Effect of data normalization on fuzzy clustering of DNA microarray data

BACKGROUND: Microarray technology has made it possible to simultaneously measure the expression levels of large numbers of genes in a short time. Gene expression data is information rich; however, extensive data mining is required to identify the patterns that characterize the underlying mechanisms of action. Clustering is an important tool for finding groups of genes with similar expression patterns in microarray data analysis. However, hard clustering methods, which assign each gene exactly to one cluster, are poorly suited to the analysis of microarray datasets because in such datasets the clusters of genes frequently overlap. RESULTS: In this study we applied the fuzzy partitional clustering method known as Fuzzy C-Means (FCM) to overcome the limitations of hard clustering. To identify the effect of data normalization, we used three normalization methods, the two common scale and location transformations and Lowess normalization methods, to normalize three microarray datasets and three simulated datasets. First we determined the optimal parameters for FCM clustering. We found that the optimal fuzzification parameter in the FCM analysis of a microarray dataset depended on the normalization method applied to the dataset during preprocessing. We additionally evaluated the effect of normalization of noisy datasets on the results obtained when hard clustering or FCM clustering was applied to those datasets. The effects of normalization were evaluated using both simulated datasets and microarray datasets. A comparative analysis showed that the clustering results depended on the normalization method used and the noisiness of the data. In particular, the selection of the fuzzification parameter value for the FCM method was sensitive to the normalization method used for datasets with large variations across samples. CONCLUSION: Lowess normalization is more robust for clustering of genes from general microarray data than the two common scale and location adjustment methods when samples have varying expression patterns or are noisy. In particular, the FCM method slightly outperformed the hard clustering methods when the expression patterns of genes overlapped and was advantageous in finding co-regulated genes. Thus, the FCM approach offers a convenient method for finding subsets of genes that are strongly associated to a given cluster

Effects of Lowering Dialysate Calcium Concentrations on Arterial Stiffness in Patients Undergoing Hemodialysis

BACKGROUND/AIMS: We assessed changes in hemodynamic and arterial stiffness parameters following reductions of dialysate calcium concentrations in patients undergoing hemodialysis. METHODS: In this prospective study, 20 patients on maintenance hemodialysis (10 females, 10 males) with dialysate calcium concentrations of 1.75 mmol/L were enrolled. At the start of the study, the dialysate calcium level was lowered to 1.50 mmol/L. Serial changes in biochemical, hemodynamic, and arterial stiffness parameters, including pulse wave velocity (PWV) and augmentation index (AIx), were assessed every 2 months for 6 months. We also examined changes in the calcification-inhibitory protein, serum fetuin-A. RESULTS: During the 6-month study period, serum total calcium and ionized calcium decreased consistently (9.5 ± 1.0 to 9.0 ± 0.7, p = 0.002 vs. 1.3 ± 0.1 to 1.1 ± 0.1, p = 0.035). Although no apparent changes in blood pressure were observed, heart-femoral PWW (hf-PWV) and AIx showed significant improvement (p = 0.012, 0.043, respectively). Repeated-measures ANOVA indicated a significant effect of lowering dialysate calcium on hf-PWV (F = 4.58, p = 0.004) and AIx (F = 2.55, p = 0.049). Accompanying the change in serum calcium, serum fetuin-A levels significantly increased (95.8 ± 45.8 pmol/mL at baseline to 124.9 ± 82.2 pmol/mL at 6 months, p = 0.043). CONCLUSIONS: Lowering dialysate calcium concentration significantly improved arterial stiffness parameters, which may have been associated with upregulation of serum fetuin-A.ope

An Antioxidant Defense System in Radiation-Resistant Bacterium <em>Deinococcus geothermalis</em> against Oxidative Stress

A radiation-resistant bacterium, Deinococcus geothermalis has various stress response mechanisms, including antioxidation. Features that maintain vitality at high radiation doses include the following: enzymatic scavengers of ROS such as catalase, SOD, and peroxidase; strain-specific DNA repair systems such as Deinococcal unique proteins; non-enzymatic responses such as manganese complexes, carotenoids, and DNA-binding proteins. This chapter summarizes the primary response mechanism by redox balance centered on the cystine transporter. It also reviews action characteristics of DNA-binding protein Dps and a putative LysR family protein, and effects on loss of function of the carotenoid biosynthesis genes by transposition of insertion sequences. Environmental adaptation and molecular evolution of radiation-resistant bacterium are also considered to explain the potentials of molecular behavior induced by oxidative stress

