Optimisation and Application of Fluorescence In Situ Hybridization in Selected Leukaemias

The overall aim of this project was to optimise and then apply the technique of dual-colour fluorescence in situ hybridization (FISH). The first main aim of this study was optimisation of dual-colour FISH by using alpha-satellite centromeric probes, chromosome specific libraries and locus specific cosmid probes. The second main aim was the application of uni- and dual-colour FISH using these probes. At the beginning, to gain experience with the non-isotopic in situ hybridization, a highly repetitive probe GMGYIO (DYS59) was applied by using the alkaline phosphatase technique and then the same probe was used for the fluorescence in situ hybridization technique. The next step was optimisation of whole chromosome specific library probes (pBS-21 and pBS-18) for chromosome 21 and chromosome 18. Less than 600 ng (per hybridization area) of the pBS-21 probe was found to be insufficient to give complete coverage of the chromosome. With a higher concentration of pBS-21 (600-700 ng), a complete coverage was obtained. Use of this probe was discontinued since each hybridization required too much of the library probe DNA. The whole chromosome specific library probe for chromosome 18 (pBS-18) was optimised using 600 ng (per hybridization area) of pBS-18 probe concentration for uni-colour FISH. Using different concentrations of this probe, it was consistently found that the centromeric area of chromosome 2 visualised more strongly than chromosome 18. The study then progressed to the development of the dual-colour FISH technique. The alpha-satellite centromeric probes and the locus specific cosmid probes were individually labelled either with biotin by using nick translation. or with digoxigenin using random primed labelling or the nick translation system. The probes to be used in the study were the a-satellite centromeric probes for chromosome 3, 8, 12 and 22, the locus specific cosmid probes for abl and bcr, and library probes 6, 8, 9, and 22. The first step was to optimise the conditions for each probe for uni-colour FISH. The centromeric probes (for chromosomes 8 and 12) always gave sharp and specific signals. The hybridization signal intensity of the abl cosmid probe was very specific and bright. In contrast, as reported by others, the locus specific bcr cosmid probes did not give specific sharp signals due to the instability of the probe. However, by manipulating each of the steps in the uni-colour FISH procedure, successful results were obtained with bcr probes. Following the optimisation of uni-colour FISH using a-satellite repetitive sequence probes for chromosome 8, 12 and 22, and the locus specific cosmid probes for ab1 and bcr, these probes were optimised for dual-colour FISH. First, in order to overcome the technical difficulties incurred by the dualcolour FISH procedure, all steps were optimised by using a-satellite repetitive sequence probes for chromosomes 8 and 12. Dual-colour FISH results were successfully optimised with those centromeric probes. Using uni-colour FISH specific parameters for cosmid probes such as probe and competitor DNA concentration and hybridization condition, these probes unfortunately could not tolerate some parameters described for the centromeric probe, such as detection, counterstaining and visualisation of signals. This failure may be due to the size and quality of the probe. Therefore, these steps were refined for dual-colour FISH of the cosmid abl and bcr probes. After optimisation of uni- and dual-colour FISH by using the a-satellite probes for chromosomes 8 and 12 , and the locus specific probes for abl and bcr , the techniques were applied to selected leukaemias. Commercial probes were also used either individually or in combination with self-prepared probes. In this project, three different groups of leukaemias were studied. These are (1) Chronic Myeloid Leukaemia (CML), (2) Acute Promyelocytic Leukaemia (AML-M3) and (3) Chronic Lymphocytic Leukaemia (CLL). The first group investigated was the CML group. Fourteen cytogenetically Philadelphia (Ph) positive CML cases were evaluated for the presence of the bcr-abl fusion using uni-colour FISH on metaphase spreads. Despite the low number of metaphases obtained, the FISH metaphase results showed the translocation of abl signal from chromosome 9 to the derivative chromosome 22q. These results were found to be in agreement with the cytogenetic results. Moreover, twelve of Ph negative patients with a provisional diagnosis of CML were studied by using uni-colour FISH on metaphase spreads. Interestingly, one case proved to be bcr-abl fusion positive, while in the remaining cases cytogenetics is in agreement with FISH result. (Abstract shortened by ProQuest.)

