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DNA methylation is an important epigenetic phenomenon that plays a key role in the regulation of expression. Most of the studies on the topic of methylation's role in cancer mechanisms include analyses based on differential methylation, with the integration of expression information as supporting evidence. In the present study, we sought to identify methylation-driven patterns by also integrating protein-protein interaction information. We performed integrative analyses of DNA methylation, expression, SNP and copy number data on paired samples from six different cancer types. As a result, we found that genes that show a methylation change larger than 32.2% may influence cancer-related genes via fewer interaction steps and with much higher percentages compared with genes showing a methylation change less than 32.2%. Additionally, we investigated whether there were shared cancer mechanisms among different cancer types. Specifically, five cancer types shared a change in AGTR1 and IGF1 genes, which implies that there may be similar underlying disease mechanisms among these cancers. Additionally, when the focus was placed on distinctly altered genes within each cancer type, we identified various cancer-specific genes that are also supported in the literature and may play crucial roles as therapeutic targets. Overall, our novel graph-based approach for identifying methylation-driven patterns will improve our understanding of the effects of methylation on cancer progression and lead to improved knowledge of cancer etiology., Competing Interests: The authors have declared that no competing interests exist.

With ongoing developments in technology, changes in DNA methylation levels have become prevalent to study cancer biology. Previous studies report that DNA methylation affects gene expression in a direct manner, most probably by blocking gene regulatory regions. In this study, we have studied the interplay between methylation and expression to improve our knowledge of cancer aetiology. For this purpose, we have investigated which genomic regions are of higher importance; hence, first exon, 5'UTR and 200 bp near the transcription start sites are proposed as being more crucial compared to other genomic regions. Furthermore, we have searched for a valid methylation level change threshold, and as a result, 25 % methylation change in previously determined genomic regions showed the highest inverse correlation with expression data. As a final step, we have examined the commonly affected genes and pathways by integrating methylation and expression information. Remarkably, the GPR115 gene and ErbB signalling pathway were found to be significantly altered for all cancer types in our analysis. Overall, combining methylation and expression information and identifying commonly affected genes and pathways in a variety of cancer types revealed new insights of cancer disease mechanisms. Moreover, compared to previous methylation-based studies, we have identified more important genomic regions and have defined a methylation change threshold level in order to obtain more reliable results. In addition to the novel analysis framework that involves the analysis of four different cancer types, our study exposes essential information regarding the contribution of methylation changes and its impact on cancer disease biology, which may facilitate the identification of new drug targets.

Purpose: Benign recurrent intrahepatic cholestasis (BRIC) is characterized by episodic cholestasis and pruritus without anatomical obstruction. The aim of this study was to evaluate the safety and efficacy of nasobiliary drainage (NBD) in patients with BRIC refractory to medical therapy and to determine whether the use of NBD prolongs the episode duration., Methods: This was a multicenter retrospective study consisting of 33 patients suffering from BRIC. All patients were administrated medical treatment and 16 patients who were refractory to standard medical therapies improved on treatment with temporary endoscopic NBD. Duration of treatment response and associated complications were analyzed., Results: Sixteen patients (43% females) underwent 25 NBD procedures. The median duration of NBD was 17 days. There were significant improvements in total and direct bilirubin and alanine aminotransferase, aspartate aminotransferase, alkaline phosphatase and gamma-glutamyl transpeptidase on the 3rd day of NBD. Longer clinical remission was monitored in the NBD group. Post-endoscopic retrograde cholangiopancreatography pancreatitis was observed in one of 16 cases., Conclusion: NBD effectively eliminates BRIC in all patients and improves biomarkers of cholestasis. It can be suggested that patients with attacks of BRIC can be treated with temporary endoscopic NBD; however, the results of this study should be confirmed by prospective studies in the future.

Purpose: We aimed to evaluate and compare the efficacy and safety of high-dose furosemide+salt orally by comparing HSS+ furosemide (i.v.) and repeated paracentesis in patients with RA., Methods: This was a prospective study of 78 cirrhotic patients with RA, randomized into three groups: Group A (n= 25) i.v. furosemide (200-300 mg bid) and 3% hypotonic saline solution (HSS) (once or twice a day); Group B (n= 26) oral furosemide tablets (360-520 mg bid) and salt (2.5 g bid); and, Group C (n= 27) repeated large-volume-paracentesis (RLVP) with albumin infusion. Patients without hyperkalemia were administrated 100 mg of spironolactone/day. During the follow-up; INR, creatinine, and total bilirubin levels were measured to determine the change in MELD (model of end stage liver disease) score., Results: Hepatic encephalopathy (HE), severe episodes of spontaneous bacterial peritonitis (SBP) and pleural effusions (PE) occurred more frequently in Group C. Improvement in Child-Pugh and MELD score was better in Group A and B than Group C. In Group B, improvements were seen in the Child-Pugh and MELD score, reduction in body weight, duration and number of hospitalization. In Groups A and B, remarkable increases in diuresis were observed (706±116 to 2425±633 mL and 691±111 to 2405±772 mL) and serum sodium levels also improved. HE and SBP were occurred more often in group C (p<0.002). Hospitalization decreased significantly in Group B (p<0.001). There was no significant difference in survival among groups., Conclusion: High dose oral furosemide with salt ingestion may be an alternative, effective, safe and well-tolerated method of therapy for RA.

We report an association between a new causative gene and spastic paraplegia, which is a genetically heterogeneous disorder. Clinical phenotyping of one consanguineous family followed by combined homozygosity mapping and whole-exome sequencing analysis. Three patients from the same family shared common features of progressive complicated spastic paraplegia. They shared a single homozygous stretch area on chromosome 6. Whole-exome sequencing revealed a homozygous mutation (c.853&#95;871del19) in the gene coding the kinesin light chain 4 protein (KLC4). Meanwhile, the unaffected parents and two siblings were heterozygous and one sibling was homozygous wild type. The 19 bp deletion in exon 6 generates a stop codon and thus a truncated messenger RNA and protein. The association of a KLC4 mutation with spastic paraplegia identifies a new locus for the disease.

Unlabelled: Due to the big data produced by next-generation sequencing studies, there is an evident need for methods to extract the valuable information gathered from these experiments. In this work, we propose GeneCOST, a novel scoring-based method to evaluate every gene for their disease association. Without any prior filtering and any prior knowledge, we assign a disease likelihood score to each gene in correspondence with their variations. Then, we rank all genes based on frequency, conservation, pedigree and detailed variation information to find out the causative reason of the disease state. We demonstrate the usage of GeneCOST with public and real life Mendelian disease cases including recessive, dominant, compound heterozygous and sporadic models. As a result, we were able to identify causative reason behind the disease state in top rankings of our list, proving that this novel prioritization framework provides a powerful environment for the analysis in genetic disease studies alternative to filtering-based approaches., Availability and Implementation: GeneCOST software is freely available at www.igbam.bilgem.tubitak.gov.tr/en/softwares/genecost-en/index.html., Contact: buozer@gmail.com, Supplementary Information: Supplementary data are available at Bioinformatics online., (© The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.)

Recently, the rapid advance in genome sequencing technology has led to production of huge amount of sensitive genomic data. However, a serious privacy challenge is confronted with increasing number of genetic tests as genomic data is the ultimate source of identity for humans. Lately, privacy threats and possible solutions regarding the undesired access to genomic data are discussed, however it is challenging to apply proposed solutions to real life problems due to the complex nature of security definitions. In this review, we have categorized pre-existing problems and corresponding solutions in more understandable and convenient way. Additionally, we have also included open privacy problems coming with each genomic data processing procedure. We believe our classification of genome associated privacy problems will pave the way for linking of real-life problems with previously proposed methods., (Copyright © 2015 Elsevier Inc. All rights reserved.)

