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You searched for +publisher:"Temple University" +contributor:("Coico, Richard"). Showing records 1 – 2 of 2 total matches.

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Temple University

1. Xu, Qifang. Statistical Analysis of Biological Interactions from Homologous Proteins.

Degree: PhD, 2008, Temple University

Computer and Information Science

Information fusion aims to develop intelligent approaches of integrating information from complementary sources, such that a more comprehensive basis is obtained for data analysis and knowledge discovery. Our Protein Biological Unit (ProtBuD) database is the first database that integrated the biological unit information from the Protein Data Bank (PDB), Protein Quaternary Server (PQS) and Protein Interfaces, Surfaces and Assemblies (PISA) server, and compared the three biological units side-by-side. The statistical analyses show that the inconsistency within these databases and between them is significant. In order to improve the inconsistency, we studied interfaces across different PDB entries in a protein family using an assumption that interfaces shared by different crystal forms are likely to be biologically relevant. A novel computational method is proposed to achieve this goal. First, redundant data were removed by clustering similar crystal structures, and a representative entry was used for each cluster. Then a modified k-d tree algorithm was applied to facilitate the computation of identifying interfaces from crystals. The interface similarity functions were derived from Gaussian distributions fit to the data. Hierarchical clustering was used to cluster interfaces to define the likely biological interfaces by the number of crystal forms in a cluster. Benchmark data sets were used to determine whether the existence or lack of existence of interfaces across multiple crystal forms can be used to predict whether a protein is an oligomer or not. The probability that a common interface is biological is given. An interface shared in two different crystal forms by divergent proteins is very likely to be biologically important. The interface data not only provide new interaction templates for computational modeling, but also provide more accurate data for training sets and testing sets in data-mining research to predict protein-protein interactions. In summary, we developed a framework which is based on databases where different biological unit information is integrated and new interface data are stored. In order for users from the biology community to use the data, a stand-alone software program, a web site with a user-friendly graphical interface, and a web service are provided.

Temple University – Theses

Advisors/Committee Members: Obradovic, Zoran, Dunbrack, Roland L., Vucetic, Slobodan, Latecki, Longin, Coico, Richard.

Subjects/Keywords: Information Science; Computer Science; biological units; homologous proteins; protbud; protein-protein interactions; structural bioinformatics; x-ray crystallography

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6th Edition):

Xu, Q. (2008). Statistical Analysis of Biological Interactions from Homologous Proteins. (Doctoral Dissertation). Temple University. Retrieved from http://digital.library.temple.edu/u?/p245801coll10,25686

Chicago Manual of Style (16th Edition):

Xu, Qifang. “Statistical Analysis of Biological Interactions from Homologous Proteins.” 2008. Doctoral Dissertation, Temple University. Accessed April 02, 2020. http://digital.library.temple.edu/u?/p245801coll10,25686.

MLA Handbook (7th Edition):

Xu, Qifang. “Statistical Analysis of Biological Interactions from Homologous Proteins.” 2008. Web. 02 Apr 2020.

Vancouver:

Xu Q. Statistical Analysis of Biological Interactions from Homologous Proteins. [Internet] [Doctoral dissertation]. Temple University; 2008. [cited 2020 Apr 02]. Available from: http://digital.library.temple.edu/u?/p245801coll10,25686.

Council of Science Editors:

Xu Q. Statistical Analysis of Biological Interactions from Homologous Proteins. [Doctoral Dissertation]. Temple University; 2008. Available from: http://digital.library.temple.edu/u?/p245801coll10,25686


Temple University

2. Moore, Andrea Rossi. COX-2 inhibition impaired resolution of chronic inflammation in a murine model of autoimmune arthritis.

Degree: PhD, 2010, Temple University

Microbiology and Immunology

Rheumatoid arthritis (RA) is a chronic disease characterized by cycles of inflammation and resolution. Previously, it was believed that the resolution of inflammation is simply dissipation of pro-inflammatory signals, although current research indicates that resolution is an active process. Acute inflammation follows defined phases of induction, inflammation and resolution, and resolution occurs by an active process that requires COX-2 activity. This study aims to address whether this paradigm extends to a recognized model of chronic inflammation. We demonstrated in murine collageninduced arthritis that chronic inflammation follows the same sequential course. While there is the normal production of pro-inflammatory cytokines during inflammation and anti-inflammatory mediators such as 15-deoxyΔ12,14PGJ2 (15d-PGJ2) during resolution, interestingly there is sustained production of both COX-2 and the presumably proinflammatory PGE2 during both phases. Blocking COX-2 activity and therefore production of PGE2 during the resolution phase perpetuated instead of attenuated inflammation. Repletion with PGE2 analogs restored homeostasis, and this function is mediated by the pro-resolving lipoxygenase metabolite, lipoxin A4 (LXA4), which is a potent stop signal. Thus, the study provided in vivo evidence for a natural, endogenous link between the cyclooxygenase-lipoxygenase pathways and showed that PGE2 serves as a feedback inhibitor essential for limiting chronic inflammation in autoimmune arthritis. These findings may explain the enigma regarding why COX-2 inhibitors are palliative rather than curative in humans because blocking resolution may mitigate the benefit of preventing induction.

Temple University – Theses

Advisors/Committee Members: Chan, Marion M., Coico, Richard, Fong, Dunne, Monestier, Marc, Safadi, Fayez F., Dun, Nae J..

Subjects/Keywords: Health Sciences, Immunology; autoimmunity; inflammation; lipid mediators; rheumatoid arthritis; rodent

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6th Edition):

Moore, A. R. (2010). COX-2 inhibition impaired resolution of chronic inflammation in a murine model of autoimmune arthritis. (Doctoral Dissertation). Temple University. Retrieved from http://digital.library.temple.edu/u?/p245801coll10,81890

Chicago Manual of Style (16th Edition):

Moore, Andrea Rossi. “COX-2 inhibition impaired resolution of chronic inflammation in a murine model of autoimmune arthritis.” 2010. Doctoral Dissertation, Temple University. Accessed April 02, 2020. http://digital.library.temple.edu/u?/p245801coll10,81890.

MLA Handbook (7th Edition):

Moore, Andrea Rossi. “COX-2 inhibition impaired resolution of chronic inflammation in a murine model of autoimmune arthritis.” 2010. Web. 02 Apr 2020.

Vancouver:

Moore AR. COX-2 inhibition impaired resolution of chronic inflammation in a murine model of autoimmune arthritis. [Internet] [Doctoral dissertation]. Temple University; 2010. [cited 2020 Apr 02]. Available from: http://digital.library.temple.edu/u?/p245801coll10,81890.

Council of Science Editors:

Moore AR. COX-2 inhibition impaired resolution of chronic inflammation in a murine model of autoimmune arthritis. [Doctoral Dissertation]. Temple University; 2010. Available from: http://digital.library.temple.edu/u?/p245801coll10,81890

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