Yu Lei

University of Texas at Arlington, Arlington, Texas, United States

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Publications (48)16.91 Total impact

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    ABSTRACT: Blood CXCR5+CD4+ T cells are defined as circulating T follicular helper (TFH) cells, which is required for effective humoral immunity. This study aimed to investigate the role of circulating TFH cells in patients with chronic hepatitis B virus (CHB) infection. The frequency and phenotype of circulating TFH cells were monitored by flow cytometry in CHB patients and in healthy controls (HC). The expression of BCL-6, IL-21, IL-4, CXCR5, and IL-6R mRNA was analyzed using real-time PCR. Serum HBsAg, HBeAg, HBeAb, HBV DNA loads, ALT and AST were determined. The potential association of the frequency of TFH cells and their surface markers with clinical parameters was assessed. The frequency of CXCR5+CD4+ T cells was increased in CHB patients and positively correlated with ALT and AST but not with HBV DNA loads. Moreover, an expansion of ICOS-, PD-1-, CD40L-, and IL-21R-expressing TFH cells occurred in CHB patients, but failed to correlate with ALT, AST and HBV DNA loads. Interestingly, the frequency of CXCR5+CD4+ T cells and ICOS+CXCR5+CD4+ T cells was significantly higher in HBeAg positive CHB patients than in HC. Additionally, the percentages of CXCR5+CD4+ T cells were positively correlated with AST, and ICOS-expressing CXCR5+CD4+ T cells were negatively correlated with HBV DNA loads. No significant differences in the frequency of CXCR5+CD4+ T cells were observed between inactive carrier (IC) patients and healthy controls. However, ICOS-, PD-1-, CD40L-expressing TFH cells were increased in IC patients and positively correlated with AST. Furthermore, the expression of BCL-6, IL-21, IL-4, CXCR5, and IL-6R mRNA in TFH cells was higher in CHB patients than in HC. These data demonstrate that circulating TFH cells may participate in HBV-related immune responses. In addition to the frequency of TFH cells, the phenotype of these cells plays an important role in CHB patients.
    Virology Journal 03/2014; 11(1):54. · 2.09 Impact Factor
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    ABSTRACT: To study the role of tumor necrosis factor-alpha (TNFalpha) in the anti-replication effects of tetracycline (Tet) on hepatitis B virus (HBV). The Tet-dependent regulatory fragment (TO) was PCR amplified from the pcDNA4TM/TO vector, inserted into the pUC118 cloning vector, and verified by sequencing. The counterpart fragment in the pVITRO3 expression vector, which contains two multiple cloning sites (MCSs), was replaced with the confirmed TO to generate a pVITRO3-TO vector. The Tet repressor (TR) gene from the pcDNA6/TR regulatory vector was incorporated into one MCS of pVITRO3-TO and the TNFalpha gene was subsequently incorporated into the other MCS. The resultant vector, pVITRO3-TOTR-TNFalpha, was transiently transfected into HepG2 cells. TNFalpha expression from the vector was induced by exposure to various concentrations of Tet and measured by enzyme-linked immunosorbent assay to determine the appropriate Tet concentration for experimentation. To investigate whether Tet inhibits TNFalpha expression as a mechanism of its anti-replication activity against HBV, the HepG2.2.15 cell line stably transfected with pVITRO3-TOTR-TNFalpha was used as an HBV replication model. Levels of hepatitis B e antigen (HBeAg) and hepatitis B surface antigen (HBsAg) were detected by immunoassay. HBV DNA level was detected by fluorescence quantitative PCR. The TNFalpha expression from the newly constructed pVITRO3-TOTR-TNFalpha vector was Tet-controllable in the eukaryotic cells examined. The optimal concentration of Tet for the experimental system was 1.0 mug/ml. HBsAg and HBeAg expression was down-regulated in the HepG2.2.15 cells stably transfected with the pVITRO3-TO-TR-TNFalpha vector. After incubation with Tet for 1, 3 and 5 days, the inhibition rate of HBsAg was 2%, 1.1% and 0, compared to 14.8%, 11.5% and 28.4% in the non-Tet control group. The corresponding inhibition rates of HBeAg were 50.0%, 26.7% and 47.9%, compared to 0.3%, 1.6% and 0.0%, in the control group. HBV DNA levels in the cells and the cell culture supernatants exposed to Tet were decreased by 70.3% and 79.9%, respectively. TNFalpha inhibited production of HBsAg mRNA. A Tet-dependent regulatory fragment double-expressing TNFalpha single vector system was constructed successfully, achieving controllable TNFalpha expression in both transiently transfected eukaryotic cells and stable cell lines. In this HBV cell model system, Tet-induced overexpression of human TNFalpha inhibited HBV DNA replication and reduced HBsAg and HBeAg expression. Inhibition of HBV transcription may be a key role of TNFalpha against HBV replication.
