Enforcing Ontological Rules in UML-Based Conceptual Modeling: Principles and Implementation (2009)
Abstract. UML is used for at least two purposes: OO software design, and conceptual modeling. However, UML's origins in software engineering may limit its appropriateness for conceptual...
ABSTRACT CP-Miner: A Tool for Finding Copy-paste and Related Bugs in Operating System Code (2008)
Zhenmin Li, Shan Lu, Suvda Myagmar, Yuanyuan Zhou
Copy-pasted code is very common in large software because programmers prefer reusing code via copy-paste in order to reduce programming effort. Recent studies show that copy-paste is prone to...
Shan Lu, Joseph Tucek, Feng Qin, Yuanyuan Zhou, Violation Bugs
...... Of all software bugs, concurrency bugs in multithreaded and multiprocess programs are among the most difficult to test for and diagnose. Their notorious nondeterminism frustrates both in-house...
A Dynamic Programming Approach to the Study of Protein Sequence Variations (2008)
Arthur W. Chou, Bioinformatics Program, Shan Lu
Abstract: We propose a dynamic programming method to design efficient algorithms to analyze the genetic variation of gene of interest from different isolates, to search for the pattern and rule of...
H.4.m [Information Systems Applications]: Miscellaneous; (2008)
Chad Verbowski, Emre K, Brad Daniels, Shan Lu, Roussi Roussev, Yi-min Wang, ...
A primary challenge to building reliable and secure computer systems is managing the persistent state (PS) of the system: all the executable files, configuration settings and other data that govern...
Shan Lu, Guido Jenster, Daniel E. Epner
Previous studies have shown that androgen upregulates expression of the p21 (WAF1, CIP1, SDI1, CAP20) gene, which contains a canonical androgen response element (ARE) in its proximal promoter region....
Kennedy, Jeffrey S., Co, Mary Dawn T., Green, Sharone, Longtine, Karen J., Longtine, Jaclyn K., O'Neill, Melissa A., ...
This report describes the safety observations following administration of a polyvalent DNA prime-protein boost HIV-1 vaccine formulated with adjuvant QS21. Local injection site reactions were the...
Lee, Kiwon, Liu, Yin, Mo, Jun, Zhang, Jinsong, Dong, Zhongyun, Lu, Shan
Abstract Background Our previous study revealed that Vav3 oncogene is overexpressed in human prostate cancer, activates androgen receptor, and stimulates growth in prostate cancer cells. The current...
Vaine, Michael, Wang, Shixia, Crooks, Emma T., Jiang, Pengfei, Montefiori, David C., Binley, James, ...
A major challenge in HIV-1 vaccine development is to elicit potent and broadly neutralizing antibodies effective against primary viral isolates. Previously, we showed that DNA prime-protein boost...
Immunogenicity of DNA vaccines in humans: it takes two to tango (2008)
Two recently completed phase I clinical trials with candidate HIV-1 vaccines demonstrated that DNA vaccines are, indeed, immunogenic in humans, even when administered through routine needle...
PUBLICATIONS REFEREED JOURNAL ARTICLES (2008)
Shan Lu, Software Systems, Computer Architecture, Shan Lu, Joe Tucek, Feng Qin, ...
ABSTRACT CP-Miner: A Tool for Finding Copy-paste and Related Bugs in Operating System Code (2008)
Zhenmin Li, Shan Lu, Suvda Myagmar, Yuanyuan Zhou
Copy-pasted code is very common in large software because programmers prefer reusing code via copy-paste in order to reduce programming effort. Recent studies show that copy-paste is prone to...
Current progress of DNA vaccine studies in humans (2008)
Lu, Shan, Wang, Shixia, Grimes-Serrano, Jill M.
Despite remarkable progress in the field of DNA vaccine research since its discovery in the early 1990 s, the formal acceptance of this novel technology as a new modality of human vaccines depends on...
Wang, Shixia, Joshi, Swati, Mboudjeka, Innocent, Liu, Fangjun, Ling, Tzufan, Goguen, Jon D., ...
Yersinia Pestis outer proteins, plasminogen activator protease and Yop secretion protein F are necessary for the full virulence of Yesinia pestis and have been proposed as potential protective...
Wang, Shixia, Kennedy, Jeffrey S., West, Kim, Montefiori, David C., Coley, Scott E., Lawrence, John M., ...
