Browsing by Subject "Cluster Analysis"

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Open Access
Application of a customized pathway-focused microarray for gene expression profiling of cellular homeostasis upon exposure to nicotine in PC12 cells
(2004) Konu Ö.; Xu X.; Ma J.Z.; Kane J.; Wang J.; Shi, S.J.; Li, M.D.
Maintenance of cellular homeostasis is integral to appropriate regulation of cellular signaling and cell growth and division. In this study, we report the development and quality assessment of a pathway-focused microarray comprising genes involved in cellular homeostasis. Since nicotine is known to have highly modulatory effects on the intracellular calcium homeostasis, we therefore tested the applicability of the homeostatic pathway-focused microarray on the gene expression in PC-12 cells treated with 1 mM nicotine for 48 h relative to the untreated control cells. We first provided a detailed description of the focused array with respect to its gene and pathway content and then assessed the array quality using a robust regression procedure that allows for the exclusion of unreliable measurements while decreasing the number of false positives. As a result, the mean correlation coefficient between duplicate measurements of the arrays used in this study (control vs. nicotine treatment, three samples each) has increased from 0.974±0.017 to 0.995±0.002. Furthermore, we found that nicotine affected various structural and signaling components of the AKT/PKB signaling pathway and protein synthesis and degradation processes in PC-12 cells. Since modulation of intracellular calcium concentrations ([Ca2+]i) and phosphatidylinositol signaling are important in various biological processes such as neurotransmitter release and tissue pathogenesis including tumor formation, we expect that the homeostatic pathway-focused microarray potentially can be used for the identification of unique gene expression profiles in comparative studies of drugs of abuse and diverse environmental stimuli, such as starvation and oxidative stress. © 2003 Elsevier B.V. All rights reserved.
Open Access
Chemical characterization and provenance studies of archeological samples
(2003) Türkmen, Işık Rıza
Data that is collected by chemical analyses of the archeological samples can be used to find out the the raw materials used and the techniques practiced in the ancient pottery production. In addition, provenance studies of archeological samples that are commercially important may give an idea on the commercial relationships between the past civilizations. This study was conducted to investigate the chemical compositions and provenance of the amphora samples that are found around Sinop and Heraclea Pontica (Black Sea Coast) in Turkey, Ibn-Hani (Eastern Mediterranean Coast) in Syria, Tanais and Gorgippia on Northern Black Sea region of Russia. Some amphorae, which are morphologically similar to those of Colchian amphorae, but having apparently distinctive clay properties, are called Pseudo-Colchian, and they were also analyzed during the studies. The mineral compositions of the samples were found out by powder X-Ray Diffraction analyses, and the elemental compositions were sought by X-Ray Fluorescence spectroscopy. Principal component analysis and cluster analysis are applied to the data collected from XRF measurements for the provenance classification of the samples. The results obtained from both statistical methods complemented each others and were in good agreement. According to the results of this study, the pink clay, red clay and white clay amphorae from Sinop are all found to be composed of the minerals quartz, feldspars, pyroxenes, calcite and hematite, but varying in amounts with respect to type and color. Considering the mineralogical compositions, it is proposed that the average baking temperature of the red clay amphorae is around 800 – 850 o C whereas it is around 950 o C for the white clay ones. The red color observed for the red clay Sinopean amphorae was attributed to the presence of hematite minerals. On the other hand white color was attributed to the formation of mineral phases such as pyroxenes, throughout the chemical reactions that take place in the clay matrix at higher baking tempertures and low oxidation environments for the white clay Sinopean amphorae. In provenance classification of the samples, it was found that the separations between the samples occur mainly due to variations in the concentration of elements Ca, Fe, Ti, Ni, Rb and Sr. White clay amphorae from Antioch and Ibn Hani, and the red clay carrot type amphora from Tanais are found to be the Sinopean production. On the other hand, the white clay amphorae from Tanais was found to be more similar to the ones from Heraclea Pontica and different from those of Sinop. The colchian amphorae from Gorgippia and Pseudo-Colchian amphorae were found to represent typical differences from all other samples, but also from each others.