    Zhonghua gan zang bing za zhi = Zhonghua ganzangbing zazhi = Chinese journal of hepatology 03/2014; 22(3):213-8.
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    ABSTRACT: A software product line is a set of software systems that share some common features. Several recent works have been reported that apply combinatorial testing, a very effective testing strategy, to software product lines. A unique challenge in these efforts is dealing with a potentially large number of constraints among different features. In this paper, we propose a novel constraint-handling strategy that uses minimum invalid tuples (MITs) as an alternative to traditional constraint solvers. Our approach systematically derives all MITs from a software product line, and uses them to quickly determine the validity of a test configuration during test generation. We implemented a test generation research tool called LOOKUP that integrates the proposed constraint-handling strategy with a general test generation algorithm called IPOG-C. Experimental results show that LOOKUP performs considerably better than two existing test generation tools in terms of test size and execution time.
    Proceedings of the 2014 IEEE 15th International Symposium on High-Assurance Systems Engineering; 01/2014
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    ABSTRACT: Security testing aims at detecting program security flaws through a set of test cases and has become an active area of research. The challenge is how to efficiently produce test cases that are highly effective in detecting security flaws. This paper presents a novel distributed demand-driven security testing system to address this challenge. It leverages how end users use the software to increase the coverage of essential paths for security testing. The proposed system consists of many client sites and one testing site. The software under test is installed at each client site. Whenever a new path is about to be exercised by a user input, it will be sent to the testing site for security testing. At the testing site, symbolic execution is used to check any potential vulnerability on this new path. If a vulnerability is detected, a signature is automatically generated and updated to all client sites for protection. The benefits are as follows. First, it allows us to focus testing on essential paths, i.e., the paths that are actually being explored by users or attackers. Second, it stops an attacker from exploiting an unreported vulnerability at the client site. A prototype system has been implemented to evaluate the performance of the proposed system. The results show that it is both effective and efficient in practice.
    Journal of Systems and Software 01/2014; 87:60–73. · 1.14 Impact Factor
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    ABSTRACT: Mother-to-child transmission (MTCT) is the main mode of spread of hepatitis B virus (HBV) in China. We performed a meta-analysis to compare the effects of three measures for prevention of MTCT. A meta-analysis was performed on randomized controlled trials and non-randomized studies comparing the index of MTCT among five groups of pregnant women: hepatitis B immunoglobulin (HBIG) administration, antiviral treatment, placebo, elective caesarean section, and vaginal delivery. Compared with the control group, the incidence of HBV intrauterine infection (RR = 0.42, 95 % CI 0.27-0.64, P < 0.0001) and the number of chronic hepatitis B (CHB) infants (RR = 0.44, 95 % CI 0.32-0.61, P < 0.00001) were lower in the HBIG administration group. In the antiviral treatment group, serum HBV DNA levels were lower (MD = -4.01, 95 % CI -5.07 to -2.94, P < 0.00001) at the time of delivery, and normalization of ALT levels was better (RR = 1.11, 95 % CI 1.06-1.17, P < 0.0001). Infant serum HBsAg positivity (RR = 0.45, 95 % CI 0.22-0.91, P = 0.03) and incidence of infant HBV transmission RR = 0.06, 95 % CI 0.01-0.24, P < 0.0001) were reduced in antiviral the treatment group. Infant serum anti-HBs positivity at birth (RR = 1.24, 95 % CI 0.89-1.74, P = 0.2) or at 6-7 months (RR = 0.98, 95 % CI 0.86-1.11, P = 0.73) was not significantly different between the caesarean section and vaginal delivery groups. The incidence of infant CHB infection may have been higher in the vaginal delivery group (RR = 2.20, 95 % CI 1.02-4.74, P = 0.04). Administration of HBIG or antiviral therapy to HBV carrier mothers during pregnancy is effective in reducing MTCT.
