• Asian Pacific Journal of Cancer Prevention
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• v.14 no.3
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• pp.1813-1817
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• 2013

Background: Multiple etiologic factors are suspected to cause gastric cancer, the most important of which is infection with virulent types of Helicobacter pylori. Materials and Methods: We have compared 102 gastric cancer patients with 122 non-ulcer, non-cancer dyspeptic patients. Gastric specimens were evaluated for H. pylori infection by tissue-based detection methods. Patient sera underwent antigen-specific ELISA and western blotting using a Helicoblot 2.1 kit and antibody responses to various H. pylori antigens were assessed. Results: The absolute majority (97-100%) of both groups were H. pylori seropositive. Multivariate regression analysis demonstrated serum antibodies to the low molecular weight 35kDa protein to be protective and reduce the risk of gastric cancer by 60% (OR:0.4; 95%CI:0.1-0.9). Conversely, seroreactivity to the 89kDa (VacA) protein was significantly higher in gastric cancer patients (OR:2.7; 95%CI:1.0-7.1). There was a highly significant association (p<0.001) between seroreactivity to the 116kDa (CagA) and 89kDa (VacA) proteins, and double positive subjects were found at nearly five fold (OR:4.9; 95%CI:1.0-24.4) enhanced risk of gastric cancer as compared to double negative subjects. Conclusions: Seroreactivity to H. pylori low (35kDa) and high (116kDa/89kDa) molecular weight antigens were respectively revealed as protective and risk indicators for gastric cancer.

• Asian Pacific Journal of Cancer Prevention
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• v.14 no.3
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• pp.1635-1642
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• 2013

Helicobacter pylori antigen was prepared from an isolate from a patient with a duodenal ulcer. Serum samples were obtained from culture-positive H. pylori infected patients with duodenal ulcers, gastric ulcers and gastritis (n=30). As controls, three kinds of sera without detectable H. pylori IgG antibodies were used: 30 from healthy individuals without history of gastric disorders, 30 from patients who were seen in the endoscopy clinic but were H. pylori culture negative and 30 from people with other diseases. OFF-GEL electrophoresis, SDS-PAGE and Western blots of individual serum samples were used to identify protein bands with good sensitivity and specificity when probed with the above sera and HRP-conjugated anti-human IgG. Four H. pylori protein bands showed good (${\geq}$ 70%) sensitivity and high specificity (98-100%) towards anti-Helicobacter IgG antibody in culture-positive patients sera and control sera, respectively. The identities of the antigenic proteins were elucidated by mass spectrometry. The relative molecular weights and the identities of the proteins, based on MALDI TOF/TOF, were as follows: CagI (25 kDa), urease G accessory protein (25 kDa), UreB (63 kDa) and proline/pyrroline-5-carboxylate dehydrogenase (118 KDa). These identified proteins, singly and/or in combinations, may be useful for diagnosis of H. pylori infection in patients.

• Structural Engineering and Mechanics
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• v.57 no.6
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• pp.1125-1142
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• 2016

Tunneling is one of the challenging tasks in civil engineering because it involves a variety of decision making and engineering judgment based on knowledge and experience. One of the challenges is to construct tunnels in risky areas under shallow overburden. In order to prevent the collapse of ceilings and walls of a large tunnels, in such conditions, either a sequential excavation method (SEM) or ground reinforcing method, or a combination of both, can be utilized. This research deals with the numerical modeling of L-profiles and pipe fore-poling pre-support systems in the adit tunnel in northwestern Iran. The first part of the adit tunnel has been drilled in alluvial material with very weak geotechnical parameters. Despite applying an SEM in constructing this tunnel, analyzing the results of numerical modeling done using FLAC3D, as well as observations during drilling, indicate the tunnel instability. To improve operational safety and to prevent collapse, pre-support systems, including pipe fore-poling and L-profiles were designed and implemented. The results of the numerical modeling coupled with monitoring during operation, as well as the results of instrumentation, indicate the efficacy of both these methods in tunnel collapse prevention. Moreover, the results of modeling using FLAC3D and SECTION BUILDER suggest a double angle with equal legs ($2L100{\times}100{\times}10mm$) in both box profile and tee array as an alternative section to pipe fore-poling system while neither $L80{\times}80{\times}8mm$ nor $2L80{\times}80{\times}8mm$ can sustain the axial and shear stresses exerted on pipe fore-poling system.

