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

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Recently, a huge amount of sulfur has been produced as a byproduct of petroleum refining processes in Korea. Sulfur concrete is made of modified sulfur binder instead of cement paste, which has advantages of reducing CO2 emission from cement industry as well as utilizing surplus sulfur. Also, sulfur concrete is a sustainable material that can be repetitively recycled. In this study, the physical properties of sulfur concrete are experimentally investigated. From the test results, sulfur concrete showed compressive strengths higher than at least 50MPa. Also, the unit weight, modulus of elasticity and splitting tensile strength of sulfur concrete was similar to that of Portland cement concrete (PCC). The coefficient of thermal expansion of sulfur concrete was a little larger than that of Portland cement concrete and sulfur concrete with mineral filler is helpful to lower the coefficient of thermal expansion. recycled aggregate sulfur concrete resulted in a slight reduction in the compressive strength, but sulfur concrete with recycled aggregate can achieve the high strength characteristics.clos

Importância dos Saca-Rabos (Herpestes Ichneumon) como Reservatório de Mycobacterium avium subsp. paratuberculosis. Deteção por Técnicas Tradicionais e Moleculares

Poster apresentado nas IV Jornadas de Genética, realizadas na UTAD, Vila Real, nos dias 1,2 e 3 de Março de 2012.Os saca-rabos (Herpestes ichneumon) também conhecidos por mangustos, são carnívoros diurnos selvagens que juntamente com a geneta (Genetta genetta) representam os exemplares da família Viverridae em Portugal. É uma espécie cinegética de caça menor que se alimenta de coelhos, roedores, aves, cobras, insectos e ovos. Neste estudo colheram-se amostras de 8 animais mortos por atropelamento e em ações de controlo de predadores, durante os anos de 2010 e 2011, nos concelhos de Idanha-a-Nova e Penamacor do distrito de Castelo Branco. As amostras colhidas foram fígado, pulmão, baço, intestino, rim, gânglio mesentérico, retrofaríngeo, mediastínico, amígdalas e fezes. As amostras foram submetidas à técnica de PCR e a cultura microbiológica em meios específicos. Em três saca-rabos (37,5%) detectou-se Mycobacterium avium subsp. paratuberculosis (Map) através da técnica de biologia molecular. Dois eram machos e um era fêmea. Map foi confirmado também em cultura nos dois machos. Sete saca-rabos (87,5%) apresentaram bactérias álcool-ácido resistentes compatíveis com Map em esfregaços de diferentes tecidos, quando corados pelo método de Ziehl-Neelsen. Estes resultados preliminares confirmam os saca-rabos como reservatório de Map no nosso país. Atualmente, estão a ser desenvolvidos mais estudos para a avaliação dos saca-rabos na dinâmica da infeção de Map em mamíferos selvagens

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

Falciform Ligament Abscess after Omphalitis: Report of a Case

A falciform ligament abscess is a rare type of intra-abdominal abscess. A 2-yr-old male, who had omphalitis two months previously, presented with a fever and right upper quadrant abdominal pain. The ultrasound and CT scan showed an abdominal wall abscess located anterior to the liver, which was refractory to conservative management with percutaneous draninage and antibiotics. On the third recurrence, surgical exploration was performed and revealed an abscess arising from the falciform ligament; the falciform ligament was excised. A follow up ultrasound confirmed complete resolution of the abscess with no further recurrence

Replication of the genetic effects of IFN regulatory factor 5 (IRF5) on systemic lupus erythematosus in a Korean population

Recently, two studies provided convincing evidence that IFN regulatory factor 5 (IRF5) gene polymorphisms are significantly associated with systemic lupus erythematosus (SLE) in several white populations. To replicate the association with SLE in an Asian population, we examined the genetic effects in our SLE cohort from a Korean population. A total of 1,565 subjects, composed of 593 cases and 972 controls, were genotyped using the TaqMan® (Applied Biosystems, Foster City, CA, USA) method. The genetic effects of polymorphisms on the risk of SLE were evaluated using χ2 tests and a Mantel–Haenszel meta-analysis. Statistical analysis revealed results in the Korean population were similar to the previous reports from white populations. The rs2004640 T allele had a higher frequency in SLE cases (0.385) than controls (0.321; odds ratio (OR) = 1.32, P = 0.0003). In combined analysis, including all seven independent cohorts from the three studies so far, robust and consistent associations of the rs2004640 T allele with SLE were observed. The estimate of risk was OR = 1.44 (range, 1.34–1.55), with an overall P = 1.85 × 10-23 for the rs2004640 T allele. The haplotype (rs2004640T–rs2280714T) involved in both the alternative splice donor site and the elevated expression of IRF5 also had a highly significant association with SLE (pooled, P = 2.11 × 10-16). Our results indicate that the genetic effect on the risk of SLE mediated by IRF5 variants can be generally accepted in both white and Asian populations