    Digestive Diseases and Sciences 11/2013; · 2.26 Impact Factor
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    ABSTRACT: Empirical data demonstrate the value of t-way coverage, but in some testing situations, it is not practical to use covering arrays. However any set of tests covers at least some proportion of t-way combinations. This paper describes a variety of measures of combinatorial coverage that can be used in evaluating aspects of t-way coverage of a test suite. We also provide lower bounds on t-way coverage of several widely-used testing strategies, and describe a tool that analyzes test suites using the measures discussed in the paper.
    Software Testing, Verification and Validation Workshops (ICSTW), 2013 IEEE Sixth International Conference on; 01/2013
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    ABSTRACT: In this paper, we introduce a combinatorial test generation research tool called Advanced Combinatorial Testing System (or ACTS). ACTS supports t-way combinatorial test generation with several advanced features such as mixed-strength test generation and constraint handling. To facilitate its use and integration with other tools, ACTS provides three types of external interface, including a graphic user interface, a command line interface, and an application programming interface. ACTS is a freely distributed research tool and has been downloaded by more than 1200 companies and organizations.
    Software Testing, Verification and Validation (ICST), 2013 IEEE Sixth International Conference on; 01/2013
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    ABSTRACT: To investigate the impact of interferon-stimulated exonuclease 20 kDa (ISG20) on replication of genotype 2a hepatitis C virus (HCV) subgenomic replicon RNA and infectivity of the cell culture-derived HCV strain JFH1 to determine the potential of exogenously expressed ISG20 as an anti-viral therapy of chronic hepatitis C. Plasma vectors containing wild-type (WT) ISG20 or a catalytically-inactive mutant ISG20m were transiently transfected into Huh7, Huh7.5 and HEK293 cells, and the replication of a monocistronic subgenomic JFH1 RNA replicon, SGRm-JFH1BlaRL, was measured. Huh7.5 cells stably expressing ISG20, ISG20m, or the control vector were established by transducing replication incompetent pCX4-Bsr-myc retroviruses encoding WT ISG20, D94G mutant ISG20, or the empty vector, respectively, and selecting with 5 mug/mL of blasticidin for approximately three weeks. The stable Huh7.5 cells were then transfected with HCV replicon RNA and infected with cell culture-derived HCV to investigate inhibition capacity of ISG20 against HCV. Huh7.5-ISG20, Huh7.5-ISG20m, and Huh7.5-Bsr controls cells stably expressing ISG20, ISG20m, or the control vector, respectively, were constructed successfully; the ectopically expressed ISG20 and ISG20m were distributed in both nucleus and cytoplasm, as detected by immuno uorescence. SGRm-JFH1BlaRL replicated efficiently and with similar kinetics in the Huh7.5-Bsr and Huh7.5-ISG20m cells, with expression levels plateauing at 48-96 h post-transfection. In contrast, at all time points examined, SGRm-JFH1BlaRL replication was 9.1% to 16.7% in the Huh7.5-ISG20 cells. The Huh7, Huh7.5 and HEK293 cells transiently expressing ISG20 also showed 16.7% to 25.0% of HCV replication that the respective controls. In addition, the amount of infectious progeny JFH1 virus released in culture supernatants was 9.1% to 12.5% from the Huh7.5-ISG20 cells than from the Huh7.5-Bsr and Huh7.5-ISG20m cells at 48-72 h post-infection, and the latter two cultures produced similar JFH1 virus yields. Finally, the expression of HCV core protein was also lower in the Huh7.5-ISG20 cells, as detected by immunoblot analysis. Exogenous expression of ISG20, either in a transient or stable manner, suppresses not only replication of genotype 2a HCV RNA replicons but also JFH1 virus propagation in cultured hepatocytes. The exonuclease activity of ISG20 is required for its antiviral activities against HCV.
    Zhonghua gan zang bing za zhi = Zhonghua ganzangbing zazhi = Chinese journal of hepatology 01/2013; 21(1):33-7.