The aim of this study was to determine the ESBL with phenotypic tests and investigate the bla(CTX-M) genes with the PCR method in Escherichia coli strains. The presence of ESBL in E. coli strains was determined with the Vitek 2 automated system. ESBL-positive 100 and ESBL-negative 50 E. coli strains were included in the study. The ESBL disk diffusion screening test (DDST) and the combined disk confirmation tests (CDCT) were performed on these strains and the results of these tests were compared with each other. bla(CTX-M) genes were investigated with the PCR method. The results of CDCT-CAZ-CZC and CDCT-CTX-CTC were found to be consistent in 90% of strains. Those of the automated system, DDST and CDCT-CAZ-CZC were compatible with each other in 83.3% of strains. Also the results of the automated system and CDCT-CTX-CTC were found to be compatible in 83.3% of strains. Based on PCR, bla(CTX-M) genes were found in 67.3% of 150 strains. According to the order of frequency, 46%, 38.7%, 20%, 7.3% of strains were determined to carry groups I, IV, II and III, respectively.

Background: Recently, a wide range of diseases have been associated with changes in DNA methylation levels, which play a vital role in gene expression regulation. With ongoing developments in technology, attempts to understand disease mechanism have benefited greatly from epigenetics and transcriptomics studies. In this work, we have used expression and methylation data of thyroid carcinoma as a case study and explored how to optimally incorporate expression and methylation information into the disease study when both data are available. Moreover, we have also investigated whether there are important post-translational modifiers which could drive critical insights on thyroid cancer genetics., Results: In this study, we have conducted a threshold analysis for varying methylation levels to identify whether setting a methylation level threshold increases the performance of functional enrichment. Moreover, in order to decide on best-performing analysis strategy, we have performed data integration analysis including comparison of 10 different analysis strategies. As a result, combining methylation with expression and using genes with more than 15% methylation change led to optimal detection rate of thyroid-cancer associated pathways in top 20 functional enrichment results. Furthermore, pooling the data from different experiments increased analysis confidence by improving the data range. Consequently, we have identified 207 transcription factors and 245 post-translational modifiers with more than 15% methylation change which may be important in understanding underlying mechanisms of thyroid cancer., Conclusion: While only expression or only methylation information would not reveal both primary and secondary mechanisms involved in disease state, combining expression and methylation led to a better detection of thyroid cancer-related genes and pathways that are found in the recent literature. Moreover, focusing on genes that have certain level of methylation change improved the functional enrichment results, revealing the core pathways involved in disease development such as; endocytosis, apoptosis, glutamatergic synapse, MAPK, ErbB, TGF-beta and Toll-like receptor pathways. Overall, in addition to novel analysis framework, our study reveals important thyroid-cancer related mechanisms, secondary molecular alterations and contributes to better knowledge of thyroid cancer aetiology.

The effects of use of adjunct cultures (Lactobacillus helveticus and Lb. casei) and ripening temperatures (6 or 12 °C) on proteolysis and angiotensin-I converting enzyme (ACE)-inhibitory activity in white-brined cheeses were investigated during 120 d ripening. Proteolysis was monitored by urea-polyacrylamide gel electrophoresis (urea-PAGE) and reversed phase-HPLC (RP-HPLC) of water-insoluble and -soluble fractions of the cheeses, respectively. Urea-PAGE patterns of the samples revealed that the intensities of the bands representing casein fractions decreased in the experimental cheeses, being more pronounced in the cheeses made with adjunct cultures. Similarly, peptide profiles and the concentrations of individual and total free amino acids were influenced by both the adjunct cultures and ripening temperatures. The ACE-inhibitory activity of the water-soluble extracts of the cheeses were higher in the cheeses made using adjunct cultures (especially Lb. helveticus) and ripened at 12 °C. The ACE-inhibitory activity did not decrease during ripening. The contribution of Lb. helveticus to the development of proteolysis and ACE-inhibitory peptide activities were higher than that of Lb. casei. To conclude, the use of Lb. helveticus as adjunct culture in white-brined cheese and ripening at 12 °C would be recommended to obtain white-brined cheese with high ACE-I-inhibitory peptides activity and higher levels of preoteolysis.

Background: Tuberculin skin test (TST) has been used for years as an aid in diagnosing latent tuberculosis infection (LTBI) but it suffers from a number of well-documented performance and logistic problems. Quantiferon-TB Gold In Tube test (QFT-GIT) has been reported to have better sensitivity and specifity than TST. In this study, it was aimed to compare the performance of a commercial IFN-gamma release assay (QFT-GIT) with TST in the diagnosis of HCWs at risk for latent TB infection in BCG vaccinated population., Material and Methods: Hundred healthy volunteer health care workers were enrolled. All were subjected to TST and QFT-GIT. Results were compared among Health Care Workers (HCWs) groups in terms of profession, workplace, working duration., Results: TST is affected by previous BCG vaccinations and number of cases with QFT-GIT positivity is increased in accordance with the TST induration diameter range. QFT-GIT result was negative in 17 of 32 TST positive (≥ 15 mm) cases and positive in 4 of 61 cases whose TST diameters are between 6-14 mm, that is attritutable to previous BCG vaccination(s). It was negative in all cases with TST diameters between 0-5 mm. HCWs with positive QFT-GIT results were significantly older than the ones with negative results. Furthermore duration of work was significantly longer in QFT-GIT positive than in negative HCWs., Conclusions: There was a moderate concordance between QFT-GIT and TST, when TST result was defined as positive with a ≥ 15 mm diameter of induration. We suggest that QFT-GIT can be used as an alternative to TST for detection of LTBI, especially in groups with high risk of LTBI and in population with routine BCG vaccination program.

The main objective of the study was to determine the effects of different fermentation parameters on kefir quality. Kefir samples were produced using kefir grains or natural kefir starter culture, and fermentation was carried out under normal or modified atmosphere (10% CO(2)) conditions. The microbiological (lactobacilli, lactococci, Lactobacillus acidophilus, Bifidobacterium spp., and yeasts), chemical (pH, lactic acid, total solids, protein, ethanol, exopolysaccharide contents), rheological, and sensory properties of kefir samples were investigated during a 21-d storage period. The use of different fermentation parameters or the choice of grain versus natural kefir starter culture did not significantly affect the content of microorganisms. Lactobacilli, lactococci, and yeast contents of kefir samples varied between 9.21 and 9.28, 9.23 and 9.29, and 4.71 and 5.53 log cfu/mL, respectively, on d 1 of storage. Contents of L. acidophilus and Bifidobacterium spp. were between 5.78 and 6.43 and between 3.19 and 6.14 log cfu/mL, respectively, during 21 d of storage. During the storage period, pH, lactic acid (%), total solids (%), protein (%), acetaldehyde, and ethanol contents of kefir samples ranged from 4.29 to 4.53, from 0.81 to 0.95%, from 7.81 to 8.21%, from 3.09 to 3.48%, from 3.8 to 23.6 mg/L, and from 76.5 to 5,147 mg/L, respectively. The exopolysaccharide contents of the samples decreased during 21 d of cold storage; the samples fermented under modified atmosphere had relatively higher exopolysaccharide contents, indicating higher potential therapeutic properties. The kefir samples exhibited non-Newtonian pseudoplastic flow behavior according to the power law model. According to the sensory results, kefir produced from natural kefir starter culture under CO(2) atmosphere had the highest overall evaluation score at d 1., (Copyright © 2013 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.)