An optimally effective AIDS vaccine would likely require the induction of both neutralizing antibody and cell-mediated immune responses, which has proven difficult to obtain in previous clinical...
Sakhatskyy, Pavlo V., Wang, Shixia, Zhang, Chuanyou, Chou, Te-Hui, Kishko, Michael G., Lu, Shan
The viral strain responsible for smallpox infection is variola major (VARV). As a result of the successful eradication of smallpox with the vaccinia virus (VACV), the general population is no longer...
Pouliot, Kimberly Lea, Pan, Ning, Wang, Shixia, Lu, Shan, Lien, Egil, Goguen, Jon D.
Pathogenic members of the Yersinia genus require the translocator protein LcrV for proper function of the type III secretion apparatus, which is crucial for virulence. LcrV has also been reported to...
Triage: Diagnosing production run failures at the users site (2007)
Joseph Tucek, Shan Lu, Chengdu Huang, Spiros Xanthos, Yuanyuan Zhou
Diagnosing production run failures is a challenging yet important task. Most previous work focuses on offsite diagnosis, i.e. development site diagnosis with the programmers present. This is...
Shan Lu, Soyeon Park, Chongfeng Hu, Xiao Ma, Weihang Jiang, Zhenmin Li, ...
Software defects significantly reduce system dependability. Among various types of software bugs, semantic and concurrency bugs are two of the most difficult to detect. This paper proposes a novel...
Triage: Diagnosing production run failures at the users site (2007)
Joseph Tucek, Shan Lu, Chengdu Huang, Spiros Xanthos, Yuanyuan Zhou
Diagnosing production run failures is a challenging yet important task. Most previous work focuses on offsite diagnosis, i.e. development site diagnosis with the programmers present. This is...
Sweeper: A lightweight end-to-end system for defending against fast worms (2007)
Joseph Tucek, James Newsome, Shan Lu, Chengdu Huang, Spiros Xanthos, David Brumley, ...
The vulnerabilities which plague computers cause endless grief to users. Slammer compromised millions of hosts in minutes; a hit-list worm would take under a second. Recently proposed techniques...
A study of interleaving coverage criteria (2007)
Shan Lu, Weihang Jiang, Yuanyuan Zhou
Concurrency bugs are becoming increasingly important due to the prevalence of concurrent programs. A fundamental problem of concurrent program bug detection and testing is that the interleaving space...
Shan Lu, Soyeon Park, Chongfeng Hu, Xiao Ma, Weihang Jiang, Zhenmin Li, ...
Software defects significantly reduce system dependability. Among various types of software bugs, semantic and concurrency bugs are two of the most difficult to detect. This paper proposes a novel...
Wang, Shixia, Taaffe, Jessica, Parker, Christopher S., Solorzano, Alicia, Cao, Hong, Garcia-Sastre, Adolfo, ...
Effective antibody responses provide crucial immunity against influenza virus infection. The hemagglutinin (HA) protein is the major target of protective antibody responses induced by viral infection...
CP-Miner: Finding Copy-Paste and Related Bugs in Large-Scale Software Code (2006)
Zhenmin Li, Shan Lu, Suvda Myagmar, Yuanyuan Zhou
Abstract—Recent studies have shown that large software suites contain significant amounts of replicated code. It is assumed that some of this replication is due to copy-and-paste activity and that...
AVIO: Detecting Atomicity Violations via Access Interleaving Invariants (2006)
Shan Lu, Joseph Tucek, Feng Qin, Yuanyuan Zhou
Abstract Concurrency bugs are among the most difficult to test and diagnoseof all software bugs. The multicore technology trend worsens this
Automatic On-line Failure Diagnosis at the End-User Site (2006)
Joseph Tucek, Shan Lu, Chengdu Huang, Spiros Xanthos, Yuanyuan Zhou
Production run software failures cause endless grief to end-users, and endless challenges to programmers as they commonly have incomplete information about the bug, facing great hurdles to reproduce...
Flight Data Recorder: Monitoring persistent-state interactions to improve systems management (2006)
Chad Verbowski, Emre Kıcıman, Arunvijay Kumar, Brad Daniels, Shan Lu, Juhan Lee, ...
Mismanagement of the persistent state of a system—all the executable files, configuration settings and other data that govern how a system functions—causes reliability problems, security...