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    ABSTRACT: Combinatorial testing has attracted a lot of attention from both industry and academia. A number of reports suggest that combinatorial testing can be effective for practical applications. However, there are few systematic, controlled studies on the effectiveness of combinatorial testing. In particular, input parameter modeling is a key step in the combinatorial testing process. But most studies do not report the details of the modeling process. In this paper, we report an experiment that applies combinatorial testing to the Siemens suite. The Siemens suite has been used as a benchmark to evaluate the effectiveness of many testing techniques. Each program in the suite has a number of faulty versions. The effectiveness of combinatorial testing is measured in terms of the number of faulty versions that are detected. The experimental results show that combinatorial testing is effective in terms of detecting most of the faulty versions with a small number of tests. In addition, we report the details of our modeling process, which we hope to shed some lights on this critical, yet often ignored step, in the combinatorial testing process.
    Software Testing, Verification and Validation Workshops (ICSTW), 2013 IEEE Sixth International Conference on; 01/2013
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    ABSTRACT: The input space of a system must be modeled before combinatorial testing can be applied to this system. The effectiveness of combinatorial testing to a large extent depends on the quality of the input space model. In this paper we introduce an input space modeling methodology for combinatorial testing. The main idea is to consider the process of input space modeling as two steps, namely, input structure modeling and input parameter modeling. The first step tries to capture the structural relationship among different components in the input space. The second step tries to identify parameters, values, relations and constraints for individual components. We also suggest strategies about how to perform unit and integration testing based on the input space structure. We applied the proposed methodology to two real-life programs. We report our experience and results that demonstrate the effectiveness of the proposed methodology.
    Software Testing, Verification and Validation Workshops (ICSTW), 2013 IEEE Sixth International Conference on; 01/2013
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    ABSTRACT: This poster presents some measures of combinatorial coverage that can be helpful in estimating residual risk related to insufficient testing of rare interactions, and a tool for computing these measures.
    Empirical Software Engineering and Measurement, 2013 ACM / IEEE International Symposium on; 01/2013
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    ABSTRACT: Combinatorial testing has been shown to be a very effective testing strategy. After a failure is detected, the next task is to identify the fault that causes the failure. In this paper, we present an approach to fault localization that leverages the result of combinatorial testing. Our approach is based on a notion called failure-inducing combinations. A combination is failure-inducing if it causes any test in which it appears to fail. Given a failure-inducing combination, our approach derives a group of tests that are likely to exercise similar traces but produce different outcomes. These tests are then analyzed to locate the faults. We conducted an experiment in which our approach was applied to the Siemens suite as well as the grep program from the SIR repository that has 10068 lines of code. The experimental results show that our approach can effectively and efficiently localize the faults in these programs.
    Software Reliability Engineering (ISSRE), 2013 IEEE 24th International Symposium on; 01/2013
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    ABSTRACT: Combinatorial testing has been shown to be a very effective testing strategy. An important problem in combinatorial testing is dealing with constraints, i.e., restrictions that must be satisfied in order for a test to be valid. In this paper, we present an efficient algorithm, called IPOG-C, for constraint handling in combinatorial testing. Algorithm IPOG-C modifies an existing combinatorial test generation algorithm called IPOG to support constraints. The major contribution of algorithm IPOG-C is that it includes three optimizations to improve the performance of constraint handling. These optimizations can be generalized to other combinatorial test generation algorithms. We implemented algorithm IPOG-C in a combinatorial test generation tool called ACTS. We report experimental results that demonstrate the effectiveness of algorithm IPOG-C. The three optimizations increased the performance by one or two orders of magnitude for most subject systems in our experiments. Furthermore, a comparison of ACTS to three other tools suggests that ACTS can perform significantly better for systems with more complex constraints.