Objective: Toxoplasmosis, cytomegalovirus and rubella may cause congenital infections. The aim of this study is to investigate toxoplasmosis, cytomegalovirus and rubella IgG antibodies in women and children who were admitted to the Hatay Women and Children Hospital between January 1 and December 31, 2009., Methods: Levels of IgG antibodies for toxoplasmosis, cytomegalovirus and rubella established with chemiluminescence immunoassay (Architect i2000, Abbott, USA) method were evaluated, retrospectively., Results: The results were obtained from 1103 cases. Seropositivity of IgG antibodies for toxoplasmosis (n = 743), cytomegalovirus (n = 929) and rubella (n = 746) were 59.9%, 98.9% and 93.6%, respectively, Conclusion: Routine serological screening should be recommended in women of childbearing age. Seronegative subjects should be vaccinated for rubella and educated for protection from toxoplasmosis.

Background & Objectives: This study was carried out to evaluate the association between the antibiotic susceptibility patterns and the antibiotic resistance genes in staphylococcal isolates obtained from various clinical samples of patients attending a teaching hospital in Hatay, Turkey., Methods: A total of 298 staphylococci clinical isolates were subjected to antimicrobial susceptibility testing. The genes implicated in resistance to oxacillin (mecA), gentamicin (aac(6')/aph(2''), aph(3')-IIIa, ant(4')-Ia), erythromycin (ermA, ermB, ermC, and msrA), tetracyclin (tetK, tetM), and penicillin (blaZ) were amplified using multiplex PCR method., Results: Methicillin resistance rate among 139 Staphlococcus aureus isolates was 16.5 and 25.9 per cent of S. aureus carried mecA gene. Of the 159 CoNS isolates, methicillin resistance rate was 18.9 and 29.6 per cent carried mecA gene. Ninety four isolates identified as gentamicin resistant phenotypically, contained at least one of the gentamicin resistance genes [aac(6')/aph(2''), aph(3')-IIIa, ant(4')-Ia], 17 gentamicin-susceptible isolates were found as positive in terms of one or more resistance genes [aac(6')/aph(2''), aph(3')-IIIa, ant(4')-Ia] by multiplex PCR. A total of 165 isolates were resistant to erythromycin, and contained at least one of the erythromycin resistance genes (ermA, ermB, ermC and msrA). Phenotypically, 106 staphylococcal isolates were resistant to tetracycline, 121 isolates carried either tetK or tetM or both resistance genes. The majority of staphylococci tested possessed the blaZ gene (89.9%)., Interpretation & Conclusions: The present results showed that the phenotypic antibiotic susceptibility patterns were not similar to those obtained by genotyping done by multiplex PCR. Rapid and reliable methods for antibiotic susceptibility are important to determine the appropriate therapy decisions. Multiplex PCR can be used for confirmation of the results obtained by conventional phenotypic methods, when needed.

The aim of this study was to determine the antimicrobial resistance rates and the resistance genes associated with efflux pumps of Pseudomonas aeruginosa strains isolated from the patients who acquired lower respiratory tract infection (LRTI) in intensive care unit (ICU). Fifty P. aeruginosa strains isolated from the lower respiratory tract specimens of the patients who acquired LRTIs in ICU were included in this study. P. aeruginosa strains were isolated from tracheal aspirate (27), bronchoalveolar lavage (14) and sputum (9). The susceptibilities of the isolates were investigated by the disk diffusion method. Multiplex PCR assay was carried out for the detection of 13 antibiotic-resistance genes. Antimicrobial resistance rates of the isolates were found high and the highest resistance rate of the isolates studied was determined against to mezlocillin (50%) followed by norfloxacin (48%), ciprofloxacin (46%), meropenem (40%). Fourty-three isolates (86%) were determined to carry one and more resistance genes. NfxB gene was most often determined in the genes that were investigated. The significant relation between the resistance to cefepime, piperacilline/tazobactam and the mexC gene, that between the resistance to mezlocillin, piperacilline/tazobactam, ceftazidime, cefepime and ampC genes, and that between the resistance to ciprofloxacin, norfloxacin and oprJ, oprN and nfxB genes was identified. Resistance caused by genes for carbapenemases, aminoglycoside-modifying enzymes and other mechanisms were not identified in this study. Understanding the prevalence and mechanism of antimicrobial resistance in P. aeruginosa may help to select empirical therapy for nosocomial LRTIs due to P. aeruginosa in our ICU.

Background: Recurrent urinary tract infections are important in children and adults with diabetes mellitus and/or incontinence due to risk of pyelonephritis (PYN) and renal damage. There is a positive correlation released free radicals during PYN and renal damage. Experimental studies showed that antioxidant agents improve renal damage when used immediately after bacterial inoculation., Objective: The aim of the present study was to evaluate whether treatment by thymoquinone (TQ) before or during Escherichia coli inoculation prevents oxidative damage in acute pyelonephritis (PYN) in an ascending obstructive rat model., Methods: In this study, 42 Wistar rats were grouped as follows: control, PYN (24, 48, and 72 hours), and TQ-PYN (24, 48, and 72 hours). E. coli (1 ×10(9) colony forming units) was inoculated into the bladder via urethral catheterization in both the PYN and TQ groups. TQ injections were performed 24 hours before bacteria inoculation and repeated at 24-hour intervals during the indicated time at a dose of 10 mg/kg body weight intraperitoneally in TQ groups., Results: Superoxide dismutase activity was statistically lower in the TQ-PYN-48 and -72 groups than the PYN-48 and -72 groups (P < 0.001, P = 0.004, respectively). Catalase activity was significantly higher in PYN-24, -48, and -72 groups than the control group (P < 0.001). In addition, there was a significant difference between the TQ-PYN-24, -48, and -72 groups and PYN groups in terms of glutathione peroxidase activity (P < 0.001, P = 0.026, P = 0.046, respectively). When the TQ-PYN-72 group was compared with the PYN-72 group, malondialdehyde levels were significantly lower in the TQ-PYN-72 group than in the PYN-72 group (P = 0.033). A histologic examination also confirmed the protective effect of TQ. In statistical analysis of histopathologic findings, there were significant differences between the PYN-24 and TQ-PYN-24, PYN-48 and TQ-PYN-48, and PYN-72 and TQ-PYN-72 groups (P = 0.008, P < 0.001, P < 0.001, respectively)., Conclusions: The results indicate that TQ administration attenuated the oxidative damage that occurred in PYN and, therefore, could be used as a supportive agent to protect the kidneys from oxidative damage caused by PYN.

Background/aim: To investigate the early effects of peginterferon alpha-2b plus ribavirin therapy on blood pressure and related cardiovascular risk parameters, and also insulin resistance in patients with chronic hepatitis C virus (HCV) infection., Methodology: Twenty-nine patients with chronic hepatitis C (CHC) were enrolled in the study. Twenty-four hour ambulatory blood pressure monitoring (ABPM) of all patients was recorded in the pre-treatment period, and after the 1st and 8th weeks of treatment. Lipid profile, insulin resistance (IR), body mass index (BMI), complete blood counts and transaminase levels were also recorded at the same time periods., Results: Fifteen of the 29 patients studied were hypertensive before treatment. The baseline, 1st week and 8th week recordings of ABPM (daytime, nighttime, mean systolic and diastolic measurements) did not show any significant change. Among hypertensive patients, differences in pretreatment, 1st and 8th week of treatment values of median systolic and diastolic blood pressures were not statistically significant. After the 8th week, total cholesterol, LDL, HDL, hemoglobin, white blood cell, platelet and AST/ALT were significantly decreased (p<0.05). Serum triglyceride levels increased significantly (p<0.0001) and HOMA-IR decreased (p=0.07)., Conclusion: Peginterferon alpha-2b plus ribavirin therapy did not cause any increase in blood pressure in hypertensive and normotensive CHC patients in the early period of treatment. This treatment resulted in early but not significant changes in the IR status of CHC patients.