Open Access
Chemical characterization of Sinopean archaeological common ware
(2004) Özal, Tuğba Arzu
Chemical characterization of archaeological common wares is important in order to make quantitative explanations about history and trade relations of nations. Chemistry uses a microscopic point of view by applying spectroscopic methods rather than macroscopic studies that archaeologists usually deal in the structural analysis. The present study is done on the common ware samples which were made of raw clays from Demirci, Sinop, Black Sea Coast of Turkey, because of the geopolitical importance of this region having trade routes. Elemental and mineralogical analyses of the clay-originated common ware samples found in the archaeological excavations and of the clay taken from Demirci region, which locates at almost 15 km southern of Sinop, were made. While the elemental compositions of the samples were obtained by the spectroscopic method, X-Ray Fluorescence (XRF), the mineral structures were investigated by Powder XRay Diffraction (PXRD) and Fourier Transform Infra Red (FT-IR) spectroscopic method. Furthermore, the characteristic reactions (dehydroxylation, decomposition, transformation) that the clays experienced between the temperatures 50 and 1000 o C were determined by Thermal Gravimetric Analysis (TGA). Characterizations of the Sinopean samples were made and the similarity and differences between other samples from different regions were investigated. Besides the provenance characterization, the distinctions between the production and firing techniques were observed. In addition to the experimental studies, chemometric techniques using statistical methods such as the standard clustering method and principal component analysis (PCA) was also applied to identify the groupings in the set of samples. As a result of this study, it is observed that the raw clays and ceramic samples have minerals of montmorillonite, quartz, feldspars, pyroxene, calcite and hematite at different amounts. From the mineralogical and elemental data, it is concluded that the color variations are resulted from the calcium element occurring in pyroxene mineral. In the light colored samples, amount of this element and mineral is high whereas it is low in red colored ones. From the interpretation of elemental data by statistical methods, it is observed that a classification among the Demirci samples is possible according to the function of the pottery. In addition, classification among ceramics from two different regions is possible by the interpretation of chemical analysis, even though the ceramics have the same morphological properties of the same period.
Open Access
Image of Turkey in the minds of Singaporians
(1995) Dicle, Coşkun K.
It has been suggested in numerous academic studies that country image forms a crucial part of consumers' product evaluations. Moreover, country image has been found to be negative for developing countries such as Turkey. However, the possibility of changing these negative images and associations through a clear understanding of the aspects of the image, sheds light on to the aim of this study. The main purpose of this study is to clearly lay out Turkey's image and current position in Singapore, extracting the favorable and unfavorable associations Singaporians have. In providing rich information with positioning implications, and a framework for future repositioning efforts, the aim is to enable Turkish stakeholders in developing suitable and effective international marketing strategies towards the region in question.
Open Access
Image of Turkey in the minds of Turks
(1995) Tanrıöver, Şafak
Country image, being an integral part of a country, tremendously affects people's perceptions, preferences and decisions about that country, itself, its products and people. It can be identified and can change over time. Once the image of a country is defined, strategies to manage that image, whether to change the existing image or to create a new one, can be developed. In this study, The image of Turkey, a developing country, in the minds of Turks is explored. It is measured in tenns of thoughts, feelings, perceptions and attitudes, and compared with Europeans' perceived image of Turkey. After defining the image of Turkey, some strategi~s how to manage it are suggested.
Open Access
A part family formation algorithm in GT environment using a multi-objective cluster analysis
(1993) Balköse, Hasan Okan
In the existing literature, the part-family formation problem is nandled either by coding systems or the cluster analysis. In this study, we propose a new method that will consider both design attributes and operation sequences simultaneously in conjunction with the related performance measures such as the machine investment, within and between cell workload variabilities, and the number of skippings. Finally the proposed method is compared with the similarity coefficent method under different experimental settings and its robustness is chocked against the varying system parameters.
Open Access
Quantification of SLIT-ROBO transcripts in hepatocellular carcinoma reveals two groups of genes with coordinate expression
(BioMed Central, 2008) Avci, M. E.; Konu, O.; Yagci, T.
Background: SLIT-ROBO families of proteins mediate axon pathfinding and their expression is not solely confined to nervous system. Aberrant expression of SLIT-ROBO genes was repeatedly shown in a wide variety of cancers, yet data about their collective behavior in hepatocellular carcinoma (HCC) is missing. Hence, we quantified SLIT-ROBO transcripts in HCC cell lines, and in normal and tumor tissues from liver. Methods: Expression of SLIT-ROBO family members was quantified by real-time qRT-PCR in 14 HCC cell lines, 8 normal and 35 tumor tissues from the liver. ANOVA and Pearson's correlation analyses were performed in R environment, and different clinicopathological subgroups were pairwise compared in Minitab. Gene expression matrices of cell lines and tissues were analyzed by Mantel's association test. Results: Genewise hierarchical clustering revealed two subgroups with coordinate expression pattern in both the HCC cell lines and tissues: ROBO1, ROBO2, SLIT1 in one cluster, and ROBO4, SLIT2, SLIT3 in the other, respectively. Moreover, SLIT-ROBO expression predicted AFP-dependent subgrouping of HCC cell lines, but not that of liver tissues. ROBO1 and ROBO2 were significantly up-regulated, whereas SLIT3 was significantly down-regulated in cell lines with high-AFP background. When compared to normal liver tissue, ROBO1 was found to be significantly overexpressed, while ROBO4 was down-regulated in HCC. We also observed that ROBO1 and SLIT2 differentiated histopathological subgroups of liver tissues depending on both tumor staging and differentiation status. However, ROBO4 could discriminate poorly differentiated HCC from other subgroups. Conclusion: The present study is the first in comprehensive and quantitative evaluation of SLIT-ROBO family gene expression in HCC, and suggests that the expression of SLIT-ROBO genes is regulated in hepatocarcinogenesis. Our results implicate that SLIT-ROBO transcription profile is bi-modular in nature, and that each module shows intrinsic variability. We also provide quantitative evidence for potential use of ROBO1, ROBO4 and SLIT2 for prediction of tumor stage and differentiation status.