    Software Testing, Verification and Validation (ICST), 2013 IEEE Sixth International Conference on; 01/2013
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    ABSTRACT: The current study explored the characteristics of γδ T cells in the blood of HBV-associated acute-on-chronic liver failure (HBV-ACLF) patients and examined the relationship between γδ T cells and the clinical parameters. Blood samples were obtained from 26 patients with HBV-ACLF, 40 patients with chronic hepatitis B virus (HBV) infection (CHBV), and 25 healthy controls (HC). The frequencies of γδ T cells, subtype Vδ1T or Vδ2T, and CD45RO(+)γδ T cells were determined using flow cytometry. Intracellular cytokine staining analysis was used to evaluate the proportion of the IFN-γ-, TNF-α-, or IL-17-producing γδ T cells, and CD107a- or granzyme B-positive γδ T cells. We found that the proportion of γδ T cells in blood samples from HBV-ACLF patients was much lower than in samples from CHBV patients or healthy controls. After stimulation with PMA and ionomycin, γδ T cells from HBV-ACLF patients produced the greatest amount of TNF-α or IL-17 among the three groups. Granzyme B- or CD107a-positive γδ T cells were significantly more frequent than in CHBV or control samples. There was a negative correlation between the percent of TNF-α(+)γδ T cells and ALT or AST levels, and between the percent of CD107a(+)γδ T cells and TBiL or DBiL levels. These results suggest that γδ T cells might participate in liver injury in HBV-ACLF patients by producing increased amounts of inflammatory cytokines and/or cytotoxicity ability. These findings provide novel information regarding the pathogenesis of HBV-ACLF.
    Journal of Clinical Immunology 03/2012; 32(4):877-85. · 3.38 Impact Factor
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    ABSTRACT: To construct a hepatitis C virus (HCV) genotype 2a moncistronic replicon and investigate its replication capabilities in the human hepatocarcinoma cell lines, Huh7.5 and Huh7.1, in order to determine its potential as a molecular tool for future in vitro studies of HCV replication and selection studies for putative anti-HCV drugs. Site-directed mutagenesis was used to delete the Core-E1-E2-p7-NS2 fragment (about 3090 bp) from plasmid pJ6JFH1BlaRL. The resultant trianglepJ6JFH1BlaRL plasmid was digested with AgeI and AvrII to release the cDNA fragment (hereafter, referred to as fragment L) containing partial 5'-untranslated region (UTR), the first 12 amino acid (aa) of HCV Core coding sequence, full-lenth coding sequences for the blasticidin-resistance gene, Renilla luciferase, foot-and-mouth disease virus (FMDV) 2a autoprotease and ubiquitin, and partial coding sequence for HCV NS3. To generate the monocistronic replicon, pSGRmJFH1BlaRL, fragment L was ligated into the pSGR-JFH1 vector that had been digested with AgeI and AvrII to remove the partial 5'-UTR, the first 19 aa of HCV Core coding sequence, the full-length coding sequence for the neomycin phosphotransferase II gene, the internal ribosomal entry site from encephalomyocarditis virus, and partial HCV NS3 coding sequence. A replication-defective mutant replicon, pSGRmJFH1BlaRL/GND, was constructed by a similar procedure using the pSGR-JFH1/GND vector. Fragment L was confirmed in both constructs by sequencing. Replicon RNAs were prepared from XbaI-linearized plasmid DNA templates with Invitrogen's T7 MEGAscript kit, and were purified by DNase I treatment and LiCl precipitation. RNAs were quanti?ed by optical density, and the quality and concentration were con?rmed by agarose gel electrophoresis. Replicon RNAs were transfected into Huh7.5 and Huh7.1 cells using Invitrogen's DMRIE-C transfection reagent at a ratio of 5 mug of lipid to 1mug of RNA. Time course assay of Renilla luciferase activity indicated the replicon's replication function. The pSGRmJFH1BlaRL monocistronic replicon and pSGRmJFH1BlaRL/GND replication-defective mutant replicon were successfully constructed. The pSGRmJFH1BlaRL replicon was replication-proficient in Huh7.5 and Huh7.1 cells, with replication peaking at 72 hours post-transfection and decreasing after 96 hours. No replication was detected at any time point post-transfection for the defective mutant replicon. A monocistronic replicon of HCV genotype 2a was constructed and shown to be replication-proficient in human hepatocarcinoma cell lines.
    Zhonghua gan zang bing za zhi = Zhonghua ganzangbing zazhi = Chinese journal of hepatology 02/2012; 20(2):103-7.
