• Journal of KIISE:Software and Applications
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• v.35 no.11
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• pp.661-670
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• 2008

In some applications of software engineering such as the verification of software model or embedded program, SAT solver is used. To practical use a SAT solver, a problem is encoded to a CNF formula, but because the formula has lower expressiveness than software models or source codes, optimal CNF encoding is required. In this paper, we propose optimal encoding techniques for the problem of "Selecting adjacent $k{\leq}n$ among n objects," Through experimental results we show the proposed constraint is efficient and correct to solve Japanese puzzle. As we know, this paper is the first study about CNF encoding for adjacency in BCC.

• Journal of KIISE:Software and Applications
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• v.35 no.2
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• pp.81-90
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• 2008

BCC(Boolean Cardinality Constraint) is to select one boolean variable from n different variables. It is widely used in many areas including software engineering. Thus, many efficient encoding techniques of BCC into CNF have been studied extensively In this paper we analyze some representative encodings with respect to flexibility as well as efficiency. In addition we use a visualization tool to draw the CNF clauses generated from each encodings. Visualizing the clauses exposes a hidden structure in encodings and makes to compare each encodings on the structure level, which is one of the prominent achievement in our work compared to other works. And we apply our analysis on the pigeon-hole problems to have confidence. In our experimental settings, the commander encoding shows the best performance.

• Journal of KIISE:Software and Applications
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• v.34 no.7
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• pp.616-624
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• 2007

Sudoku can be regarded as a SAT problem. Various encodings are known for encoding Sudoku as a Conjunctive Normal Form (CNF) formula, which is the standard input for most SAT solvers. Using these encodings for large Sudoku, however, generates too many clauses, which impede the performance of state-of-the-art SAT solvers. This paper presents an optimized CNF encodings of Sudoku to deal with large instances of the puzzle. We use fixed cells in Sudoku to remove redundant clauses during the encoding phase. This results in reducing the number of clauses and a significant speedup in the SAT solving time.

• Journal of KIISE:Software and Applications
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• v.34 no.8
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• pp.743-751
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• 2007

Model checking has been successfully applied to hardware verification. Software is more subtle than hardware with respect to formal verification due to its infinite state space. Although there are many research activities in this area, bounded model checking is regarded as a promising technique. Bounded model checking uses an upper bound to unroll its model, which is the main advantage of bounded model checking compared to other model checking techniques. In this paper, we applied bounded model checking to verify BIR which is the input model for the model checking tool BOGOR. Some BIR examples are verified with our technique. Experimental results show that bounded model checking is better than explicit model checking provided by BOGOR. This paper presents the formalization of BIR and the encoding algorithm of BIR into CNF.

• Biomedical Science Letters
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• v.18 no.2
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• pp.146-151
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• 2012

Urinary tract infection (UTI) is one of the most common bacterial infections and is predominantly caused by uropathogenic Escherichia coli (UPEC). UPEC strains generally possess several genes encoding virulent factors, which are mostly adhesins, toxins, bacteriocin and siderophores. E. coli is composed of four main phylogenetic group (A, B1, B2, D) and virulent extra-intestinal strains mainly belong to groups B2 and D. Prescription of ciprofloxacin, a kind of fluoroquinolone group antibiotics, is increasing now a days, but resistance to this drug is also increasing. A total of 188 strains of E. coli were collected. Thirteen strains were collected from healthy students in 2011 and 175 strains from patients with urinary tract infection in 2010. Virulence factor genes (papC, fimG/H, sfaD/E, hlyA, cnf1, and usp) were amplified by polymerase chain reaction (PCR) methods for phylogenetic group (A, B1, B2, D) detection. Ciprofloxacin susceptibility test was performed by disk diffusion method. The identified virulence factors (VFs), phylogenetic groups and ciprofloxacin resistance in 13 E. coli strains isolated from healthy students were papC (15.4%), fimG/H (76.9%), sfaD/E (30.8%), hlyA (23.1%), cnf1 (23.1%), usp (7.7%), phylogenetic group A (23%), B1 (8%), B2 (46%), D (23%) and ciprofloxacin resistance (7.7%), while those of in 175 E. coli strains isolated from patients with UTI were papC (41.1%), fimG/H (92.5%), sfaD/E (30.3%), hlyA (10.3%), cnf1 (30.3%), usp (27.4%), phylogenetic group A (9.1%), B1 (5.1%), B2 (60.6%), D (25.1%) and ciprofloxacin resistance (29.7%). In this study, 10 out of 13 E. coli strains (76.9%) from healthy students were found to possess more than one virulence factor associated with adhesion. In addition, one E. coli strain isolated from healthy students who had never been infected with UPEC showed ciprofloxacin resistance. According to these results between the virulence factors and phylogenetic groups it was closely associated, and UPEC strains isolated from patients showed high level of ciprofloxacin resistance.

• Biomedical Science Letters
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• v.28 no.2
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• pp.127-136
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• 2022

Uropathogenic Escherichia coli (UPEC) is main causative agent of urinary tract infections. They are classified based on various types of O antigen. UPEC strains commonly possess many genes encoding virulece-associated factors. E. coli strains are generally divided into four main phylogenetic groups. The virulence factor (VF) profiles of UPEC are related with their O-serogroups in each strains. A total of 681 strains of UPEC clinical isolates were collected from Korean healthcare facility (1989: 123 strains and 2010-2014: 558 strains). The UPEC clinical isolates were analyzed by polymerase chain reaction (PCR) methods. A total of 14 O-serotypes (O1, O2, O4, O6, O7, O8, O15, O16, O18, O21, O22, O25, O75 and O83), 6 virulence factors (papC, fimG/H, sfaD/E, hly1, cnf1 and usp) and phylogenetic groups were identified. The most prevalent O-serogroups were O6 (11.1%) in 1989 UPEC strains and O25 (21.0%) in 2010-2014 UPEC strains. The identified VFs, phylogenetic groups in 1989 UPEC strains and 2010-2014 UPEC strains were fimG/H and B2 group. In this study, O6 serotype was revealed the close relationships with VFs. Also, the distribution of prevalence O-serogroups of UPEC has been changed from O6 to O25 and virulence of UPEC strains was increased during past twenty-one years.