Çin’de Sosyal Devlet Sorunsalı: Hukou Problemi

1958 yılında yürürlüğe giren hukou sistemi, Çin'in göç terminolojisinde yer alan, kır ve kent kavramlarını birbirinden ayrıştırarak yurttaşları arasında sınıfsal fark gözeten hane halkı kayıt sistemidir. Çin’de vatandaşın adına kayıtlı ikametgâh belgesi (Hùkǒu běn: 户口本), doğum yerine göre belirlenir. Bu çalışma, toplamda dört bölümden oluşmaktadır. Birinci bölümde, hukou sisteminin kavramsal çerçevesi açıklanmıştır. Hukounun tanımı, kökenleri ve amaçları üzerinde durulmuştur ve hukou sisteminin hazırlanış safhası incelenmiş ve böyle bir sisteme neden ihtiyaç duyulduğu açıklanmaya çalışılmıştır. İkinci bölümde, bu sistemin temel sıkıntıları irdelenmiştir. Üçüncü bölümde, hukou sisteminin tarihsel gelişimi ve dönüşümü ile ilgili detaylı araştırmalar yapılmış ve dönemin reform hareketleri incelenmiştir. Son bölümde ise güncel sorunlar açıklanmıştır. Bu çalışmada hukou ile ilgili yazılmış birincil ve ikincil kaynaklar ile Çin Ulusal İstatistik Bürosu’nun verileri kullanılmıştır

Effects of the Chernobyl Disaster on Thyroid Cancer Incidence in Turkey after 22 Years

Background. Separate studies involving people who survived atomic bombs have shown that the risk for cancer remains high after 40 years, compared with the risk in the general population. An elevated risk may also remain in regions of Turkey near the Chernobyl disaster. Patients and Methods. A multidisciplinary study conducted in 2008, 22 years after the Chernobyl disaster, examined the thyroid cancer incidence in Rize, a province of Turkey located on the shore of the middle Black Sea. Approximately 100,000 people were screened, and a fine-needle aspiration biopsy was performed in 89 patients. Results. Based on postoperative histopathological examinations, thyroid cancer was diagnosed in six of the 100,000 people screened. Conclusion. Given a thyroid cancer frequency of approximately 8 in 100,000 in the Turkish population, according to the Turkish Cancer Research Association, the rate in Rize reflects no increase in the thyroid cancer incidence 22 years after the Chernobyl disaster

Alcoholic extract of Tarantula cubensis (Theranekron®) induce autophagy on gastric cancer cells

Aim: To evaluate the effects of theranekron in respect of autophagy on gastric cancer that is the fifth leading cancer type worldwide. Metods: In the present study, metastatic AGS and non-metastatic MKN-45 human gastric cell lines were used together with HEK-293 non-cancer cells as controls. Cytotoxic effect of theranekron besides appropriate treatment time was investigated through cell proliferation by using Cell Proliferation assay Kit (MTT) using different concentrations of the drug. The autophagic effect of the drug was determined using the LC3-GFP translocation assay and western blot analysis. All experiments were performed also using the ethanol since Tarantula cubensis spider was processed and diluted in 60% alcohol to generate as a drug. Results: MTT assay results demonstrated that the half maximal inhibitory concentration of theranekron was ~100 μM, its effect was found to be significant at 6 hrs, and theranekron decreased the cell viability in all cell lines without specificity in respect to the increasing concentrations. Additionally, a significantly increased GFP accumulation was detected in the autophagosomes of the cells treated with theranekron compared to non-treated cells, indicating the presence of autophagy. Conclusion: These findings were confirmed by LC3-I to LC3-II conversion with the western blot analysis. The data of ethanol experiments; however, demonstrated that ethanol also induced a cytotoxic effect and autophagic cell death. Our results suggested that theranekron results in cell death and stimulate autophagy process, but it is not specific for cancer cells since it represented similar results on non-cancer control cells. Moreover, the effect of theranekron on cell death might mostly occur through alcohol in which it is extracted

Ilık Hidromekanik Derin Çekme Prosesinin Sonlu Elemanlar Analizi Ve Parametrik Optimizasyonu