• Geomechanics and Engineering
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• v.19 no.5
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• pp.393-405
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• 2019

This paper evaluates the geotechnical and geo-engineering properties of the South Pars Zone (SPZ) marls in Assalouyeh, Iran. These marly beds mostly belong to the Aghajari and Mishan formations which entail the gray, cream, black, green, dark red and pink types. Marls can be observed as rock (soft rock) or soil. Marlstone outcrops show a relatively rapid change to soils in the presence of weathering. To geotechnically characterise the marls, field and laboratory experiments such as particle-size distribution, hydrometer, Atterberg limits, uniaxial compression, laboratory direct-shear, durability and carbonate content tests have been performed on soil and rock samples to investigate the physico-mechanical properties and behaviour of the SPZ marls in order to establish empirical relations between the geo-engineering features of the marls. Based on the experiments conducted on marly soils, the USCS classes of the marls is CL to CH which has a LL ranging from 32 to 57% and PL ranging from 18 to 27%. Mineralogical analyses of the samples revealed that the major clay minerals of the marls belong to the smectite or illite groups with low to moderate swelling activities. The geomechanical investigations revealed that the SPZ marls are classified as argillaceous lime, calcareous marl and marlstone (based on the carbonate content) which show variations in the geomechanical properties (i.e., with a cohesion ranging from 97 to 320 kPa and a friction angle ranging from 16 to 35 degrees). The results of the durability tests revealed that the degradation potential showed a wide variation from none to fully disintegrated. According to the results of the experiments, the studied marls have been classified as calcareous marl, marlstone and argillaceous lime due to the variations in the carbonate and clay contents. The results have shown that an increase in the carbonate content leads to a decrease in the degradation potential and an increase in the density and strength parameters such as durability and compressive strength. A comparison of the empirical relationships obtained from the regression analyses with similar studies revealed that the results obtained herein are reasonably reliable.

• Asian Pacific Journal of Cancer Prevention
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• v.16 no.17
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• pp.7819-7824
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• 2015

Purpose: To subtype breast cancer (BC) in Saudi women according to the recent molecular classification and to correlate these subtypes with available clinicopathological parameters. Materials and Methods: Estrogen receptor (ER), progesterone receptor (PR) and human epidermal growth factor receptor (Her2/neu) immunostaining was semi-quantitatively assessed to define molecular subtypes of luminal A and B, HER-2 and triple negative (basal-like) in BC paraffin embedded sections from 115 Saudi female patients diagnosed between 2005 to 2015 at the Department of Pathology, King Fahd Hospital, Almadinah, Saudi Arabia. Results: The most common subtypes were luminal A (47%), followed by luminal B (27.8%) and basal like subtypes (18.3%), whereas HER-2 was the least common subtype (6.9%). Luminal A was predominantly found in the old age group, with low tumor grade (p<0.001) and small tumor size, whereas HER-2 and basal-like subtypes were significantly associated with young age, high tumor grade, lymph node metastasis and lymphovascular invasion (p<0.03, 0.004, 0.05 and 0.04 respectively). All subtypes showed advanced clinical stage at the time of presentation. Conclusions: Molecular subtypes of Saudi BC patients in Almadinah region are consistent with most of the worldwide subtyping. The biological behaviour of each molecular subtype could be expected based on its characteristic clinicopathological features. Along with other prognostic indicators, molecular subtyping would be helpful in predicting prognosis and management of our BC patients. We recommend screening and early diagnosis of BC in our population.

• Asian Pacific Journal of Cancer Prevention
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• v.16 no.17
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• pp.7883-7887
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• 2015

Background: Colorectal cancer is one of the most common cancers worldwide. Viruses including human papillomavirus (HPV) have been reported to be associated with different cancers but any association with colorectal cancers remains controversial. Aim: To evaluate any association between HPV infection and adenocarcinoma of the colon and adenomatous polyps. Materials and Methods: Paraffin-embedded tissue specimens of 70 colorectal adenocarcinomas, 70 colorectal adenomatous polyps, and 70 colorectal normal tissues were subjected to DNA extraction. The quality of the extracted DNA was confirmed by amplification of a ${\beta}$-globin fragment using polymerase chain reaction (PCR). PCR using specific primers were performed to detect HPV DNA. Specific primers targeting the E6 region of the HPVs 16 and 18 were used for genotyping. Results: HPV DNA was detected in 2 (2.85%) out of 70 adenocarcinoma colorectal tissues and 4 (5.71 %) out of 70 adenomatous colorectal tissues. All normal colorectal tissues were negative for HPV DNA. HPV-16 was the most predominant genotype (5 sample) followed by HPV-18 (4 sample). Despite the above observations, statistical analyses indicated no significant differences in the frequencies of HPV positive subjects between the cancerous and normal samples. Conclusions: Although the differences observed in the frequencies of HPV positive cases in our study was not significant relative to those of control subjects, the fact of 6 positive samples among cancerous tissues, may still suggest a role of HPV in colorectal carcinogenesis. The study collectively indicated that some colorectal cancerous tissues are infected with high risk HPV genotype. The findings merit more investigation.