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    ABSTRACT: Combinatorial Testing (CT) is a systematic way of sampling input parameters of the software under test (SUT). A t-way combinatorial test set can exercise all behaviors of the SUT caused by interactions between t input parameters or less. Although combinatorial testing can provide fault detection capability, it is often desirable to isolate the input combinations that cause failures. Isolating these failure-inducing combinations aids developers in understanding the causes of failures. Previous work directly uses classification tree analysis on the results of combinatorial testing to model the failure inducing combinations. But in many scenarios, the effectiveness of classification depends upon whether the analyzed test set is sufficient for classification. In addition, generating combinatorial tests for more-than-6-way combination is generally expensive. To address these issues, we propose an approach that uses existing combinatorial testing results to generate additional tests that enhance the effectiveness of classification. In addition, our approach also includes a technique to reduce the complexity of the resulting classification tree so that developers can understand the nature of failure-inducing combinations. We present the preliminary results of our approach applied on the TCAS benchmark.
    01/2012;
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    ABSTRACT: A t-way combinatorial test set is designed to detect failures that are triggered by combinations involving no more than t parameters. Assume that we have executed a t-way test set and some tests have failed. A natural question to ask is: What combinations have caused these failures? Identifying such combinations can facilitate the debugging effort, e.g., by reducing the scope of the code that needs to be inspected. In this paper, we present an approach to identifying failure-inducing combinations, i.e., combinations that have caused some tests to fail. Given a t-way test set, our approach first identifies and ranks a set of suspicious combinations, which are candidates that are likely to be failure-inducing combinations. Next, it generates a set of new tests, which can be executed to refine the ranking of suspicious combinations in the next iteration. This process can be repeated until a stopping condition is satisfied. We conducted an experiment in which our approach was applied to several benchmark programs. The experimental results show that our approach can effectively and efficiently identify failure-inducing combinations in these programs.
    01/2012;
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    ABSTRACT: In this paper we present a case study of applying combinatorial testing to test a combinatorial test generation tool called ACTS. The purpose of this study is two-fold. First, we want to gain experience and insights about how to apply combinatorial testing in practice. Second, we want to evaluate the effectiveness of combinatorial testing applied to a real-life system. ACTS has 24637 lines of uncommented code, and provides a command line interface and a fairly sophisticated graphic user interface. The main challenge of this study was to model the input space in terms of a set of parameters and values. Once the model was designed, we generated test cases using ACTS, which were then later used to test ACTS. The results of this study show that input space modeling can be a significant undertaking, and needs to be carefully managed. The results also show that combinatorial testing is effective in terms of achieving high code coverage and fault detection.
    01/2012;
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    ABSTRACT: Many software testing problems involve sequences of events. This paper applies combinatorial methods to testing problems that have n distinct events, where each event occurs exactly once. The methods described in this paper were motivated by testing needs for systems that may accept multiple communication or sensor connections and generate output to several communication links and other interfaces, where it is important to test the order in which connections occur. Although pair wise event order testing (both A followed by B and B followed by A) has been described, our algorithm ensures that any t events will be tested in every possible t-way order.
    01/2012;
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    ABSTRACT: Combinatorial testing has been shown to be a very effective testing strategy. Most work on combinatorial testing focuses on t-way test data generation, where each test is an unordered set of parameter values. In this paper, we study the problem of t-way test sequence generation, where each test is an ordered sequence of events. Using a general labeled transition system as the system model, we formally define the notion of t-way sequence coverage, and introduce an efficient algorithm to compute all valid t-way target sequences, i.e., sequences of t events that must be covered by at least one test sequence. We then report several algorithms to generate a set of test sequences that achieves the proposed t-way sequence coverage. These algorithms are developed as the result of a systematic exploration of the possible approaches to t-way test sequence generation, and are compared both analytically and experimentally. The results show that while these algorithms have their own advantages and disadvantages, one of them is more scalable than others while exhibiting very good performance.
    Engineering of Complex Computer Systems (ICECCS), 2012 17th International Conference on; 01/2012

Publication Stats

358 Citations
16.91 Total Impact Points

Institutions

  • 2004–2014
    • University of Texas at Arlington
      • Department of Computer Sciences & Engineering
      Arlington, Texas, United States
  • 2012–2013
    • Chongqing Medical University
      Ch’ung-ch’ing-shih, Chongqing Shi, China
  • 2010
    • University of Texas at Austin
      • Department of Computer Science
      Austin, Texas, United States