capability.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/87263/4/Saitou88.pd

Automated extraction of chemical structure information from digital raster images

Background: To search for chemical structures in research articles, diagrams or text representing molecules need to be translated to a standard chemical file format compatible with cheminformatic search engines. Nevertheless, chemical information contained in research articles is often referenced as analog diagrams of chemical structures embedded in digital raster images. To automate analog-to-digital conversion of chemical structure diagrams in scientific research articles, several software systems have been developed. But their algorithmic performance and utility in cheminformatic research have not been investigated. Results: This paper aims to provide critical reviews for these systems and also report our recent development of ChemReader -- a fully automated tool for extracting chemical structure diagrams in research articles and converting them into standard, searchable chemical file formats. Basic algorithms for recognizing lines and letters representing bonds and atoms in chemical structure diagrams can be independently run in sequence from a graphical user interface-and the algorithm parameters can be readily changed-to facilitate additional development specifically tailored to a chemical database annotation scheme. Compared with existing software programs such as OSRA, Kekule, and CLiDE, our results indicate that ChemReader outperforms other software systems on several sets of sample images from diverse sources in terms of the rate of correct outputs and the accuracy on extracting molecular substructure patterns. Conclusion: The availability of ChemReader as a cheminformatic tool for extracting chemical structure information from digital raster images allows research and development groups to enrich their chemical structure databases by annotating the entries with published research articles. Based on its stable performance and high accuracy, ChemReader may be sufficiently accurate for annotating the chemical database with links to scientific research articles.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/90875/1/Saitou8.pd

Growth dynamics of reactive-sputtering-deposited AlN films

8 pages, 7 figures.-- PACS nrs.: 81.05.Ea, 68.47.Fg, 81.15.Cd, 68.55.Ac, 68.55.Jk, 68.35.Bs.-- Issue title: "Structural, mechanical, thermodynamical and optical properties of condensed matter".We have studied the surface kinetic roughening of AlN films grown on Si(100) substrates by dc reactive sputtering within the framework of the dynamic scaling theory. Films deposited under the same experimental conditions for different growth times were analyzed by atomic force microscopy and x-ray diffraction. The AlN films display a (002) preferred orientation. We have found two growth regimes with a crossover time of 36 min. In the first regime, the growth dynamics is unstable and the films present two types of textured domains, well textured and randomly oriented, respectively. In contrast, in the second regime the films are homogeneous and well textured, leading to a relative stabilization of the surface roughness characterized by a growth exponent β=0.37±0.03. In this regime a superrough scaling behavior is found with the following exponents: (i) Global exponents: roughness exponent α=1.2±0.2 and β=0.37±0.03 and coarsening exponent 1/z=0.32±0.05; (ii) local exponents: α(loc)=1, β(loc)=0.32±0.01. The differences between the growth modes are found to be related to the different main growth mechanisms dominating their growth dynamics: sticking anisotropy and shadowing, respectively.Financial support from Spanish MCyT: Projects No. MAT 2002-04037-C03-03 and BFM 2003-07749-C05-01, BFM 2003-07749-C05-02, and BFM 2003-07749-C05-05, European Community: Project No. G5RD-CT-2000-00333, Slovak governmental Project No. 2003-SO 51/03R0600/01, and Slovak Grant Agency for Science VEGA, Project No. 2/3149/23, are acknowledged.Publicad

Endoscopy in the Diagnosis of Small Intestinal Tumors

The importance of endoscopy in the diagnosis of small intestinal tumors was evaluated in 15 patients with small intestinal tumors treated in our hospital. Two tumors were benign, and 13 were malignant (carcinoma in 5 patients, malignant lymphoma in 5 and leiomyosarcoma in 3). The presence of lesions could be determined by X-rays before surgery, but definitive diagnoses were difficult. When preoperative endoscopy of the small intestine was possible accurate preoperative diagnoses could be made based on the endoscopic findings and biopsies taken under direct vision. Endoscopy is therefore very important for the diagnosis of small intestinal tumors. It is necessary to develop small intestinal endoscopes that are easier to insert

