New gene selection method for classification of cancer subtypes considering within-class variation

AbstractIn this work we propose a new method for finding gene subsets of microarray data that effectively discriminates subtypes of disease. We developed a new criterion for measuring the relevance of individual genes by using mean and standard deviation of distances from each sample to the class centroid in order to treat the well-known problem of gene selection, large within-class variation. Also this approach has the advantage that it is applicable not only to binary classification but also to multiple classification problems. We demonstrated the performance of the method by applying it to the publicly available microarray datasets, leukemia (two classes) and small round blue cell tumors (four classes). The proposed method provides a very small number of genes compared with the previous methods without loss of discriminating power and thus it can effectively facilitate further biological and clinical researches

A strategy for production of 1,4-pentanediol from cellulose and hemicellulose of lignocellulose biomass

Many studies have developed simulation models of bio-based process for production of liquid transportation fuels (bio-gasoline and biodiesel) from lignocellulosic biomass (containing cellulose, hemicellulose and lignin) and conducted economic analysis of the process. However, because of a sharp decrease in the price of crude oil based liquid transportation fuels in entire world today, lignocellulosic biofuels process cannot yet compete with the crude oil based process. Alternatively, production of value-added chemicals instead of biofuels has been considered as a viable option using lignocellulosic biomass. In this study we develop a catalytic process and perform an economic analysis for production of 1,4-pentanediol from lignocellulosic biomass. 1,4-pentanediol was used in the preparation of poly(ortho ester). In the process, the cellulose and hemicellulose are simultaneously converted to levulinic acid (LA) using γ-valerolactone (GVL) as a solvent. The LA is then converted to GVL in the presence of GVL and subsequently to 1,4-pentandiol. The simulation models of bio-based process are developed using ASPEN Plus simulator. Moreover, in order to reduce the total process energy requirements, heat integration of the process has conducted using Aspen Energy Analyzer. Our energy analysis shows that the total energy requirements could be satisfied from combustion of the biomass residues (lignin). Our economic analysis shows that minimum selling price of 1,4-pentanediol is $1.57 per kg which is compete with the market price of crude oil based one.Papers presented to the 12th International Conference on Heat Transfer, Fluid Mechanics and Thermodynamics, Costa de Sol, Spain on 11-13 July 2016

A role of DNA-dependent protein kinase for the activation of AMP-activated protein kinase in response to glucose deprivation

AbstractThe catalytic subunit of DNA-dependent protein kinase (DNA-PKcs) plays an essential role in double-strand break repair by initially recognizing and binding to DNA breaks. Here, we show that DNA-PKcs interacts with the regulatory γ1 subunit of AMP-activated protein kinase (AMPK), a heterotrimeric enzyme that has been proposed to function as a “fuel gauge” to monitor changes in the energy status of cells and is controlled by the upstream kinases LKB1 and Ca2+/calmodulin-dependent kinase kinase (CaMKK). In co-immunoprecipitation analyses, DNA-PKcs and AMPKγ1 interacted physically in DNA-PKcs-proficient M059K cells but not in DNA-PKcs-deficient M059J cells. Glucose deprivation-stimulated phosphorylation of AMPKα on Thr172 and of acetyl-CoA carboxylase (ACC), a downstream target of AMPK, is substantially reduced in M059J cells compared with M059K cells. The inhibition or down-regulation of DNA-PKcs by the DNA-PKcs inhibitors, wortmannin and Nu7441, or by DNA-PKcs siRNA caused a marked reduction in AMPK phosphorylation, AMPK activity, and ACC phosphorylation in response to glucose depletion in M059K, WI38, and IMR90 cells. In addition, DNA–DNA-PKcs−/− mouse embryonic fibroblasts (MEFs) exhibited decreased AMPK activation in response to glucose-free conditions. Furthermore, the knockdown of DNA-PKcs led to the suppression of AMPK (Thr172) phosphorylation in LKB1-deficient HeLa cells under glucose deprivation. Taken together, these findings support the positive regulation of AMPK activation by DNA-PKcs under glucose-deprived conditions in mammalian cells

Abnormal Integrity of Corticocortical Tracts in Mild Cognitive Impairment: A Diffusion Tensor Imaging Study

Mild cognitive impairment (MCI) has been defined as a transitional state between normal aging and Alzheimer disease. Diffusion tensor imaging (DTI) can estimate the microstructural integrity of white matter tracts in MCI. We evaluated the microstructural changes in the white matter of MCI patients with DTI. We recruited 11 patients with MCI who met the working criteria of MCI and 11 elderly normal controls. The mean diffusivity (MD) and fractional anisotropy (FA) were measured in 26 regions of the brain with the regions of interest (ROIs) method. In the MCI patients, FA values were significantly decreased in the hippocampus, the posterior limb of the internal capsule, the splenium of corpus callosum, and in the superior and inferior longitudinal fasciculus compared to the control group. MD values were significantly increased in the hippocampus, the anterior and posterior limbs of the internal capsules, the splenium of the corpus callosum, the right frontal lobe, and in the superior and the inferior longitudinal fasciculus. Microstructural changes of several corticocortical tracts associated with cognition were identified in patients with MCI. FA and MD values of DTI may be used as novel biomarkers for the evaluation of neurodegenerative disorders

Development of a protocol to detect and diagnose the chattering in the hot rolling process

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Data Reconcilation (DR) and Gross Error Detection (GED) in Utility System

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Process Monitoring and Diagnosis using Autoencoder Self-Organization Map for an EVA production process

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Optimal operation and pump regeneration plan of fusion fuel cycle based on the state-task network representation

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