Background: Nosocomial infections are one of the most serious complications in intensive care unit patients because they lead to high morbidity, mortality, length of stay and cost. The aim of this study was to determine the nosocomial infections, risk factors, pathogens and the antimicrobial susceptibilities of them in intensive care unit of a university hospital., Material/methods: The patients were observed prospectively by the unit-directed active surveillance method based on patient and the laboratory., Results: 20.1% of the patients developed a total of 40 intensive care unit-acquired infections for a total of 988 patient-days. The infection sites were the lower respiratory tract, urinary tract, bloodstream, wound, and the central nervous system. The respiratory deficiency, diabetes mellitus, usage of steroid and antibiotics were found as the risk factors. The most common pathogens were Enterobacteriaceae, Staphylococcus aureus, Candida species. No vancomycin resistance was determined in Gram positive bacteria. Imipenem and meropenem were found to be the most effective antibiotics to Enterobacteriaceae., Conclusions: Hospital infection rate in intensive care unit is not very high. The diabetes mellitus, length of stay, usage of steroids, urinary catheter and central venous catheter were determined as the risk factors by the final logistic regression analysis. These data, which were collected from a newly established intensive care unit of a university hospital, are important in order to predict the infections and the antimicrobial resistance profile that will develop in the future.

Propolis is a honeybee product with a very complex chemical composition and various pharmacological properties. This study was aimed to investigate antileishmanial activities of "Bursa" and "Hatay" propolis samples against Leishmania infantum and Leishmania tropica strains. Propolis samples were analysed with the gas chromatography-mass spectrometry technique. Promastigotes were incubated in Roswell Park Memorial Institute culture medium in the absence and presence of several concentrations (50, 100, 250, 500, 750, and 1,000 μg/mL) of each propolis sample. The viability and cell morphology of promastigotes in each concentration were examined after 24, 48, 72, and 96 h of incubation. The growth of leishmania parasites was significantly suppressed in the presence of 500, 750, and 1,000 μg/mL of Hatay propolis. Bursa propolis was found to be efficient in inhibiting the growth of leishmania promastigotes in culture media at these concentrations, 250, 500, 750, and 1,000 μg/mL. Thus, the in vitro results showed that the Hatay and Bursa propolis samples decreased significantly the proliferation of L. infantum and L. tropica parasites (p < 0.001); however, Bursa propolis was found to be more effective than Hatay propolis against leishmania promastigotes. These two natural products may be useful agents in the prevention of leishmanial infections.

Background: The purposes of the present study were (1) to determine the prevalence of mecA and femA genes, (2) to investigate the presence of icaA and icaD genes responsible for slime synthesis, and (3) to search in vitro slime synthesis by staphylococcal strains isolated from the nares of patients with orthopaedic implants using the Congo red agar (CRA) plate test., Material/methods: Staphylococci strains were defined by multiplex polymerase chain reaction (PCR) technique to determine intercellular adhesion genes icaA and icaD. Slime production capability was searched by the CRA plate test, phenotypically. Also, the presence of mecA and femA genes was determined by PCR in all strains., Results: The presence of icaA and icaD was detected in 101 isolates of 134 (75.4%) strains. This ratio was 74.8% (89 of 119) among the Staphylococcus epidermidis and 80% (12 of 15) among the Staphylococcus aureus isolates. A total of 63.4% of all the strains were found to be icaA and icaD positive as well as slime-forming on the CRA plate test. The percentage of icaA- and icaD-negative strains was 36.6%, and all of them were negative on the CRA plate test. Although femA presence was detected in all 15 (11.2%) S. aureus isolates, a total of 5 (3.7%) isolates carried the mecA gene., Conclusions: The frequency of icaA and icaD genes was determined to be of high prevalence among staphylococcal isolates. The staphylococcal strains that were found in the nasal flora of patients with orthopaedic implants may be important potential sources of infection for these patients.

Background: Beta-thalassemia major affects multiple organs and is associated with considerable morbidity and mortality. The goal of this analysis was to document the frequency of skin diseases among patients with beta-thalassemia major., Methods: A sample of 78 patients with beta-thalassemia major was recruited and interviewed at the thalassemia clinic between April and June 2008. A dermatologist completed a skin examination of each patient and recorded any skin disease present. The patients' laboratory results and treatment modalities were recorded from the charts., Results: Sixty-five (83.3%) of the 78 patients examined had a diagnosed skin disease: pruritus (37.2%), xerosis (34.6%), scars (24.4%), ephelides (23.1%), skin irritation/erythema caused by deferoxamine pump (12.8%), idiopathic guttate hypomelanosis (6.4%), pityriasis alba (6.4%), tinea infections (5.1%), verruca vulgaris (5.1%), urticaria (3.8%), hyperhidrosis, contact dermatitis, and acne (2.6%), necrobiosis lipoidica (1.3%), melasma (1.3%), and others (14.1%). Pruritus and xerosis increased in frequency with age. The mean serum ferritin level was higher in patients with xerosis than in those without (5607.7 +/- 2997.5 ng/mL and 4285.2 +/- 4732.4 ng/mL, respectively) (P1/4 0.005). Moreover, xerosis was observed significantly more frequently inpatients using deferoxamine and deferiprone than in those using deferasirox (P1/4 0.047, P1/4 0.027, and P1/4 0.273, respectively)., Conclusion: Skin diseases, especially pruritus and xerosis, are observed highly frequently inpatients with beta-thalassemia major. Treatment is needed for these patients who already have other significant morbidities.

Aspergillus species are widely distributed in nature, and more than 30 species have been reported to be involved in human and animal infection. Cutaneous infections due to Aspergillus terreus are particularly rare. In this report, we describe a case of cutaneous infection caused by A. terreus in a paediatric patient who underwent surgical treatment for an open tibial fracture secondary to an agricultural accident.

Objective: We aimed to evaluate the ghrelin levels in the children with adenoid or tonsil hyperthrophies., Methods: The study included 27 children (17 boys and 10 girls). Mean age was 6.9+/-3.5 years, ranging from 3 to 16. Ghrelin levels in the patients and their weight and height measurements were evaluated before surgery and after 3 months later of the operation., Results: While 18 (67%) children were operated for adenoid hypertrophy, 9 (33%) children were operated for adenoid and tonsil hypertrophy. It was found that postoperative ghrelin levels were significantly decreased whereas weight and BMI scores were significantly increased (p<0.01). A weak correlation was observed between preoperative ghrelin and weight (r=-0.29). This negative correlation became more profound at the postoperative 3rd month examination (r=0.85) (p<0.01)., Conclusions: The present study showed that the surgical treatment provides positive contributions on the growing of children with adenoid and tonsil hypertrophies. The ghrelin levels were significantly decreased at the postoperative period in the children, and a negative relationship was observed between the ghrelin levels and the weight. These findings suggest that blood ghrelin levels may be useful as a parameter for following the development of the children.

The aim of this study was to evaluate the association of Staphylococcal enterotoxins (se) a through e, exfoliative toxin (et) a and b, toxin and toxic shock syndrome toxin (tst) and mecA with psoriasis. We also investigated the distribution of Staphylococcus aureus (S. aureus) in the skin and nares. Fifty consecutive patients with chronic plaque-type psoriasis and 50 sex- and age-matched healthy controls were included in this study. There was a statistical difference in cultivation of S. aureus between lesional (64%) and non-lesional skin (14%) in patients with psoriasis (p = 0.037). S. aureus was cultivated from the nares in 25 (50%) of 50 patients with psoriasis and in 17 (34%) of 50 healthy controls (p > 0.05). In psoriasis patients, 31 (96.8%) out of the 32 strains isolated from the lesional skin and 3 (42.3%) out of the 7 strains isolated from the non-lesional skin were toxigenic (p = 0.01). Isolated strains from the nares were toxigenic in 96% (24/25) for patients with psoriasis and in 41.2% (7/17) for healthy controls, respectively (p = 0.006). Patients with cultivation-positive in lesional skin had a significantly higher PASI score than patients who were cultivation-negative in lesional skin (8.28 +/- 3.97 vs. 5.89 +/- 2.98, p = 0.031). Our results confirm that S. aureus colonization and its toxigenic-strains are associated with psoriasis. According to our findings, non-classical superantigens such as methicillin resistance gene (mecA), see and etb may also be associated with psoriasis.

