• Journal of the Institute of Electronics and Information Engineers
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• v.51 no.6
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• pp.110-116
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• 2014

Pattern matching algorithms are widely used in computer security systems such as computer networks, ubiquitous networks, sensor networks, and so on. However, the advances in information technology causes grow on the amount of data and increase on the computation complexity of pattern matching processes. Therefore, there is a strong demand for a novel high performance pattern matching algorithms. In light of this fact, this paper newly proposes a suffix tree based pattern matching algorithm. The suffix tree is constructed based on the suffix values of all patterns. Then, the shift nodes which informs how many characters can be skipped without matching operations are added to the suffix tree in order to boost matching performance. The proposed algorithm reduces memory usage on the suffix tree and the amount of matching operations by the shift nodes. From the performance evaluation, our algorithm achieved 24% performance gain compared with the traditional algorithm named as Wu-Manber.

• Biomedical Science Letters
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• v.21 no.4
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• pp.227-232
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• 2015

Epstein-Barr virus (EBV) has a pathogenic role in several lymphomas including diffuse large B-cell lymphoma (DLBCL). In this study, we detected EBV from formalin-fixed paraffin embedded (FFPE) tissues of DLBCL patients by RT-PCR and compared the sensitivity of the RT-PCR method to in situ hybridization (ISH) method. The RNA was extracted from 91 FFPE samples with DLBCL and amplified with primers targeting EBV-encoded small RNA (EBER) by RT-PCR. When using the RT-PCR method, 13 of 91 patients (14.3%) were positive and among these 13 cases, 7 cases (7.7%) were from > 50-year-old patients that is classified as EBV positive DLBCL of the elderly. In previous results using ISH method, 3 of 91 patients (3.3%) were positive and 2 case (2.4%) were older than 50-year-old. These results indicate that RT-PCR method used in this study shows a higher sensitivity than ISH method. The ratio of male versus female among the EBV positive samples was 1.2:1 with the ratio of male higher. If RT-PCR method having high sensitivity is used simultaneously as well as the ISH method providing the information of the EBV positive cellular location, it is expected that EBV will be more accurately detected.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.49 no.2
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• pp.109-115
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• 2016

The efficacy of depuration following growing area translocation for the defecation of norovirus was evaluated under experimental conditions using oysters Crassostrea gigas previously subjected to bioaccumulation of this virus at a waste treatment plant discharge site. Three trials were assayed in an open experimental system with a commercial oyster farm located in a shellfish growing area approved by the Korean Shellfish Sanitation Program. Real-time reverse-transcription polymerase chain reaction (RT-PCR) was used to quantify viruses in the digestive glands of oysters. The final viral loads in oysters after 12 days remained under the detection limit (10 copies/g digestive gland) of the real-time RT-PCR. This reduction trend showed two-phase removal kinetics, with an initial slow reduction or slight increase in viruses during the first 2 days of depuration and subsequent stabilization with 0.12 to 2.64 log unit norovirus copies/g digestive gland per 2 days of depuration for the remaining time.

• The Korean Journal of Nuclear Medicine
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• v.38 no.2
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• pp.152-160
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• 2004

Radioiodide uptake in thyroid follicular epithelial cells, mediated by a plasma membrane transporter, sodium iodide symporter (NIS), provides a first step mechanism for thyroid cancer detection by radioiodide injection and effective radioiodide treatment for patients with invasive, recurrent, and/or metastatic thyroid cancers after total thyroidectomy. NIS gene transfer to tumor cells may significantly and specifically enhance internal radioactive accumulation of tumors following radioiodide administration, and result in better tumor control. NIS gene transfers have been successfully performed in a variety of tumor animal models by either plasmid-mediated transfection or virus (adenovirus or retrovirus)-mediated gene delivery. These animal models include nude mice xenografted with human melanoma, glioma, breast cancer or prostate cancer, rats with subcutaneous thyroid tumor implantation, as well as the rat intracranial glioma model. In these animal models, non-invasive imaging of in vivo tumors by gamma camera scintigraphy after radioiodide or technetium injection has been performed successfully, suggesting that the NIS can serve as an imaging reporter gene for gene therapy trials. In addition, the tumor killing effects of I-131, ReO4-188 and At-211 after NIS gene transfer have been demonstrated in in vitro clonogenic assays and in vivo radioiodide therapy studies, suggesting that NIS gene can also serve as a therapeutic agent when combined with radioiodide injection. Better NIS-mediated imaging and tumor treatment by radioiodide requires a more efficient and specific system of gene delivery with better retention of radioiodide in tumor. Results thus far are, however, promising, and suggest that NIS gene transfer followed by radioiodide treatment will allow non-invasive in vivo imaging to assess the outcome of gene therapy and provide a therapeutic strategy for a variety of human diseases.