Zhenmin Li, Lin Tan, Xuanhui Wang, Shan Lu, Yuanyuan Zhou, Chengxiang Zhai
Software errors are a major cause for system failures. To effectively design tools and support for detecting and recovering from software failures requires a deep understanding of bug 1...
Flight Data Recorder: Monitoring persistent-state interactions to improve systems management (2006)
Chad Verbowski, Emre Kıcıman, Arunvijay Kumar, Brad Daniels, Shan Lu, Juhan Lee, ...
Mismanagement of the persistent state of a system—all the executable files, configuration settings and other data that govern how a system functions—causes reliability problems, security...
PathExpander: Architectural Support for Increasing the Path Coverage of Dynamic Bug Detection (2006)
Shan Lu, Pin Zhou, Wei Liu, Yuanyuan Zhou, Josep Torrellas
Dynamic software bug detection tools are commonly used because they leverage run-time information. However, they suffer from a fundamental limitation, the Path Coverage Problem: they detect bugs only...
Yeast Model Uncovers Dual Roles of Mitochondria in the Action of Artemisinin (2005)
Wei Li, Weike Mo, Dan Shen, Libo Sun, Juan Wang, Shan Lu, ...
Artemisinins, derived from the wormwood herb Artemisia annua, are the most potent antimalarial drugs currently available. Despite extensive research, the exact mode of action of artemisinins has not...
Wang, Shixia, Arthos, James, Lawrence, John M., Van Ryk, Donald I., Mboudjeka, Innocent, Shen, Siyuan, ...
Strategies are needed for human immunodeficiency virus type 1 vaccine development that improves the neutralizing antibody response against primary isolates of the virus. Here we examined recombinant...
Wang, Shixia, Chou, Te-hui W., Sakhatskyy, Pavlo V., Huang, Song, Lawrence, John M., Cao, Hong, ...
The Spike (S) protein of the severe acute respiratory syndrome-associated coronavirus (SARS-CoV) plays important roles in viral pathogenesis and potentially in the development of an effective vaccine...
Design of computerized drug delivery control system / (2005)
"Supervisor, Associate Prof. Zhu Kuanyi."
Bugbench: Benchmarks for evaluating bug detection tools (2005)
Shan Lu, Zhenmin Li, Feng Qin, Lin Tan, Pin Zhou, Yuanyuan Zhou
Benchmarking provides an effective way to evaluate different tools. Unfortunately, so far there is no good benchmark suite to systematically evaluate software bug detection tools. As a result, it is...
Blob Analysis of the Head and Hands: A Method for Deception Detection (2005)
Shan Lu, Gabriel Tsechpenakis, Dimitris N. Metaxas
Behavioral indicators of deception and behavioral state are extremely difficult for humans to analyze. Blob analysis, a method for analyzing the movement of the head and hands based on the...
AccMon: Automatically Detecting Memory-related Bugs via Program Counter-based Invariants (2004)
Pin Zhou, Wei Liu, Long Fei, Shan Lu, Feng Qin, Yuanyuan Zhou, ...
This paper makes two contributions to architectural support for software debugging. First, it proposes a novel statistics-based, onthe -fly bug detection method called PC-based invariant detection....
AccMon: Automatically Detecting Memory-related Bugs via Program Counter-based Invariants (2004)
Pin Zhou, Wei Liu, Long Fei, Shan Lu, Feng Qin, Yuanyuan Zhou, ...
This paper makes two contributions to architectural support for software debugging. First, it proposes a novel statistics-based, onthe-fly bug detection method called PC-based invariant detection....
Using multiple cues for hand tracking and model refinement (2003)
We present a model based approach to the integration of multiple cues for tracking high degree of freedom articulated motions and model refinement. We then apply it to the problem of hand tracking...
Model-based Integration of Visual Cues for Hand Tracking (2002)
Shan Lu, Gang Huang, Dimitris Samaras, Dimitris Metaxas
We present a model based approach to the integration of multiple cues for tracking high degree of freedom articulated motions. We then apply it to the problem of hand tracking using a single camera...
Typescript.
Lu, Shan, Wyatt, Richard T., Richmond, Joan F. L., Mustafa, Farah, Wang, Shixia, Weng, Jiayu, ...