Objective: To evaluate whether there is a relationship between HLA-A, -B, -Cw, and -DRB1 alleles and developing nasal polyposis (NP)., Study Design: Data from 66 patients with NP were compared with data from 100 healthy randomly selected controls. Asthma, ASA (acetylsalicylic acid) triad, polyp score, and previous sinonasal surgery were also recorded., Subjects and Methods: Genotyping of the HLA-A, -B, -Cw, and -DRB1 alleles were performed with polymerase chain reaction (PCR) with the sequence-specific primer (SSP) method. Data were analyzed by using a Pearson chi(2) test., Results: The HLA-B*07 and -Cw*12 alleles were found to be significantly higher in the NP patients compared with the control group, whereas the HLA-B*57 and HLA-Cw*04 alleles were significantly lower (P < 0.05). The HLA-A*24, HLA-Cw*12, and HLA-DRB1*04 alleles were determined to be significantly higher in the NP patients with asthma and ASA triad (P < 0.05)., Conclusions: Our results show that some of the HLA alleles seem to be associated with the genetic susceptibility to develop NP in the Turkish population.

Background/aims: Helicobacter pylori-induced gastritis increases serum nitrate and nitrite concentrations. The relationship between splanchnic hemodynamics and nitrate and nitrite levels has been demonstrated. We aimed to determine the effect of Helicobacter pylori eradication treatment on portal hemodynamics., Methods: Nineteen patients with liver cirrhosis and Helicobacter pylori gastritis were included. Nine patients had esophageal varices indicating over portal hypertension. After histopathologic examination of gastric mucosa, Doppler ultrasonographic measurement of the portal veins and serum sampling to determine nitrate and nitrite concentration, treatment for Helicobacter pylori eradication was initiated for each patient. Evaluation of histopathology, Doppler measurements and sampling for serum nitrate and nitrite levels were repeated six weeks after the end of therapy., Results: The rate of eradication of Helicobacter pylori was 73.7%. The median inflammation score, Helicobacter pylori density, and the median serum concentration of nitrate and nitrite decreased significantly after therapy (p values were 0.021, 0.001, and 0.018, respectively). After treatment, the patients with varices showed significant decreases in serum nitrate and nitrite levels whereas those without varices did not. Considering portal measurements, alteration in the congestion index approached statistical significance (0.15 versus 0.1; p=0 .066) in the patient group with varices., Conclusions: Reducing effect of Helicobacter pylori eradication treatment on serum nitrate and nitrite concentration seems to have some beneficial influence on portal hemodynamics.

Background: Chronic exposure to relatively high levels of n-hexane either by inhalation or skin contact can result in peripheral nerve lesions. We present the clinical and electrophysiological features of 5 patients who have been exposed to n-hexane at similar industrial occupations in the progressive phase., Methods: All patients underwent routine laboratory tests, cerebrospinal fluid examination, and sural nerve biopsy. Conventional sensory and motor nerve conduction studies were applied at admission and at the end of the 12 month., Results: The average incubation period of the 5 cases was 10.2 months and the average period of the initial symptoms was 3.8 months. Numbness and weakness of the lower extremities were the initial symptoms that had ascended to the upper extremities in three of the patients. Deep tendon reflexes were either diminished or abolic. There was distal atrophy only in patient 5. All were treated with vitamin B complex and physical therapy and training. They were removed from further exposure to n-hexane after aetiological confirmation, but motor disturbance continued to worsen in the patient 5. The patients were visited every 3 months. Sensory functions were regained earlier than motor functions. All the patients, including one who was severe quadriparetic in the early stages, regained their full motor capabilities within 6 months to 21 months., Conclusion: Occupational n-hexane causes subacute neuropathy and the duration of exposure is important for the neurological outcome. We suggest that the prognosis of n-hexane induced neuropathy is well if correct diagnosis is made and further exposure is ceased.

Background/aims: We aimed to compare the level of thrombocytopenia in cirrhotic patients with HBV and those with HCV, and to investigate whether the reduced serum level of IL-6 in patients with HCV is responsible for the lower platelet count compared to those with HBV through the effect on serum thrombopoietin level., Methodology: Fifty-three patients with liver cirrhosis, 28 of who were HBV- seropositive (Group A), 25 of who were HCV- seropositive (Group B) and 15 healthy controls were enrolled in this study., Results: Platelet count in group B [75 (1.5-99) K/microL] were lower than those of group A [140 (62-374) K/microL] (p < 0.001). The median levels of serum thrombopoietin in patients [group A: 31.9 (31-113) pg/mL and group B: 38.0 (31.2-102) pg/mL] and controls [31.3 (31-153) pg/mL] did not show statistically significant difference. The patients compared to controls, had higher serum IL-6 levels [3.6 (2-1150) vs. 2.0 (2-9.9) pg/mL], (p < 0.01), which showed similarity in group A and B patients [3.65 (2-1150) vs. 3.3 (2-45) pg/mL], (p=NS). Serum thrombopoietin level was not correlated with serum IL-6 levels in any group. Serum thrombopoietin and IL-6 levels had no relationship with platelet count and with Child-Pugh score., Conclusions: Our study showed that cirrhotic patients with HCV had lower platelet count than those with HBV and controls, and this difference does not appear to be related with either serum thrombopoietin or IL-6 level.

A mutation in the methylenetetrahydrofolate reductase (MTHFR) gene is known as one of the causes of hyperhomocyteinemia. The oxidation products of homocysteine can initiate lipid peroxidation, which has a central role in the pathogenesis of nonalcoholic fatty liver disease (NAFLD). We aimed to assess the possible role of the MTHFR C677T mutation in the progression of simple steatosis to an advanced form of NAFLD. Thirty-four patients with NAFLD diagnosed by histologic analysis and 282 healthy controls were included in the study. The discrimination of nonalcoholic steatohepatitis (NASH) from another NAFLD was made by NAFLD activity score (NAS), and a NAS>or=5 was considered NASH. Patients with either NASH or nonalcoholic fatty liver (NAFL) and controls were evaluated for frequency of the MTHFR C677T mutation. The frequency of the MTHFR C677T mutation was 53.5% (CT, 44.7%; TT, 8.9%) in controls and 41.5% (CT, 37.7%; TT, 3.8%) in patients (odds ratio [OR], 0.62; 95% confidence interval [CI], 0.34-1.12). There was no statistical difference in the frequency of this genotype between patients with NAFL and those with NASH (36% [CT, 28%; TT, 8%] vs 46.4% [CT, 46.4; TT, 0%]; OR, 0.65; 95% CI, 0.22-1.96). According to this study, the MTHFR C677T mutation does not seem to be a risk factor for the progression of NAFL to NASH.

