Cenk Sokmensuer

Automatic segmentation of colon glands using object-graphs

Gland segmentation is an important step to automate the analysis of biopsies that contain glandular structures. However, this remains a challenging problem as the variation in staining, fixation, and sectioning procedures lead to a considerable amount of artifacts and variances in tissue sections, which may result in huge variances in gland appearances. In this work, we report a new approach for gland segmentation. This approach decomposes the tissue image into a set of primitive objects and segments glands making use of the organizational properties of these objects, which are quantified with the definition of object-graphs. As opposed to the previous literature, the proposed approach employs the object-based information for the gland segmentation problem, instead of using the pixel-based information alone. Working with the images of colon tissues, our experiments demonstrate that the proposed object-graph approach yields high segmentation accuracies for the training and test sets and significantly improves the segmentation performance of its pixel-based counterparts. The experiments also show that the object-based structure of the proposed approach provides more tolerance to artifacts and variances in tissues.

Color Graphs for Automated Cancer Diagnosis and Grading

This paper reports a new structural method to mathematically represent and quantify a tissue for the purpose of automated and objective cancer diagnosis and grading. Unlike the previous structural methods, which quantify a tissue considering the spatial distributions of its cell nuclei, the proposed method relies on the use of distributions of multiple tissue components for the representation. To this end, it constructs a graph on multiple tissue components and colors its edges depending on the component types of their endpoints. Subsequently, it extracts a new set of structural features from these color graphs and uses these features in the classification of tissues. Working with the images of colon tissues, our experiments demonstrate that the color-graph approach leads to 82.65% test accuracy and that it significantly improves the performance of its counterparts.

Screening of tissue transglutaminase antibody in healthy blood donors for celiac disease screening in the Turkish population.

Celiac disease (CD) is a disease having the characteristic pathology of the mucosa of the small intestine. The prevalence of CD in the Turkish population has not been investigated previously. The present study was designed to determine the prevalence of CD in healthy blood donors. Serum samples of 2000 healthy blood donors presenting to Hacettepe University Faculty of Medicine Hospital Blood Bank were tested for tissue transglutaminase (tTG) IgA and IgG antibodies with enzyme-linked immunosorbent assay (ELISA; Euroimmune, Germany). The histopathological findings for the cases with positive serology were evaluated. The distribution of sex was 95.7% male, and 4.3% female. The mean age was 33±9. Among 2000 donors, 23 (1.15%) were positive for tTG IgA antibody and 3 (0.15%) were positive for tTG IgG antibody. None of the samples was positive for both antibodies. Serum total IgA was measured in two cases with only tTG IgG positivity and was found to be low in one case. Twelve subjects positive for tTG agreed to endoscopy and biopsy. Histopathological examination revealed changes classified as Marsh III–II in one, Marsh II in two, Marsh I in seven, and Marsh 0 in two donors. This was the first study conducted to determine the prevalence of tTG positivity in the Turkish population. The tTG antibody positivity prevalence in healthy blood donors was as high as 1.3%. This study shows that the prevalence of CD in the Turkish population is relatively high in comparison to that in the Western world.

Object-oriented texture analysis for the unsupervised segmentation of biopsy images for cancer detection

Staining methods routinely used in pathology lead to similar color distributions in the biologically different regions of histopathological images. This causes problems in image segmentation for the quantitative analysis and detection of cancer. To overcome this problem, unlike previous methods that use pixel distributions, we propose a new homogeneity measure based on the distribution of the objects that we define to represent tissue components. Using this measure, we demonstrate a new object-oriented segmentation algorithm. Working with colon biopsy images, we show that this algorithm segments the cancerous and normal regions with 94.89 percent accuracy on the average and significantly improves the segmentation accuracy compared to its pixel-based counterpart.