Konferans Bildirisi -- Teorik ve Uygulamalı Mekanik Türk Milli Komitesi, 2015Conference Paper -- Theoretical and Applied Mechanical Turkish National Committee, 2015Bu çalışmada otomotiv sanayiinde taşıt ağırlığını azaltmak için giderek artan şekilde kullanılan alüminyum alaşımlarının şekillendirilmesinde kullanılan geleneksel yöntemlerin yerini almaya başlayan ılık hidromekanik derin çekme prosesinin kapsamlı bir sonlu elemanlar modeli oluşturulmuştur. Farklı eleman sayıları ve eleman formülasyonları, temasta bulunan bileşenler için farklı sürtünme katsayıları ve malzeme modelleri sistematik bir şekilde denenerek sonlu eleman modeli için en uygun tercihler ve değerler belirlenmeye çalışılmıştır. Çalışmanın ikinci kısmında ise, oluşturulan sonlu elemanlar modeli ile ılık hidromekanik derin çekme işlemindeki takım sıcaklıklarının ve yükleme profillerinin (hidrolik basıncı ve baskı plakası kuvveti) en iyi şekillendirilebilirliği veren değerleri belirlenmeye çalışılmıştır. Bu çalışmalar neticesinde, malzeme davranışını en iyi elastik-viskoplastik-termal malzeme modelinin yansıttığı belirlenmiştir. Coulomb sürtünme katsayıları sac-kalıp ara yüzeyi için 0.05, sac-baskı plakası için 0.05 ve sac-zımba sürtünme yüzeyleri arasında 0.25 olarak tespit edilmiştir. En iyi şekillendirmenin sağlanabilmesi için kalıp ve zımbaya ait sıcaklık değerleri sırasıyla 300 ve 25 °C olarak belirlenmiştir. Hidrolik basıncın baskı plakasının kuvvetine göre daha etkin bir parametre olduğu görülmüştür.In current study, a comprehensive finite element modeling was established for warm hydromechanical deep drawing process which is a promising technique in forming of aluminum alloys that are expected to be increasingly exploited in automotive industry along with lightweighting efforts. Different number of elements and element formulations, coefficients of friction for contacting surfaces and material models were systematically tested and optimum choices and values were determined. In the second part of the study, optimum tool temperature, and loading profiles (hydraulic pressure and blank holder force) were obtained parametrically to achieve highest formability in warm hydromechanical deep drawing process by using established FE model. As a result, elastic-viscoplastic-thermal material model was found to be reflecting the material behavior better compared to other material models utilized. Coulomb friction coefficient for contacting surfaces blank-die, blank-blank holder and blank-punch were determined as 0.05, 0.05 and 0.25, respectively. Optimal temperatures values for die and punch were determined as 300 and 25°C, respectively when highest formability is taken into account. Hydraulic pressure was found to be more effective on formability than blank holder force

DEVLET ORMAN FİDANLIK İŞLETMELERİNDE MALİYET YÖNETİMİ ÇABALARI VE MALİYET YÖNETİMİNİN İŞLETME BAŞARISINDAKİ ROLÜ

ABSTRACT Businesses that must think and act strategically in today's competitive environment have to plan their costs along with their production process. Over the last two decades, a large number of businesses in the developed countries have implemented advanced cost management systems in order to introduce effective cost management. On the other hand, the public sector's businesses of the our country are not aware about thus going on developments. For instance, at state forest nursery businesses is not only the cost management, but also the determination of actual costs procedures have not been sufficiently carrying out so far.In this respect, the first part of study covers the problems of state forest nursery businesses in term of management economics. The second part of the study covers the implication of cost management in the state forest nursery businesses.Günümüz rekabetçi ortamında stratejik düşünmek ve hareket etmek zorunda olan işletmeler, maliyetlerini üretimle birlikte planlamak zorundadır. 20 yılı aşkın süredir gelişmiş ülkelerdeki işletmelerin bir çoğu etkin maliyet yönetimi için ileri maliyet yönetimi sistemlerini kullanmaktadır. Ancak, ülkemizdeki özellikle kamu sektörü işletmeleri söz konusu gelişmelerden haberdar bile değildir. Örneğin; devlet orman fidanlık işletmelerinde değil maliyet yönetimi; fiili maliyetleri belirleme işleri bile sağlıklı bir şekilde yapılamamaktadır. Bu bağlamda, çalışmada ilk önce, geçmişten günümüze kadar zarar eden ve halen büyük çoğunluğunda zarar durumu devam eden Devlet Orman Fidanlık İşletmelerinde işletme ekonomisi bakımından yaşanan mevcut sorunlar belirlenmeye çalışılmıştır. İkinci olarak da maliyet yönetiminin bu işletmelerde etkin bir şekilde uygulanabilirliği araştırılmıştır