Aim: To investigate the influence of anti-HCV positivity on markers of malnutrition and inflammation in hemodialysis (HD) patients., Methods: Stable HD patients who had persistently negative or positive HCV antibodies (at least three) and without elevated aminotransferase levels in routine periodical tests with a duration of more than 12 months were included. Patients with conditions known to be associated with acute-phase responses or clinically active (HCV RNA positive) or advanced liver failure were excluded. Thirty-six anti-HCV-positive patients (22 male, 14 female, mean age 47.3 +/- 14.5 years, mean time on HD 72.0 +/- 39.0 months), were compared with 36 anti-HCV negative patients with similar age and HD duration (25 male, 11 female, mean age 49.2 +/- 13.8 years, mean time on HD 59.7 +/- 27.1 months). Malnutrition-Inflammation Score (MIS), a fully quantitative score adopted from subjective global assessment, was recorded for each patient (ranges from 0 to 30). High sensitivity serum C-reactive protein (hs-CRP), interleukin-6 (IL-6), erythrocyte sedimentation rate (ESR), and hematocrit-corrected ESR were compared as indices of the degree of inflammation beyond anthropometric evaluation and routine laboratory tests., Results: There was no significant difference in MIS of two groups (6.1 +/- 3.2 vs. 5.6 +/- 3.2, p > 0.05). In the comparison of components of MIS, co-morbidity including number of years on dialysis was higher in anti-HCV-positive patients (p = 0.04). Anthropometric values and serum levels of hs-CRP, IL-6, ESR, and hematocrit-corrected ESR of two groups were not statistically different from each other (p > 0.05 for all). ALT (p = 0.0001) and AST (p = 0.001) levels were higher in anti-HCV-positive patients., Conclusion: Anti-HCV positivity without active infection seems to have no additional negative effect on malnutrition and inflammation in maintenance HD patients.

The purpose of the present study was to investigate GSTM1 and GSTT1 genotypes by using multiplex polymerase chain reaction (PCR) in patients with laryngeal squamous cell carcinoma (LSCC). The genotypes of 110 patients with LSCC and of 197 healthy subjects as the control group were determined by PCR analysis for GSTM1 and GSTT1 genes. Results showed that frequencies of GSTM1-null, GSTT1-null, and both GSTs-null genotypes were 51.8, 30, and 16.4%, respectively, in the patients with LSCC and 37.6, 15.7, and 5.6% in the control group. There was a significant difference between the genotype distributions of all GSTs in patients and in control groups (P < 0.05). The results support the hypothesis that null genotypes of GSTM1 and GSTT1 can reduce detoxification capacity of GSTs as members of the xenobiotic enzyme system. GSTM1-null, GSTT1-null, and both GSTs-null genotypes were more common in the patients with LSCC than in the control group. Patients with both GSTs-null genotypes had the highest risk for supraglottic LSCC in the early period, even if they were light-to-medium smokers. Investigation and determination of the genetic basis of LSCC may contribute to detection of risk groups and to prevent LSCC in the population.

Background: The aim of the present study was to evaluate gallbladder function in irritable bowel syndrome (IBS) patients., Methods: The functions of gallbladder were investigated every 30 min for 4 h. In addition, ejection fraction of the gallbladder was calculated from the fasting and post-prandial volumes., Results: In IBS patients and healthy controls, fasting gallbladder volumes were 19.64 +/- 3.09 mL and 20.04 +/- 1.82 mL, and residual volumes after 3 h were 3.36 +/- 6.82 mL and 9.74 +/- 1.50 mL. Except for the residual volume after 3 h, all these results were not statistically significant. Residual volume after 3 h was statistically significantly lower in the IBS patients than in the controls (P < 0.001). Ejection fraction of the gallbladder was significantly higher in the IBS patients than in the controls (84% vs 55%, P < 0.001)., Conclusions: Gallbladder contraction in patients with IBS was not different from that of a control group at post-prandial second hour but was signigicantly more pronounced at the end of 3 h when compared with controls. Ejection fraction of the gallbladder was higher in IBS patients when compared with controls.

Objectives: The purpose of the study is to investigate whether there is any association between pharyngeal reflux and adenoid hyperplasia by using 24-h esophageal pH monitoring with a dual probe in children., Methods: The study group consisted of 30 children with adenoid hyperplasia, and the control group consisted of 12 healthy children, studied prospectively. All children underwent 24-h esophageal pH monitoring with a dual probe (distal and proximal esophageal pH monitoring). The results were evaluated by the Measurement and Analysis Software of Medical Measurement System program (Version: 7.2a)., Results: In the study group, the frequency of pharyngeal reflux was 46.7% and the gastroesophageal reflux (GER) was 64.5%, while, in the control group, they were 8.3% and 25%, respectively. There was a significant difference between study and control groups for frequencies of pharyngeal reflux and GER. Mean adenoid nasopharyngeal ratio (ANR) was 0.78+/-0.11 in children with adenoid hyperplasia. There was not a significant difference between positive pharyngeal reflux, positive GER and mean ANR (p>0.05)., Conclusions: Children with adenoid hyperplasia had higher frequency of pharyngeal reflux than children at the same age healthy group. These results supported that pharyngeal reflux may play an important role in the etiology of adenoid hyperplasia.

Aim: To determine whether Helicobacter pylori (H pylori)infection caused hyperhomocysteinemia by altering serum vitamin B(12), serum folate and erythrocyte folate levels and whether eradication of this organism decreased serum homocysteine level., Methods: The study involved 73 dyspeptic H pylori-positive patients, none of them had gastric mucosal atrophy based on rapid urease test and histology. Out of 73 patients, 41 (56.2%) showed a successful eradication of H pylori 4 wk after the end of treatment. In these 41 patients, fasting serum vitamin B(12), folate and homocysteine levels, and erythrocyte folate levels before and 4 wk after H pylori eradication therapy were compared., Results: The group with a successful eradication of H pylori had significantly higher serum vitamin B(12) and erythrocyte folate levels in the post-treatment period compared to those in pre-treatment period (210+/-97 pg/mL vs 237+/-94 pg/mL, P<0.001 and 442+/-212 ng/mL vs 539+/-304 ng/mL, P = 0.024, respectively), but showed no significant change in serum folate levels (5.6+/-2.6 ng/mL vs 6.0+/-2.4 ng/mL, P = 0.341). Also, the serum homocysteine levels in this group were significantly lower after therapy (13.1+/-5.2 micromol/L vs 11.9+/-6.2 micromol /L, P = 0.002). Regression analysis showed that serum homocysteine level was positively correlated with age (P = 0.01) and negatively with serum folate level before therapy (P = 0.003)., Conclusion: Eradication of H pylori decreases serum homocysteine even in patients who do not exhibit gastric mucosal atrophy. It appears that the level of homocysteine in serum is related to a complex interaction among serum vitamin B(12), serum folate and erythrocyte folate levels.

Background: Stenotrophomonas maltophilia is inherently resistant to many antimicrobials. So far, antimicrobial susceptibility tests for S. maltophilia have not been fully standardized. The purpose of the study was to compare the susceptibility of S. maltophilia isolates against seven different antimicrobials using three different methods and to investigate their genetic relatedness., Results: Although trimethoprim/sulfamethoxazole (SXT) and ciprofloxacin have the lowest MIC values, SXT (98.1%) and ticarcillin/clavulanate (TLc) (73.1%) were found to be the most effective antimicrobials by agar dilution method, which was in accordance with the breakpoints established by NCCLS. Disc diffusion and E-test was in agreement with agar dilution method for SXT. When the isolation dates, clinics, antibiotyping, and AP-PCR data were investigated, two small outbreaks consisting of five and three cases were determined., Conclusion: By using the NCCLS criteria, disc diffusion and E-test were unreliable alternative methods for S. maltophilia, except for SXT. However, the significance of these data should be confirmed by further experimental and clinical studies.

