Oxygen sensitive paper

Paper is impregnated with mixture of methylene blue and ethylenediaminetetraacetic acid. Methylene blue is photo-reduced to leuco-form. Paper is kept isolated from oxygen until ready for use. Paper can be reused by photo-reduction after oxygen exposure

Citation Handling: Processing Citation Texts in Scientific Documents

Citation sentences (sentences that cite other papers) play a key role in the summarization of scientific articles. However, a citation-based summarization system that depends on generic natural language processing components, such as parsers or sentence compressors, will perform poorly if those components cannot handle citations correctly. In this thesis, I examine the effect of citation handling on parsing, sentence compression, and multi-document summarization. There are two types of citations that occur in citation sentences: constituent citations and parenthetical citations. I propose an automatic citation classifier based on training data created through Mechanical Turk tasks. I demonstrate that the use of type-specific citation handling as pre-processing improves the performance of a state-of-the-art generic parser, both for quality of the parse trees and running time. Extrinsic evaluations demonstrate that improving the performance of a parser on citation sentences in turn improves the performance of a sentence compressor, Trimmer (Zajic et al., 2007), and a multi-document summarization system, MASCS, according to several summarization measures

Citation Handling for Improved Summarization of Scientific Documents

In this paper we present the first steps toward improving summarization of scientific documents through citation analysis and parsing. Prior work (Mohammad et al., 2009) argues that citation texts (sentences that cite other papers) play a crucial role in automatic summarization of a topical area, but did not take into account the noise introduced by the citations themselves. We demonstrate that it is possible to improve summarization output through careful handling of these citations. We base our experiments on the application of an improved trimming approach to summarization of citation texts extracted from Question-Answering and Dependency-Parsing documents. We demonstrate that confidence scores from the Stanford NLP Parser (Klein and Manning, 2003) are significantly improved, and that Trimmer (Zajic et al., 2007), a sentence-compression tool, is able to generate higher-quality candidates. Our summarization output is currently used as part of a larger system, Action Science Explorer (ASE) (Gove, 2011)

The Disulfide Bonds in Glycoprotein E2 of Hepatitis C Virus Reveal the Tertiary Organization of the Molecule

Hepatitis C virus (HCV), a major cause of chronic liver disease in humans, is the focus of intense research efforts worldwide. Yet structural data on the viral envelope glycoproteins E1 and E2 are scarce, in spite of their essential role in the viral life cycle. To obtain more information, we developed an efficient production system of recombinant E2 ectodomain (E2e), truncated immediately upstream its trans-membrane (TM) region, using Drosophila melanogaster cells. This system yields a majority of monomeric protein, which can be readily separated chromatographically from contaminating disulfide-linked aggregates. The isolated monomeric E2e reacts with a number of conformation-sensitive monoclonal antibodies, binds the soluble CD81 large external loop and efficiently inhibits infection of Huh7.5 cells by infectious HCV particles (HCVcc) in a dose-dependent manner, suggesting that it adopts a native conformation. These properties of E2e led us to experimentally determine the connectivity of its 9 disulfide bonds, which are strictly conserved across HCV genotypes. Furthermore, circular dichroism combined with infrared spectroscopy analyses revealed the secondary structure contents of E2e, indicating in particular about 28% β-sheet, in agreement with the consensus secondary structure predictions. The disulfide connectivity pattern, together with data on the CD81 binding site and reported E2 deletion mutants, enabled the threading of the E2e polypeptide chain onto the structural template of class II fusion proteins of related flavi- and alphaviruses. The resulting model of the tertiary organization of E2 gives key information on the antigenicity determinants of the virus, maps the receptor binding site to the interface of domains I and III, and provides insight into the nature of a putative fusogenic conformational change

A novel strategy for expressing recombinant HCV glycoproteins in cell culture: toward biochemical, biophysical, and immunological studies

Almost 4 million people are infected with hepatitis C virus (HCV) in the United States alone, with 170 million infected worldwide. It is the leading cause of liver transplantation in the US. Although infection is initially asymptomatic, HCV often leads to chronic liver disease, cirrhosis, and/or liver cancer. Many cases are treatable with combination therapy (interferon, ribavirin, and new protease inhibitors), but efficacy is dependent on the infecting strain and there is currently no vaccine. Without more effective antiviral and immunological treatments, the Centers for Disease Control and Prevention (CDC) predicts that deaths due to HCV will double or triple in the next 15 to 20 years due to prolonged disease and continued spread. The high prevalence of infection, lack of highly effective HCV-specific inhibitors, and poor response rate to the current treatment underscore the importance of developing new therapeutic strategies. The mechanism of viral entry is an important subject of study with respect to preventing and treating infection. Two of the four HCV structural proteins, envelope 1 (E1) and envelope 2 (E2), heterodimerize on the surface of the virion. Experimental evidence supports the roles of E1 and E2 in receptor binding, virus-cell fusion, and entry into the host cell. These factors make E1 and E2 key determinants of pathogenicity and optimal targets of vaccine design. We hypothesize that a thorough biophysical understanding of E2, as well as improvements in the available biochemical tools for the study of HCV E2 will provide a significant advancement in the understanding of viral infection.Ph. D.Includes bibliographical referencesby Jillian L. Whidb

Precision machining of a turbine nozzle segment

M.S.Thomas R. Kurfes