Effect of Montelukast and MK-886 on Hepatic Ischemia-Reperfusion Injury in Rats

BACKGROUND Hepatic ischemia-reperfusion injury (I/R) may occur in transplantation, trauma, and elective hepatic resections. Leukotrienes have been shown to play a major role in hepatic I/R injury. Five-lipoxygenase enzyme is an important enzyme in the production of leukotrienes from arachidonic acid. MK-886 is an inhibitor of 5-lipoxygenase, and montelukast is a cysteinyl leukotriene receptor antagonist. The aim of this study was to investigate whether MK-886 and montelukast are effective in preventing hepatic I/R injury. MATERIALS AND METHODS Rats were divided into five groups consisting of seven rats in each: (1) Control I/R, (2) Control-montelukast, (3) Control-MK-886, (4) I/R+montelukast, and (5) I/R+MK-886. Thirty min of total hepatic vascular occlusion and then 60 min reperfusion were performed to animals in groups 1, 4, and 5. In groups 2 and 4, montelukast, and in groups 3 and 5, MK-886 was applied intraperitoneally before and during the surgical procedures. RESULTS Apoptosis in the liver and intestine decreased significantly in the I/R+montelukast and I/R+MK-886 groups compared with the I/R group. Tissue malondialdehyde levels and glutathione consumptions also decreased significantly in the I/R+montelukast and I/R+MK-886 groups compared with the I/R group. The difference in serum alanine aminotransferase and aspartate aminotransferase levels between the groups did not reach significance. CONCLUSIONS Montelukast and MK-886 were found to be effective in prevention of liver and intestine injury by reducing apoptosis and oxidative stress in a hepatic I/R model. Anti-inflammatory properties and inhibition of lipid peroxidation by montelukast and MK-886 could be protective for these organs in I/R injury.

Is Congenital Hepatic Fibrosis a Pure Liver Disease

OBJECTIVES:An association between congenital hepatic fibrosis (CHF) and several different conditions is being increasingly recognized. We aimed to investigate, prospectively, these associated disorders and the clinical consequences for patients with CHF.MATERIALS AND METHODS:CHF was diagnosed using liver biopsy, abdominal ultrasound (US), Doppler US, upper endoscopy, and abdominal computed tomography (CT) in 19 patients (13 women, 6 men). CT portography and splenoportography with digital subtraction angiography were performed if indicated. Endoscopic retrograde cholangiopancreatography (ERCP) was performed to investigate the extent of portal vein involvement of the common bile duct if it existed, to remove a stone located in the common bile duct when documented, and to confirm the diagnosis of Carolis syndrome. Cranial MRI was done when clinical findings suggested brain involvement.RESULTS:The mean age of the patients was 29.47 ± 12.06, ranging from 13 to 57. CHF-associated diseases were Carolis syndrome, polycystic kidney disease, cavernous transformation of the portal vein, Jouberts syndrome, von Meyenburg complex, polydactyly, medullary sponge kidney, and pancreatic duct atrophy. In two cases, cholangiocarcinoma had developed. There was only one case with pure CHF. Portosystemic shunt, TIPS, or splenectomy were performed in some cases to control bleeding from esophageal varices. Papillotomy and stone extraction from the common bile duct were performed in four patients with Carolis syndrome complicated by cholangitis. Three patients died of complications of CHF. Two patients with Carolis syndrome underwent liver transplantation.CONCLUSION:In this prospective study, it seems that CHF is not a pure liver disease but rather a multiorgan disorder involving the brain, portal vein, kidneys, and bile ducts. In most cases, the clinical picture includes other organ involvement, rather than purely the liver parenchyma.

Multilevel Segmentation of Histopathological Images Using Cooccurrence of Tissue Objects

This paper presents a new approach for unsupervised segmentation of histopathological tissue images. This approach has two main contributions. First, it introduces a new set of high-level texture features to represent the prior knowledge of spatial organization of the tissue components. These texture features are defined on the tissue components, which are approximately represented by tissue objects, and quantify the frequency of two component types being cooccurred in a particular spatial relationship. As they are defined on components, rather than on image pixels, these object cooccurrence features are expected to be less vulnerable to noise and variations that are typically observed at the pixel level of tissue images. Second, it proposes to obtain multiple segmentations by multilevel partitioning of a graph constructed on the tissue objects and combine them by an ensemble function. This multilevel graph partitioning algorithm introduces randomization in graph construction and refinements in its multilevel scheme to increase diversity of individual segmentations, and thus, improve the final result. The experiments on 200 colon tissue images reveal that the proposed approach-the object cooccurrence features together with the multilevel segmentation algorithm-is effective to obtain high-quality results. The experiments also show that it improves the segmentation results compared to the previous approaches.