The aim is to examine histopathological changes and expression of epidermal growth factor receptor (EGFR) in tracheal epithelia caused by application of topical mitomycin-C (MMC) in rabbit model after the tracheotomy procedure. The conventional tracheotomy was performed in 16 rabbits. They were randomly divided into two equal groups. The first group was applied MMC at a concentration of 0.4 mg/ml around tracheotomy for 5 min, and the other group was not taken a treatment as a control. The animals were sacrificed at the end of 4 weeks. Their tracheas were evaluated with H&E and Masson's trichrome histochemically, and with antiepidermal growth factor receptor immunohistochemically. Results showed that there was no significant difference between MMC and control group for inflammatory cells (P=0.09). The numbers of fibroblasts and subepithelial tissue thickness in the group exposed to MMC were significantly lower than the control group (P<0.05). In contrast, the percentage of EGFR in the application of MMC group was significantly higher than the control group (P<0.05). The application of topical MMC on airway epithelia after tracheotomy showed significant elevation in the levels of epithelial EGFR expression compared to controls in a rabbit model. The activation of epithelial EGFR may facilitate epithelial healing, but further studies are needed to assess the effect of topical MMC on respiratory epithelia.

Objective: To investigate whether there is an association between chronic otitis media (COM) with effusion and pharyngeal reflux in children by using 24-h pH monitoring with a dual probe., Material and Methods: This was a prospective study. The study group consisted of 25 children with COM with effusion and the control group comprised 12 healthy children. All children underwent 24-h esophageal pH monitoring with a dual probe (distal and proximal esophageal pH monitoring)., Results: In the study group, the frequencies of pharyngeal and gastroesophageal reflux (GER) were 48% and 64%, respectively, and the corresponding values in the control group were 8.3% and 25%. Both of these differences were significant (p <0.05). In the study group, 28% of patients were positive for at least 1 symptom of GER; 72% of the patients did not have any symptoms but 56% of these patients had silent GER., Conclusions: These findings indicate that pharyngeal reflux may play an important role in the etiology of COM with effusion. If patients have typical symptoms of GER, such as pyrosis, regurgitation, dysphagia and emesis, the presence of GER should be considered. The presence of silent GER and pharyngeal reflux should also be considered.

Objective: To determine the micronucleus (MN) frequency of acquired cholesteatoma tissue using an MN assay., Material and Methods: Eighteen patients were diagnosed as having chronic otitis media with acquired cholesteatoma and were divided into primary and secondary acquired cholesteatoma groups. Cholesteatoma tissue and normal tissue specimens from the external ear canal skin were taken from the patients during surgical operations. MN frequencies of cholesteatoma and control samples were determined according to standard criteria., Results: The MN frequencies of the cholesteatoma and control tissues were 0.54%+/-0.31% and 0.24%+/-0.11%, respectively (p<0.01). MN frequencies for the primary and secondary acquired cholesteatoma groups were 0.63%+/-0.36% and 0.46%+/-0.26%, respectively (p>0.05). MN frequencies in cholesteatoma patients without and with complications were 0.42%+/-0.19% and 0.85%+/-0.37%, respectively (p<0.05)., Conclusion: MN frequencies were found to be increased in cholesteatoma tissues when compared with external ear canal skin. The MN frequency in five cases with complications was higher than in cases without complications. These results indicate that there could be associations between MN frequency and acquired cholesteatoma and between MN frequency and complications.

Aim: Our aims were to determine the normal limits of subepithelial basement membrane (SEBM) thickness in order to more accurately diagnose collagenous colitis in the population from southern Turkey and to investigate into links between SEBM thickness and age, and sex., Methods: The study included 100 patients (mean age 50.0+/-13.3 years; male, 34; female, 66) with miscellaneous gastrointestinal symptoms, and normal colonic mucosal appearance in colonoscopic evaluation. Biopsies were taken from five different regions of the colon. SEBM was measured with a calibrated eyepiece on specimens prepared with specific stains for collagen. Intensity of inflammatory cells was graded semiquantitatively. Differences in SEBM thickness among the different colon regions, and relationships between SEBM thickness and age, sex, and density of inflammatory cells were statistically evaluated., Results: The cecum and rectum showed the largest amounts of infiltrate. None of the specimens showed histologic findings of collagenous colitis. The SEBM thicknesses measured for each case ranged from 3-20 microm. The biggest thickness was observed in rectal mucosa (median value: 10 microm). Cecum and ascending colon showed similar SEBM thickness (median value: 5 microm). SEBM thickness was not correlated with patient age or sex, but was positively correlated with the intensity of inflammatory cells in each colon segment., Conclusion: In this patient group from southern Turkey, SEBM was thickest in the rectum. Our results indicate that, in this population, SEBM thickness is not correlated with age or sex, but is positively correlated with severity of inflammation. The findings also support the concept that measuring SEBM thickness at one segment in the colon is inadequate and may be misleading.

Aim: The eradication rate of Helicobacter pylori (H pylori) shows variation among countries and regimens of treatment. We aimed to study the eradication rates of different regimens in our region and some factors affecting the rate of eradication., Methods: One hundred and sixty-four H pylori positive patients (68 males, 96 females; mean age: 48+/-12 years) with duodenal or gastric ulcer without a smoking history were included in the study. The patients were divided into three groups according to the treatment regimens. Omeprazole 20 mg, clarithromycin 500 mg, amoxicillin 1 g were given twice daily for 1 week (Group I) and 2 weeks (Group II). Patients in Group III received bismuth subsitrate 300 mg, tetracyline 500 mg and metronidazole 500 mg four times daily in addition to Omeprazole 20 mg twice daily. Two biopsies each before and after treatment were obtained from antrum and corpus, and histopathologically evaluated. Eradication was assumed to be successful if no H pylorus was detected from four biopsy specimens taken after treatment. The effects of factors like age, sex, H pylori density on antrum and corpus before treatment, the total H pylori density, and the inflammation scores on the rate of H pylori eradication were evaluated., Results: The overall eradication rate was 42%. The rates in groups II and III were statistically higher than that in group I (P<0.05). The rates of eradication were 24.5%, 40.7% and 61.5% in groups I, II and III, respectively. The eradication rate was negatively related to either corpus H pylori density or total H pylori density (P<0.05). The median age was older in the group in which the eradication failed in comparison to that with successful eradication (55 yr vs 39 yr, P<0.001). No correlation between sex and H pylori eradication was found., Conclusion: Our rates of eradication were significantly lower when compared to those reported in literature. We believe that advanced age and high H pylori density are negative predictive factors for the rate of H pylori eradication.

The aim of this study was to investigate the source and the size of a tularemia outbreak in a village located in a non-endemic area. Five patients from the same village were admitted to hospital with the same complaints all within one week of September 2001. Tularemia was suspected and a diagnosis was made after physical and anamnesis examinations. The village was visited the same week that the patients were admitted to the hospital, in the January and April 2002. The villagers were examined and screened serologically by microagglutination method and the water sources were investigated bacteriologically. A total of 14 people were found to be infected from the outbreak and the oropharyngeal form was the only clinical presentation. Antibody titers ranged between 1 : 80 and 1 : 640. The patients responded well to the aminoglycoside plus tetracycline therapy. Examination of the pipewater and three springs revealed that all the water sources were contaminated by coliforms, however, Francisella tularensis could not be isolated in glucose-cystine medium. Antibody levels stayed stable or decreased seven months after. Tularemia had not been reported in this area before, so the first patients were misdiagnosed. In conclusion tularemia should be considered in differential diagnosis of patients with fever, sore throat and cervical lymphadenopaties.