DNA vaccines that express the human immunodeficiency virus type 1 HXB-2 envelope glycoprotein (Env) with or without deletions of the major variable regions V1/V2 and V3 were tested for the ability to...
Richmond, Joan F. L., Mustafa, Farah, Lu, Shan, Santoro, Joseph C., Weng, Jiayu, O'Connell, Maryellen, ...
HIV-1 envelopes from two series of primary isolates (from Swedish patients 5 and 6), from JR-FL and BaL (prototypic monocyte/macrophage tropic viruses) and from HXB-2 (a prototypic...
Mustafa, Farah, Richmond, Joan F. L., Fernandez-Larsson, Roberto, Lu, Shan, Fredriksson, Robert, Fenyo, Eva Maria, ...
Seven envelope regions from two series of patient isolates have been molecularly cloned and analyzed for replication phenotypes and immunogenicity. Growth potential was analyzed for env sequences...
Simian immunodeficiency virus DNA vaccine trial in macaques (1996)
Lu, Shan, Arthos, James, Montefiori, David C., Yasutomi, Yasuhiro, Manson, Kelledy, Mustafa, Farah, ...
An experimental vaccine consisting of five DNA plasmids expressing different combinations and forms of simian immunodeficiency virus-macaque (SIVmac) proteins has been evaluated for the ability to...
Robinson, Harriet L., Lu, Shan, Feltquate, David Marc, Torres, Celia Aurora Tiglao, Richmond, Joann M., Boyle, Christine Margaret, ...
Yasutomi, Yasuhiro, Robinson, Harriet L., Lu, Shan, Mustafa, Farah, Lekutis, Christine, Arthos, James, ...
In view of the growing evidence that virus-specific cytotoxic T lymphocytes (CTL) play an important role in containing the early spread of human immunodeficiency virus type 1 (HIV-1) in infected...
NONLINEAR MODELING AND PROCESSING OF SPEECH WITH APPLICATIONS TO SPEECH CODING (1995)
IN recent years there has been increasing interest in nonlinear speech modeling. In our approach, a speech signal is modeled as a sum of jointly amplitude (AM) and frequency (FM) modulated cosines...
Characterization of the human tissue transglutaminase gene promoter (1995)
Transglutaminases are a family of calcium-dependent enzymes, that catalyze the covalent cross-linking of proteins by forming $\varepsilon(\gamma$-glutamyl)lysine isopeptide bonds. In order to...
Lu, Shan, Putney, Scott D., Robinson, Harriet L.
The entry of human immunodeficiency virus type 1 into two T-cell lines has been analyzed to determine the relative time courses with which virus entry can be blocked (i) by washing, (ii) by adding a...
Fernandez-Larsson, Roberto, Srivastava, Kishore K., Lu, Shan, Robinson, Harriet L.
Isolates of human immunodeficiency virus type 1 (HIV-1) undergo many different rates of replication, with the time course of replication being determined by the host cell and the virus. Recently, we...
Biophysical mechanism of the scavenger site near T cell-presented epitopes (1992)
Lu, Shan, Reyes, Victor E., Bositis, Christopher M., Goldschmidt, Thomas G., Lam, Valery, Torgerson, Rochelle R., ...
We seek to identify consensus sequences in digested fragments of antigenic proteins regulating selection and major histocompatibility complex (MHC)-restricted presentation to T cells of epitopes...
Common principles in protein folding and antigen presentation (1991)
Lu, Shan, Reyes, Victor E., Torgerson, Rochelle R., Lew, Robert A., Humphreys, Robert E.
The regular recurrence of hydrophobic amino acid residues along a peptide sequence determines the formation of a longitudinal hydrophobic strip when the peptide forms an alpha-helix. An understanding...
Lu, Shan, Ciardelli, Thomas, Reyes, Victor E., Humphreys, Robert E.
alpha-Helix formation of a peptidyl sequence is stabilized by hydrophobic residues recurring at positions which create a longitudinal hydrophobic strip upon folding of the sequence as a helix against...
Cathepsin B cleavage of Ii from class II MHC alpha- and beta-chains (1991)
Reyes, Victor E., Lu, Shan, Humphreys, Robert E.
Class II MHC-associated invariant chain (Ii) might regulate binding of digested peptides to the Ag binding site (desetope) of class II MHC proteins by directly or allosterically blocking that site...