• Asian Pacific Journal of Cancer Prevention
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• v.17 no.9
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• pp.4357-4361
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• 2016

Background: Whether there is any relationship between human papilloma virus (HPV) and breast carcinoma is not clear. Some previous studies have indicated a possible role in oncogenesis in the breast. In this study, we therefore analyzed the presence of HPV infection in breast tissues of Iranian women from Yazd city. Materials and Methods: In a cross-sectional study, formalin-fixed paraffin-embedded tissues from 87 patients with breast cancer and 84 cases with breast fibrocystic lesions (control group) were selected from a tissue archive. Grade of tumors and fibrocystic tissues were determined by two pathologists. The nested-PCR method was performed for detection of HPVs in samples. HPV genotypes were determined by sequencing and the phylogenetic tree depicted by MEGA software. Results: Of the 87 women with breast cancer, 22.9% (20 isolates) had positive results for HPV DNA. In the control group no HPV was detected. The HPV genotypes in positive samples were HPV-16 (35%) HPV-18 (15%), HPV-6 (45%) and HPV-11 (5%). The data did not approved a significant correlation between tissue pathology of breast cancer and the HPV genotype frequency. Conclusions: The data did not provide any evidence for a role of high risk HPV types in oncogenesis in the breast.

• Tuberculosis and Respiratory Diseases
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• v.81 no.3
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• pp.233-240
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• 2018

Background: Non-conversion of sputum smear and culture prolongs the infectivity of the patient and has been associated with unfavorable outcomes. We aimed to evaluate factors associated with persistent sputum positivity at the end of two months of treatment of new case pulmonary tuberculosis (TB). Methods: Data of 87 human immunodeficiency virus-negative patients with culture-positive drug-susceptible pulmonary TB admitted to local university hospital between September 2015 and September 2016 were reviewed. Factors associated with sputum smear and/or culture positivity at the end of the second month of treatment were analyzed. Results: Twenty-two patients (25.3%) remained smear and/or culture-positive. Male sex, lower body mass index (BMI), unemployment, alcohol abuse, higher number of lobes involved and cavities on chest X-rays, shorter time to detection (TTD) on liquid cultures, higher respiratory sample smear grading and colony count in solid cultures, higher C-reactive protein, erythrocyte sedimentation rate, leukocytosis, thrombocytosis, and anemia were all significantly associated with persistent sputum positivity. However, in the logistic regression analysis only male sex, lower BMI, alcohol abuse, higher radiological involvement, cavitation, higher smear grading, higher colony count in solid cultures and shorter TTD were determined as independent factors associated with persistent sputum positivity at the end of 2 months of treatment. Conclusion: In conclusion, higher sputum smear and culture grading at diagnosis, shorter TTD, higher number of lobes involved, cavitation, male sex, alcohol abuse, and lower BMI were independently associated with persistent sputum positivity. These factors should be sought when distinguishing which patients will remain infectious longer and possibly have worse outcomes.

• BMB Reports
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• v.33 no.1
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• pp.92-95
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• 2000

The HIV-1 p24(202-221) sequence ETINNEEEWDRVHPV HAGP contains a B-cell epitope with the earliest immune response and the highest antibody titer against anti-mouse sera obtained by immunization with p24 antigens. A novel mouse monoclonal antibody (mAb) was generated against the immunodominant B-cell epitope of the HIV-1 p24 capsid protein, p24(202-221). BALB/c mice were immunized with the four branched multiple antigenic peptide (MAP) containing the HIV-1p24(202-221) sequence, and antibody-secreting hybridoma were produced by fusion of mouse splenocytes with P3X63Ag8.653, mouse myeloma cells. One clone which produced the antigen-specific mAb named KI-24 (Isotype IgG1, light chain: ${\kappa}$) was identified. mAb KI-24 was highly specific for both the p24(202-221) and p24 proteins when analyzed by ELISA and Western blotting. Since p24(202-221) also contains a cytotoxic T-lymphocyte epitope, this specfic peptide epitope and the monoclonal antibody with specific reactivity against the p24 protein and p24(202-221) can be used in peptide vaccine development and p24 antigen detection from HIV patients.