Acinetobacter baumannii is becoming increasingly resistant to antibiotics often requiring combination therapy. Annual changes of resistance to selected antimicrobials of 150 A. baumannii strains, isolated as nosocomial pathogens between 1994 and 2000 were investigated. The synergistic effects of antimicrobials were studied using a microdilution checkerboard technique in eight selected isolates resistant to third-generation cephalosporins and beta-lactam/beta-lactamase inhibitor combinations and to at least one aminoglycoside. Rates of resistance of cefepime, ceftazidime, ampicillin/sulbactam, amikacin and ciprofloxacin (before 1996 and between 1996-2000) were 29.7% - 72.6, 37.8% - 81.4%, 35.1% - 72.6%, 8.1% - 56.6%, 5.4% - 46.0% respectively (p < 0.001 for each one). Synergy was observed in at least one of the combinations of antibiotics from seven of eight isolates (87%), no antagonism was detected with any combination. Ceftazidime-amikacin (50%) and ampicillin/sulbactam-tobramycin (50%) were the most effective combinations. Due to the effectiveness of sulbactams to Acinetobacter, ampicillin/sulbactam-tobramycin combination is recommended as the first line of choice.

Tuberculosis of skeletal system is frequently located in spine and is called as "Pott disease". Pott disease is frequently located in lumbar vertebrates and it can be interfered with the other diseases which cause low back pain. Our patient which was operated because of breast cancer nearly 10 years ago, has had waist and leg pain for 6 weeks. The story of breast cancer reminded us the possibility of a metastasis. But there were no findings in favour of metastasis except the high scores of sedimentation rate. There was a disc herniation according to the MR imaging of lumbar region. Therefore we performed epidural steroid injection but 10 days later the patient was unable to walk. We present this case to understand the importance of the differential diagnosis of Pott disease.

In the present study the prevalence of nightmare disorder (ND) was examined in patients with dissociative disorders (DD), and comparison was made between those with ND and those without nightmares in terms of clinical characteristics. The 30 patients with DD (5 male and 25 female) were recruited over 12 months in the Yüzüncü Yil University Research Hospital Department of Psychiatry. The subjects were diagnosed according to the Diagnostic and Statistical Manual of Mental Disorders (4th edn) criteria for ND. The Dissociative Experiences Scale, Beck Depression Inventory, and a semistructured interview schedule for childhood traumatic events were administered to the subjects. A 57% prevalence of ND was found among patients with DD. Among patients with DD, those with ND had a higher rate of self-mutilative behavior, a history of suicide attempt in the last year, and comorbidity with borderline personality disorder than those without ND. Nightmares or dreams should be considered in the therapy of DD patients.

Goals: The role that vitamin B12 deficiency plays in upper gastrointestinal motor dysfunction is not clear. The aim of this study was to determine whether B12 replacement therapy improves prolonged gastric emptying time in dyspeptic patients with Helicobacter pylori infection., Materials and Methods: The study included 34 H. pylori-positive patients who had low serum levels of B12 but had no other factors associated with altered gastric motility. Each patient underwent a radionuclide gastric emptying study before and after 3 months of B12 replacement therapy. Dyspepsia scores were calculated pretherapy and posttherapy using a semiquantitative scale. A vitamin B12 preparation (1000 microg/d) was given intramuscularly for the first 10 days and then orally for 80 days. H. pylori eradication therapy was delayed for 3 months until the posttreatment radionuclide study was completed., Results: The mean gastric emptying time before B12 treatment was significantly longer than that after treatment (230 +/- 190 minutes vs. 98 +/- 29 minutes, respectively; P < 0.0001). The mean dyspepsia score was also significantly improved by treatment (5.4 +/- 1.0 vs. 1.2 +/- 1.0, respectively; P < 0.0001)., Conclusion: Vitamin B12 deficiency appears to play an important role in the development of gastric dysmotility and its clinical consequences. Replacement therapy will improve gastric emptying in some patients with dyspepsia.

Background/aims: The aim of this study was to determine the characteristics of hepatocellular carcinoma at a major health center in southern Turkey. Computed tomography was compared to the combination of ultrasonography and serum alpha-fetoprotein determination in the diagnosis of hepatocellular carcinoma., Methods: Of 226 patients with liver cirrhosis, 35 were diagnosed with hepatocellular carcinoma on first admission or during follow-up in the period between 1999 and 2002. The features investigated were, age at time of hepatocellular carcinoma diagnosis, etiology of cirrhosis, severity of cirrhosis at presentation, tumor pattern, stage of hepatocellular carcinoma, serum alpha-fetoprotein level, and dynamic computed tomography findings. Results were compared to previous findings in Turkey and elsewhere., Results: In the hepatocellular carcinoma patients, the male:female ratio was 4:1 and the mean age at presentation was 61 years. Chronic hepatitis B virus infection (65.7%) and chronic hepatitis C virus infection (28.6%) were the most frequently identified risk factors for hepatocellular carcinoma. Forty percent of the patients had Child-Pugh A cirrhosis when they were diagnosed with hepatocellular carcinoma. Sixty-seven percent of patients had fewer than three hepatocellular carcinoma nodules in the liver at the time of diagnosis. Only three of the hepatocellular carcinoma cases were Okuda stage I. The combination of ultrasonography and serum alpha-fetoprotein >20 ng/ml identified hepatocellular carcinoma in 32 of the 35 total cases., Conclusions: The results indicate that hepatitis B virus infection in patients with cirrhosis is still the leading risk factor for the development of hepatocellular carcinoma. Also, early-stage hepatocellular carcinoma is rarely diagnosed in cirrhosis patients from this region of Turkey. Surveillance with computed tomography for early diagnosis of hepatocellular carcinoma seems not to be mandatory.

The effects of activation of the lactoperoxidase (LPO) system by H2O2-NaSCN and hydrogen peroxide (H2O2) on the accessibility of sulphydryl groups (SH) in skimmed milk, and on the dynamic rheological properties of the resulting yoghurt were investigated. Four different concentrations of each reagent (20-80 mg H2O2-NaSCN/kg milk and 100-400 mg H2O2/kg milk) were compared. Clear negative correlations were noted between the accessibility of SH groups and both LPO activation rate and H2O2 concentration. Also the native PAGE pattern of the heat-treated samples showed that with increase in the H2O2-NaSCN and H2O2 concentrations, the level of interaction between beta-lactoglobulin (beta-lg) and kappa-casein (kappa-CN) decreased. The complex modulus (G*) of skimmed milk yoghurts declined gradually with the decrease in the concentration of accessible SH groups accordingly. Tan delta values of yoghurt samples were found to be different from the control, but close to each other, indicating that protein interaction forces taking place in the formation of gel networks of treated yoghurts were different from the control.

Aim: To investigate and compare frequencies of serum positive cagA in patients from two separate regions of Turkey who were grouped according to the presence of peptic ulcer disease or non-ulcer dyspepsia., Methods: One hundred and eighty Helicobacter pylori-positive patients with peptic ulcer disease or non-ulcer dyspepsia were included in the study. One hundred and fourteen patients had non-ulcer dyspepsia and 66 had peptic ulcer disease (32 with gastric ulcers and/or erosions and 34 with duodenal ulcers). Each patient was tested for serum antibody to H. pylori cagA protein by enzyme immunoassay., Results: The total frequency of serum positive cagA in the study group was 97.2 %. The rates in the patients with peptic ulcers and in those with non-ulcer dyspepsia were 100 % and 95.6 %, respectively. These results were similar to those reported in Asian studies, but higher than those that have been noted in other studies from Turkey and Western countries., Conclusion: The high rates of serum positive cagA in these patients with peptic ulcer disease and non-ulcer dyspepsia were similar to results reported in Asia. The fact that there was high seroum prevalence regardless of ulcer status suggests that factors other than cagA might be responsible for ulceration or other types of severe pathology in H. pylori-positive individuals.