• Asian Pacific Journal of Cancer Prevention
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• v.13 no.12
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• pp.6469-6474
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• 2012

Background: DNA repair is one of the crucial defense mechanism against mutagenic exposure. Inherited SNPs of DNA repair genes may contribute to variation in DNA repair capacity and susceptibility to cancer. Due to the presence of these variants, inter-individual and ethnic differences in DNA repair capacity have been established in various populations. India harbors enormous genetic and cultural diversity. Materials and Methods: In the present study we aimed to determine the genotypes and allele frequencies of XRCC1 Arg399Gln (rs25487), XRCC3 Thr241Met (rs861539), XPD Lys751Gln (rs13181), and OGG1 Ser326Cys (rs1052133) gene polymorphisms in 186 healthy individuals residing in the Hyderabad region of India and to compare them with HapMap and other populations. Results and Conclusions: The genotype and allele frequency distribution at the four DNA repair gene loci among Hyderabad population of India revealed a characteristic pattern. Comparison of these gene polymorphisms with other populations revealed a distinctiveness of Hyderabad population from the Deccan region of India. To the best of our knowledge, this is the first report of such DNA repair gene polymorphisms in the Deccan Indian population.

• Asian Pacific Journal of Cancer Prevention
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• v.15 no.4
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• pp.1617-1620
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• 2014

Background: Evidence shows direct link of HER2 to increased glycolysis and over production of lactate dehydrogenase (LDH). HER2 overexpression, high LDH and low glucose pleural levels are associated with poor prognosis in lung cancer. Here, their relationships were investigated. Materials and Methods: HER2 positivity was studied using immunohistochemistry in non-small cell lung cancer. Glucose and LDH levels were measured using commercial colorimetric kits. Results: Of 42 patients (29 adenocarcinoma and 13 squamous cell carcinoma), 28 (66.7%) were HER2-negative, 14 (33.3%) were HER2- positive, including 9 (21.4%) weakly stained (1+) and 5 (11.9%) moderately stained (2+) samples. The relationship between HER2 and glucose and LDH levels were tested in 20 newly diagnosed lung cancer patients who had simultaneous pleural and serum samples. Pleural and serum LDH levels were increased, and pleural glucose levels were decreased with the scale of HER2 positivity, and that the difference in glucose levels between HER2-negative group and HER2-positive patients scored at 2+ reached statistical significance (p=0.02). This latter group all had pleural glucose levels below 40 mg/dl. Conclusions: For the first time, we showed a significant association between low pleural glucose level and overexpression of HER2 in lung cancer. Further investigations are warranted to disclose the association of HER2 with low pleural glucose levels in other populations, with a larger sample size, in malignant pleural effusions caused by other types of cancer, and finally to assess employment as a screening tool for finding HER2-positive cases of lung cancer.

• Asian Pacific Journal of Cancer Prevention
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• v.17 no.9
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• pp.4527-4531
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• 2016

Background: PTEN protein is one of the most important tumour suppressor factors which is detectable by immunohistochemistry. The goal of the present study was to investigate the prognostic role of PTEN gene expression in breast cancer patients. Materials and Methods: This descriptive-analytical study was conducted on 100 breast cancer patients referred to Sabzevar hospitals in the north-east of Iran between 2010 and 2011, who were followed up to 2015. PTEN gene expression in tissue samples was determined using specific monoclonal antibodies and data were analyzed using Chi-square test and Fisher's exact test. Patient survival was analyzed after 4 years of follow-up using the Cox regression model. Results: PTEN gene expression was evident in 70 of 100 cnacer samples but was found at high levels in all non-cancer samples. There was an inverse significant relationship between PTEN gene expression and tumour stage or tumour grade (p<0.001). The expression of PTEN in invasive ductal tumours was lower than in non-invasive tumours. There was also an inverse significant relationship between the hazard of death and PTEN gene expression (p<0.001). In addition, there was an inverse significant relationship between tumour stage and hazard of death (p<0.001). Conclusion: These findings indicate that lack of PTEN gene expression can be a sign of a worse prognosis and poor survival in breast cancer cases.

• Korean Journal of Agricultural Science
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• v.47 no.1
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• pp.119-130
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• 2020

With the current rapid growth and increase in the world's population, the demand for nutritious food and fibers and fuel will increase. Therefore, there is a serious need for the use of breeding programs with the full potential to produce high-yielding crops. However, existing breeding techniques are unable to meet the demand criteria even though genotyping techniques have significantly progressed with the discovery of molecular markers and next-generation sequencing tools, and conventional phenotyping techniques lag behind. Well-organized high-throughput plant phenotyping platforms have been established recently and developed in different parts of the world to address this problem. These platforms use several imaging techniques and technologies to acquire data for quantitative studies related to plant growth, yield, and adaptation to various types of abiotic or biotic stresses (drought, nutrient, disease, salinity, etc.). Phenotyping has become an impediment in genomics studies of plant breeding. In recent years, phenomics, an emerging domain that entails characterizing the full set of phenotypes in a given species, has appeared as a novel approach to enhance genomics data in breeding programs. Imaging techniques are of substantial importance in phenomics. In this study, the importance of current imaging technologies and their applications in plant phenotyping are reviewed, and their advantages and limitations in phenomics are highlighted.