Reyes, Victor E., Lu, Shan, Humphreys, Robert E.
In order to determine how T cell-presented peptides associate with the antigen binding sites (desetopes) of class I major histocompatibility complex (MHC) molecules and how they might be scavenged...
Reyes, Victor E., Lew, Robert A., Lu, Shan, Humphreys, Robert E.
Recurrent aliphatic hydrophobic amino acids which occur in the sequence of a protein or a peptide at positions which form an axial, hydrophobic strip when the sequence is coiled as an alpha helix...
The overall objective of this study was to understand the mechanisms that control antigen processing and binding of peptides to major histocompatibility complex (MHC) molecules. Towards this goal I...
Comparison of three related methods to select T cell-presented sequences of protein antigens (1990)
Reyes, Victor E., Fowlie, Elisabeth J., Lu, Shan, Phillips, Lisa, Chin, L. Thomas, Humphreys, Robert E., ...
A comparison of three methods to predict T cell-presented sequences within antigenic proteins led to the view that recurrent hydrophobic residues might nucleate excised peptides as alpha-helices...
Lu, Shan, Reyes, Victor E., Lew, Robert A., Anderson, Jacqueline K., Mole, John E., Humphreys, Robert E., ...
We tested the hypothesis that the recurrence of hydrophobic amino acids in a polypeptide at positions falling in an axial, hydrophobic strip if the sequence were coiled as an alpha helix, can lead to...
Elliot, William L., Lu, Shan, Nguyen, Que, Reisert, Patricia S., Sairenji, Takeshi, Sorli, Christopher H., ...
The p35 protein which is hyperexpressed on hairy leukemic cells was determined to be Ii, the electrophoretically invariant glycoprotein that is associated with class II major histocompatibility...
Pouliot, Kimberly, Pan, Ning, Wang, Shixia, Lu, Shan, Lien, Egil, Goguen, Jon D.
Pathogenic members of the Yersinia genus require the translocator protein LcrV for proper function of the type III secretion apparatus, which is crucial for virulence. LcrV has also been reported to...
Lu, Shan, Van Eck, Joyce, Zhou, Xiangjun, Lopez, Alex B., O'Halloran, Diana M., Cosman, Kelly M., ...
Despite recent progress in our understanding of carotenogenesis in plants, the mechanisms that govern overall carotenoid accumulation remain largely unknown. The Orange (Or) gene mutation in...
Vlasova, Anastasia N., Zhang, Xinsheng, Hasoksuz, Mustafa, Nagesha, Hadya S., Haynes, Lia M., Fang, Ying, ...
In 2002, severe acute respiratory syndrome-associated coronavirus (SARS-CoV) emerged in humans, causing a global epidemic. By phylogenetic analysis, SARS-CoV is distinct from known CoVs and most...
Recycling of Shiga Toxin 2 Genes in Sorbitol-Fermenting Enterohemorrhagic Escherichia coli O157:NM▿
Mellmann, Alexander, Lu, Shan, Karch, Helge, Xu, Jian-guo, Harmsen, Dag, Schmidt, M. Alexander, ...
Using colony blot hybridization with stx2 and eae probes and agglutination in anti-O157 lipopolysaccharide serum, we isolated stx2-positive and eae-positive sorbitol-fermenting (SF) enterohemorrhagic...
Bansal, Anju, Jackson, Bethany, West, Kim, Wang, Shixia, Lu, Shan, Kennedy, Jeffrey S., ...
A phase I clinical vaccine study of a human immunodeficiency virus type 1 (HIV-1) vaccine regimen comprising a DNA prime formulation (5-valent env and monovalent gag) followed by a 5-valent Env...
Vaine, Michael, Wang, Shixia, Crooks, Emma T., Jiang, Pengfei, Montefiori, David C., Binley, James, ...
A major challenge in human immunodeficiency virus type 1 (HIV-1) vaccine development is to elicit potent and broadly neutralizing antibodies that are effective against primary viral isolates....
Cao, Cong, Lu, Shan, Kivlin, Rebecca, Wallin, Brittany, Card, Elizabeth, Bagdasarian, Andrew, ...
AMP-activated protein kinase or AMPK is an evolutionarily conserved sensor of cellular energy status, activated by a variety of cellular stresses that deplete ATP. However, the possible involvement...