The Atrial Fibrillation in Turkey: Epidemiologic Registry (AFTER)

Background: AFTER (Atrial Fibrillation in Turkey: Epidemiologic Registry) is a prospective,multicenter study designed with the aim of describing the prevalence and epidemiology ofAF practice in Turkey. This study aims to evaluate stroke risk in non-valvular atrial fi brillation(AF) and anticoagulant drug utilization within conformity to AF guidelines.Methods: Patients were recruited in 17 referral hospitals refl ecting all the population of7 geographical regions of Turkey. 2242 consecutive patients who had been admitted with AFon ECG were included in the study. 1745 of these patients, who had non-valvular AF, wereincluded in the statistical evaluation. Stroke risk was evaluated with the CHA2DS2-VASc score.Results: The average age of participants was determined to be 69.2 ± 11.5 years (56%female). Persistent-permanent AF was found to be the most common type of non-valvularAF (78%). The most common comorbid disorder was hypertension (73%). It was found thatoral anticoagulant therapy was used by 40% of all patients, 37% of whom had effective INR(2.0–3.0). Upon multivariate analysis, age was found to be the only independent predictorof stroke among the variables’ effects on thromboembolic events that created CHA2DS2-VAScabbreviations (OR 1.026, p < 0.001).Conclusions: These results suggest that stroke risk scores should be thoroughly heededbased on guidelines, and that anticoagulation must be applied according to their guidance

Investigation of the Distribution of Fetal Nasal Bone Percentile Values in First-Trimester Fetal Anomaly Screening

INTRODUCTION: We aim to determine the fetal nasal bone length (NBL) percentile values that can be used in the prediction of the fetal anomaly at 11-14 weeks of gestation in a low-risk population. METHODS: Our prospective and cross-sectional study included four hundred and eighty-six singleton pregnancies who applied for the first-trimester aneuploidy screening test at 11-14 weeks of gestation. We excluded pregnant women with fetal structural or chromosomal anomaly, nuchal translucency >3mm, an absent nasal bone, and in utero fetal death. Reference and percentile values of the NBL were calculated separately for 11,12,13,and 14. gestational weeks. RESULTS: Standard NBL measurements were performed in 486 pregnancies according to inclusion and exclusion criteria. Median NBL values were computed for each gestational age (GA), for 11,12,13 and 14. weeks of gestation was found 1.6mm (range=1.1-2.5), 1.8mm (range=1.1-3.0), 2.0mm (range=1.4-3.1), and 2.2mm (range=1.7-2.8), respectively. A positive significant correlation was found between NBL and the crown-rump length (CRL) (NBL (mm) = [0.02xCRL(mm)] + 0.73, r=.483; p<.001). The 5th percentile of NBL for GA was calculated, for 11,12, 13, and 14. weeks of gestation was found 1.2mm,1.4mm,1.5mm, and 1.7mm respectively. DISCUSSION AND CONCLUSION: We revealed the reference value of NBL for each gestational week in the first trimester of the low-risk population. The data obtained in our study can be used in the screening of genetic syndromes, especially Down syndrome, associated with nasal bone hypoplasia. Our reference value of NBL for the first trimester in singleton pregnancy varies from both previous racial and ethnic groups studies, and other Turkish studies

Tracing where and who provenance in linked data - a calculus -

Linked Data provides some sensible guidelines for publishing and consuming data on the Web. Data published on the Web has no inherent truth, yet its quality can often be assessed based on its provenance. This work introduces a new approach to provenance for Linked Data. The simplest notion of provenance-viz., a named graph indicating where the data is now-is extended with a richer provenance format. The format reflects the behaviour of processes interacting with Linked Data, tracing where the data has been published and who published it. An executable model is presented based on abstract syntax and operational semantics, providing a proof of concept and the means to statically evaluate provenance driven access control using a type system