• BMB Reports
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• v.31 no.1
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• pp.58-63
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• 1998

In this study, a mouse monoclonal antibody (mAb) against gp41(584-618), the immunodominant epitope protein, was generated. For this purpose, BALB/c mice were immunized with double branched multiple antigenic peptides derived from the HIV-1 gp41(584-618) sequence, and antibody-secreting hybridoma were produced by fusion of mice splenocytes with SP2/0 myeloma cells. One clone producing an antigen specific mAb, termed KI-41(isotype IgG1) was identified, whose specific reactivity against gp41(584-618) could be confirmed by ELISA and Western blot analysis. Epitope mapping revealed the recognition site of the mAb KI-41 to be located around the sequence RILAVERYLKDQQLLG, which comprises the N-terminal region within the immunized gp41(584-618) peptied. Since this mAb recognizes this specific epitope within the HIV-1 gp41 without any cross-reactivity to other immunodominant regions in the HIV-2 gp35, KI-41 will provide some alternative possibilities in further applications such as the development of indirect or competitive ELISA for specific antibody detection in HIV-1 infection or for other basic researches regarding the role and function of HIV-1 gp41.

• Asian Pacific Journal of Cancer Prevention
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• v.16 no.3
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• pp.1289-1293
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• 2015

Background: Anal intraepithelial lesions (AIL) are likely to represent a precursor for anal cancer. Women infected with human immunodeficiency virus (HIV) may be at higher risk of anal cancer but a screening program for AIL still is not routinely recommended. We here studied the relationship of dysplastic cells from cervical and anal cytology in HIV-infected women. Materials and Methods: This prospective study was conducted in Prapokklao Hospital, Thailand during 2013-2014. Five hundred and ninety nine HIV-infected women were recruited. Participants who had cytological reports of equally or over "abnormal squamous/glandular cells of undetermined significance" (ASC-US) were classified as abnormal cervical or anal cytology. Descriptive statistics and logistic regression analysis were used to evaluate correlations between groups. Results: HIV-infected women with abnormal cervical cytology had 3.8 times more risk (adjusted odd ratio 3.846, 95% confidence interval 1.247-11.862, p-value. 019) for abnormal anal cytology. The major problem of the anal Pap test in this study was the inadequacy of the collected specimens for evaluation (34.4%, 206/599). Sensitivity, specificity, positive predictive value, negative predictive value and accuracy of cervical and anal Pap tests were 93.9/12.0, 87.3/96.9, 39.7/21.4, 99.4/94.1 and 88.1/91.4 percent, respectively. Conclusions: Abnormal cervical cytology in HIV-infected women indicates elevated risk for abnormal anal cytology. The sensitivity of the anal Pap test for detection of AIL 2/3 in HIV-infected women was quite low while specificity was excellent. Inadequacy of specimen collection for evaluation was a major limitation. Improvement of sample collection is recommended for future investigations.

• Asian Pacific Journal of Cancer Prevention
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• v.13 no.5
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• pp.2299-2304
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• 2012

Since there is evidence that human papillomavirus (HPV) may play some role in oral carcinogenesis, we investigated the presence of HPV in a group of Pakistani subjects with normal oral cavity using real-time PCR analysis. Two-hundred patients attending the Dental Department, Sandaman Provincial Hospital, Balochistan, Pakistan, were recruited. After interview, oral epithelial cells were collected by scraping and subjected to DNA extraction. The HPV-positive DNA samples were further analyzed using primer sets specific for HPV-16 and -18. It was found that out of 200 DNA samples, 192 were PCR-positive for the ${\beta}$-globin gene and these were subsequently examined for the presence of HPV DNA. Among these, 47 (24.5%) were HPV-positive with the virus copy number ranged between 0.43-32 copies per 1 ${\mu}g$ of total DNA (9-99 copies per PCR reaction). There were 4 and 11 samples containing HPV-16 and -18, respectively. Additionally, one sample harbored both types of HPV. Among the investigated clinical parameters, smoking habit was associated with the presence of HPV (p = 0.001) while others indicated no significant association. The prevalence of HPV in normal oral cavity in our Pakistani subjects appears to be comparable to other studies. However, the association between the presence of HPV and smoking warrants further investigations whether both of these factors can cooperate in inducing oral cancer in this group of patients.