Search results for "Clusterin"
showing 10 items of 478 documents
Fast dendrogram-based OTU clustering using sequence embedding
2014
Biodiversity assessment is an important step in a metagenomic processing pipeline. The biodiversity of a microbial metagenome is often estimated by grouping its 16S rRNA reads into operational taxonomic units or OTUs. These metagenomic datasets are typically large and hence require effective yet accurate computational methods for processing.In this paper, we introduce a new hierarchical clustering method called CRiSPy-Embed which aims to produce high-quality clustering results at a low computational cost. We tackle two computational issues of the current OTU hierarchical clustering approach: (1) the compute-intensive sequence alignment operation for building the distance matrix and (2) the …
A Fuzzy Logic C-Means Clustering Algorithm to Enhance Microcalcifications Clusters in Digital Mammograms
2011
The detection of microcalcifications is a hard task, since they are quite small and often poorly contrasted against the background of images. The Computer Aided Detection (CAD) systems could be very useful for breast cancer control. In this paper, we report a method to enhance microcalcifications cluster in digital mammograms. A Fuzzy Logic clustering algorithm with a set of features is used for clustering microcalcifications. The method described was tested on simulated clusters of microcalcifications, so that the location of the cluster within the breast and the exact number of microcalcifications is known.
Parallelized Clustering of Protein Structures on CUDA-Enabled GPUs
2014
Estimation of the pose in which two given molecules might bind together to form a potential complex is a crucial task in structural biology. To solve this so-called "docking problem", most algorithms initially generate large numbers of candidate poses (or decoys) which are then clustered to allow for subsequent computationally expensive evaluations of reasonable representatives. Since the number of such candidates ranges from thousands to millions, performing the clustering on standard CPUs is highly time consuming. In this paper we analyze and evaluate different approaches to parallelize the nearest neighbor chain algorithm to perform hierarchical Ward clustering of protein structures usin…
ERBB2 Induces an Antiapoptotic Expression Pattern of Bcl-2 Family Members in Node-Negative Breast Cancer
2010
AbstractPurpose: Members of the Bcl-2 family act as master regulators of mitochondrial homeostasis and apoptosis. We analyzed whether ERBB2 influences the prognosis of breast cancer by influencing the proapoptotic versus antiapoptotic balance of Bcl-2 family members.Experimental Design: ERBB2-regulated Bcl-2 family members were identified by inducible expression of ERBB2 in MCF-7 breast cancer cells and by correlation analysis with ERBB2 expression in breast carcinomas. The prognostic relevance of ERBB2-regulated and all additional Bcl-2 family members was determined in 782 patients with untreated node-negative breast cancer. The biological relevance of ERBB2-induced inhibition of apoptosis…
Gp80 (clusterin; TRPM-2) mRNA level is enhanced in human renal clear cell carcinomas
1994
The gp80 glycoprotein complex (clusterin, apolipoprotein J, TRPM-2) is a widely expressed protein that has been attributed functions in tissue remodelling, immune defense and transport of lipids and biologically active peptides. The expression of the protein appears to be elevated in several neurodegenerative, apoptotic and malignant processes. We show here that in patients with renal clear cell carcinoma gp80 mRNA is 3-fold overexpressed in tissue of the tumors compared with adjacent non-tumor tissue.
Toll-like receptor 3 mediates expression of clusterin/apolipoprotein J in vascular smooth muscle cells stimulated with RNA released from necrotic cel…
2010
Clusterin/Apolipoprotein J is a protein that is upregulated in a broad spectrum of diverse pathological processes. The predominant form is a secreted glycoprotein (sCLU) with cytoprotective and anti-inflammatory properties which shows enhanced expression in vascular smooth muscle cells (VSMC) following aortic injury and in atherosclerotic disease. Recent evidence indicates that during atherosclerosis, Toll-like receptors (TLRs) are activated in vascular cells by endogenous ligands. Here, we analyzed whether CLU expression in VSMC is controlled by TLRs, and stimulated by factors associated with or released by necrotic cells. Activation of TLR3 by the synthetic RNA analogue polyinosinic-polyc…
Differential regulation of the clusterin gene by Ha-ras and c-myc oncogenes and during apoptosis
1998
Clusterin (ApoJ) is an extracellular glycoprotein expressed during processes of tissue differentiation and regression that involve programmed cell death (apoptosis). Increased clusterin expression has also been found in tumors, however, the mechanism underlying this induction is not known. Apoptotic processes in tumors could be responsible for clusterin gene activation. Alternatively, oncogenic mutations could modulate signal transduction, thereby inducing the gene. We examined the response of the rat clusterin gene to two oncogenes, Ha-ras and c-myc, in transfected Rat1 fibroblasts. While c-myc overexpression did not modify clusterin gene activity, the Ha-ras oncogene produced a seven to t…
Chapter 7 Cell Protective Functions of Secretory Clusterin (sCLU)
2009
Secretory clusterin (sCLU) is found as an 80-kDa glycoprotein in virtually all body fluids, in serum it is associated with high-density lipoprotein (HDL). Here, we discuss demonstrated and proposed mechanisms of the cytoprotective functions of sCLU in instances of apoptosis, necrosis, and disease. These include prevention from cell damage by lipid oxidation in blood vessels, removal of dead cell remnants in tissues undergoing various forms of cell death, and clearance of harmful extracellular molecules such as amyloid beta (Aβ) by endocytosis or transcytosis. All these functions may reflect the propensity of sCLU to bind to a wide spectrum of hydrophobic molecules on one hand and to specifi…
Multiple signal transduction pathways regulate clusterin (gp 80) gene expression in MDCK cells
1996
ABSTRACT Clusterin (gp 80, apolipoprotein J, TRPM-2) is a widely expressed multifunctional glycoprotein. Its demonstrated and proposed functions include the transport of lipids and membrane fragments, the inhibition of the cytolytic action of the terminal complement complex and the modulation of cell—cell interactions. The expression of the gene is enhanced during tissue injury and remodelling and by hormone-withdrawal-induced apoptosis of prostate and mammary cells. We show here that, in the kidney-derived epithelial cell line MDCK, clusterin mRNA is repressed by glucocorticoids and by progesterone. Treatment with epidermal growth factor also represses clusterin gene expression in MDCK cel…
Cellular automata and urban development simulation : a transition rules creation process based on statistical analysis
2015
National audience; Nowadays land use evolution study has become a major stake in urban planning. The main focus is to understand the way in which land use evolves across time and to understand processes that take place. This understanding would allow to plan urban developments based on a knowledge as complete as possible covering as many fields as possible (i.e. urban planning, politics, sociology, etc.). Simulation tools can be used to merge and display different points of view and stakes from different stakeholders (Parrott & Meyer, 2012).