Microstaging of pT1 Transitional Cell Carcinoma of the Bladder

Introduction: Our objective was to evaluate the feasibility and value of microstaging in pT1 transitional cell carcinoma (TCC) of the bladder in a well-defined group of patients treated with transurethral resection (TUR) only. Materials and Methods: The clinical records of 152 patients who underwent TUR for the treatment of primary superficial TCC of the bladder between 1983 and 1997 were reviewed. Patients with primary carcinoma in situ and who received adjuvant intravesical treatments were excluded from study. We subclassified the pT1 tumors into two groups according to muscularis mucosae (MM) invasion (pT1 and pT1b). The recurrence and progression rate of cancers was analyzed according to the stage, grade, multiplicity and tumor size. Mean follow-up was 68 months. Estimation of the cumulative distribution of the disease-free interval in separate groups was calculated according to the Kaplan-Meier method. Multivariate analysis of the data was performed by using Cox regression method. A value of p < 0.05 was taken to be statistically significant with odds ratios. Results: Of the 152 patients, tumor stage was pTa in 62 (40.8%) patients and pT1 in 90 (59.2%) patients. Among those pT1 tumors, MM was identified in 50 (55.5%) of cases (pT1a = 34, pT1b = 16). In the remaining 40 (44.5%) patients, MM could not be assessed. Kaplan-Meier analysis revealed that recurrence and progression were statistically significant for stage, multiplicity and grade of tumor. However, multivariate analysis revealed that stage was the only prognostic factor for recurrence and progression (p = 0.0001). Conclusion: The present study underscores the fact that pT1b tumors have a distinct natural history. If initial conservative treatment is selected, the patients must be followed very cautiously.

Celiac Disease in the Turkish Population

Celiac disease (CD) is characterized by malabsorption of nutrients in the small intestine. The availability of highly specific and sensitive serologic tests has facilitated its diagnosis, increasing the disease prevalence. The aim of this study was to determine the clinical, laboratory, and histopathological features of CD in Turkish adults. Between 1968 and 2002, CD patients presenting to the Gastroenterology Unit were evaluated retrospectively. From 2002, newly diagnosed patients were prospectively followed up. Sixty patients (39 female, 21 male) were included in the study. Mean body mass index was 22.2 ± 5.4 kg/m2. The most common symptoms were diarrhea, weight loss, and flatulence. Most common comorbidities were anemia, osteoporosis, type 1 diabetes mellitus, and steatohepatitis. Six (10.0%) patients had a family history of diabetes mellitus; one (1.7%) patient had a family history of CD. Plasma glucose and serum γ-glutamyltransferase levels were significantly higher in females than males. Most common histopathological findings were increased lymphocytes in the lamina propria (76.2%) and villus epithelium (59.5%). Over the years, the cumulative frequency of CD increased more in females than males. This is the first study in the literature showing the characteristics of CD in Turkish adults. In our previous recent study, the prevalence of tissue transglutaminase antibody positivity in Turkish healthy blood donors was 1.3%, indicating a high prevalence of CD in our population. In this study, the cumulative frequency of CD increased more in females than males. With the better understanding and increased suspicion of the disease, more patients are being diagnosed in our population.

Urgent liver transplantation for Amanita phalloides poisoning.

Abstract:  Amanita phalloides is a deadly wild mushroom causing severe damage in man ranging from diarrhea to organ dysfunction. If not treated, mortality is as high as 80%. Treatment includes supportive measures, inactivation of the toxin and if liver failure occurs liver transplantation. The indications for transplantation are debatable.