Crude Extracts of Caenorhabditis elegans Suppress Airway Inflammation in a Murine Model of Allergic Asthma

Epidemiological studies suggest an inverse relationship between helminth infections and allergic disease, and several helminth-derived products have been shown to suppress allergic responses in animals. This study was undertaken to evaluate the effect of a crude extract of Caenorhabditis elegans on allergic airway inflammation in a murine model of asthma. Allergic airway inflammation was induced in BALB/c mice by sensitization with ovalbumin. The effect of the C. elegans crude extract on the development of asthma and on established asthma was evaluated by analyzing airway hyperresponsiveness, serum antibody titers, lung histology and cell counts and cytokine levels in the bronchoalveolar lavage fluid. The role of IFN-γ in the suppression of asthma by the C. elegans crude extract was investigated in IFN-γ knockout and wild-type mice. When mice were sensitized with ovalbumin together with the crude extract of C. elegans, cellular infiltration into the lung was dramatically reduced in comparison with the ovalbumin-treated group. Treatment of mice with the C. elegans crude extract significantly decreased methacholine-induced airway hyperresponsiveness and the total cell counts and levels of IL-4, IL-5 and IL-13 in the bronchoalveolar lavage fluid but increased the levels of IFN-γ and IL-12. Sensitization with the C. elegans crude extract significantly diminished the IgE and IgG1 responses but provoked elevated IgG2a levels. However, the suppressive effect of the C. elegans crude extract was abolished in IFN-γ knockout mice, and the Th2 responses in these mice were as strong as those in wild-type mice sensitized with ovalbumin. The crude extract of C. elegans also suppressed the airway inflammation associated with established asthma. This study provides new insights into immune modulation by the C. elegans crude extract, which suppressed airway inflammation in mice not only during the development of asthma but also after its establishment by skewing allergen-induced Th2 responses to Th1 responses

Experimental Study on Reinforced Concrete Column Incased in Prefabricated Permanent Thin-Walled Steel Form

Conventional construction methods of reinforced concrete (RC) structures generally require a long construction period and high costs due to many on-site temporary form works. In this study, a prefabricated permanent thin-walled steel form integrated with reinforcement cage (PPSFRC) was developed, and it makes for a fast-built construction by reducing the temporary form works. Axial compression tests were conducted on a total of 9 test specimens to investigate the structural performances of the newly developed columns. The proposed column construction method utilized relatively thinner steel plates compared to conventional concrete-filled tube (CFT) columns, but it was designed to have sufficient resistance performances against the lateral pressure of fresh concrete and to prevent the buckling of the thin plates by utilizing the steel angles and channel stiffeners prefabricated in the permanent thin-walled steel form. The experimental results showed that the column specimens fabricated by the PPSFRC method had better local buckling resistance and behaved in a more ductile manner compared to the conventional CFT columns. In addition, the axial strengths of the test specimens were compared with those estimated by design provisions, and the flexural moments induced by initial imperfection or accidental eccentricity of axial loads were also discussed in detail

Dopant dependent band gap tailoring of hydrothermally prepared cubic SrTi(x)M(1-x)O(3) (M=Ru,Rh,Ir,Pt,Pd) nanoparticles as visible light photocatalysts

Nanostructured cubic SrTiO(3) particles were hydrothermally synthesized and studied experimentally/theoretically for photoreduction of water. The particles were doped with metal atoms (M=Ru,Rh,Ir,Pt,Pd), which acquired high cyrstallinity after thermal treatment. SrTiO(3):Rh showed the highest rate of H(2) evolution under lambda>420 nm photons. The density functional theory calculations of SrTi(x)M(1-x)O(3) (M=Ru,Rh,Ir,Pt) implied that the photocatalytic activity of SrTi(x)Rh(1-x)O(3) was due to its suitable band energetics, and the induced hybridized Ti/Rh orbitals in the bandgap of SrTiO(3). (C) 2008 American Institute of Physicsclose353