Limit-cycle behavior in one-zone convective models

We present the results of a detailed set of one-zone models that account for the coupling between pulsation and convection following the original prescriptions of Stellingwerf (1986). Motivated by the arbitrary nature of the input parameters adopted in this theoretical framework, we computed several sequences of models that cover a substantial fraction of the parameter space and a longer integration time. We also included a turbulent pressure term and found that this physical mechanism plays a crucial role in the pulsation characteristics of the models by removing the sharp discontinuities along the light and the velocity curves showed by models that do not account for turbulent pressure. Finally, we investigated the vibrational and the pulsational stability of completely convective models. We consider as the most important finding of the present work the identification of a well-defined region in the parameter space where they approach limit-cycle stability. Several numerical experiments performed by adopting different values of the adiabatic exponent and of the shell thickness indicate that the coupling between pulsation and convection is the key driving mechanism for LPVs, a finding supported by recent theoretical predictions.Comment: 11 pages, 10 figures; accepted for publication in Astrophysical Journa

Widespread association between the ericoid mycorrhizal fungus Rhizoscyphus ericae and a leafy liverwort in the maritime and sub-Antarctic

A recent study identified a fungal isolate from the Antarctic leafy liverwort Cephaloziella varians as the ericoid mycorrhizal associate Rhizoscyphus ericae. However, nothing is known about the wider Antarctic distribution of R. ericae in C. varians, and inoculation experiments confirming the ability of the fungus to form coils in the liverwort are lacking. Using direct isolation and baiting with Vaccinium macrocarpon seedlings, fungi were isolated from C. varians sampled from eight sites across a 1875-km transect through sub- and maritime Antarctica. The ability of an isolate to form coils in aseptically grown C. varians was also tested. Fungi with 98–99% sequence identity to R. ericae internal transcribed spacer (ITS) region and partial large subunit ribosomal (r)DNA sequences were frequently isolated from C. varians at all sites sampled. The EF4/Fung5 primer set did not amplify small subunit rDNA from three of five R. ericae isolates, probably accounting for the reported absence of the fungus from C. varians in a previous study. Rhizoscyphus ericae was found to colonize aseptically-grown C. varians intracellularly, forming hyphal coils. This study shows that the association between R. ericae and C. varians is apparently widespread in Antarctica, and confirms that R. ericae is at least in part responsible for the formation of the coils observed in rhizoids of field-collected C. varians

Stable phantom-divide crossing in two scalar models with matter

We construct cosmological models with two scalar fields, which has the structure as in the ghost condensation model or k-essence model. The models can describe the stable phantom crossing, which should be contrasted with one scalar tensor models, where the infinite instability occurs at the crossing the phantom divide. We give a general formulation of the reconstruction in terms of the e-foldings N by including the matter although in the previous two scalar models, which are extensions of the scalar tensor model, it was difficult to give a formulation of the reconstruction when we include matters. In the formulation of the reconstruction, we start with a model with some arbitrary functions, and find the functions which generates the history in the expansion of the universe. We also give general arguments for the stabilities of the models and the reconstructed solution. The viability of a model is also investigated by comparing the observational data.Comment: 12 pages, 1 figur

Thiophaeococcus mangrovi gen. nov., sp. nov., a photosynthetic marine gammaproteobacterium isolated from Bhitarkanika mangrove forest, India

A coccoid, phototrophic purple sulfur bacterium was isolated in pure culture from a mud sample collected from brackish water in the Bhitarkanika mangrove forest of Orissa, India, in a medium containing 2 % NaCl (w/v). This bacterium, strain JA304T, was Gram-negative and had a requirement for NaCl. Intracellular photosynthetic membranes were of the vesicular type. The colour of the phototrophically grown culture was saddle-brown. Bacteriochlorophyll a and the carotenoid lycopene were present as photosynthetic pigments. Strain JA304T was able to grow photolithoautotrophically and could photoassimilate a number of organic substrates. Yeast extract was required for growth of strain JA304T. The DNA G+C content was 68.1–68.9 mol%. 16S rRNA gene sequence comparisons indicate that the isolate represents a member of the Chromatiaceae within the class Gammaproteobacteria. According to sequence comparison data, strain JA304T is positioned distinctly outside the group formed by the four genera Thiocystis, Chromatium, Allochromatium and Thermochromatium, with only 86.7–91.0 % sequence similarity. Distinct morphological, physiological and genotypic differences from these previously described taxa support the classification of this isolate as a representative of a novel species in a new genus, for which the name Thiophaeococcus mangrovi gen. nov., sp. nov. is proposed. The type strain of Thiophaeococcus mangrovi is JA304T (=JCM 14889T =DSM 19863T). PABA, para-aminobenzoic acid The GenBank/EMBL/DDBJ accession number for the 16S rRNA gene sequence of strain JA304T is AM748925. A phase-contrast micrograph and whole-cell absorption spectrum and an acetone spectrum of extracted pigments of strain JA304T are available as supplementary material with the online version of this paper