Multi-scale directional-filtering-based method for follicular lymphoma grading

Cataloged from PDF version of article.Follicular lymphoma (FL) is a group of malignancies of lymphocyte origin that arise from lymph nodes, spleen, and bone marrow in the lymphatic system. It is the second most common non-Hodgkins lymphoma. Characteristic of FL is the presence of follicle center B cells consisting of centrocytes and centroblasts. Typically, FL images are graded by an expert manually counting the centroblasts in an image. This is time consuming. In this paper, we present a novel multi-scale directional filtering scheme and utilize it to classify FL images into different grades. Instead of counting the centroblasts individually, we classify the texture formed by centroblasts. We apply our multi-scale directional filtering scheme in two scales and along eight orientations, and use the mean and the standard deviation of each filter output as feature parameters. For classification, we use support vector machines with the radial basis function kernel. We map the features into two dimensions using linear discriminant analysis prior to classification. Experimental results are presented

Content-adaptive color transform for image compression

Cataloged from PDF version of article.In this paper, an adaptive color transform for image compression is introduced. In each block of the image, coefficients of the color transform are determined from the previously compressed neighboring blocks using weighted sums of the RGB pixel values, making the transform block-specific. There is no need to transmit or store the transform coeffi- cients because they are estimated from previous blocks. The compression efficiency of the transform is demonstrated using the JPEG image coding scheme. In general, the suggested transformation results in better peak signal-to-noise ratio (PSNR) values for a given compression level. ( C) 2011 Society of Photo-Optical Instrumentation Engineer

Bandwidth selection for kernel density estimation using Fourier domain constraints

Kernel density estimation (KDE) is widely-used for non-parametric estimation of an underlying density from data. The performance of KDE is mainly dependent on the bandwidth parameter of the kernel. This study presents an alternative method of estimating the bandwidth by incorporating sparsity priors in the Fourier transform domain. By using cross-validation (CV) together with an l1 constraint, the proposed method significantly reduces the under-smoothing effect of traditional CV methods. A solution for all free parameters in the minimisation is proposed, such that the algorithm does not need any additional parameter tuning. Simulation results indicate that the new approach is able to outperform classical and more recent approaches over a set of distributions of interest. © The Institution of Engineering and Technology

Unraveling the functional role of the orphan solute carrier, SLC22A24 in the transport of steroid conjugates through metabolomic and genome-wide association studies.

Variation in steroid hormone levels has wide implications for health and disease. The genes encoding the proteins involved in steroid disposition represent key determinants of interindividual variation in steroid levels and ultimately, their effects. Beginning with metabolomic data from genome-wide association studies (GWAS), we observed that genetic variants in the orphan transporter, SLC22A24 were significantly associated with levels of androsterone glucuronide and etiocholanolone glucuronide (sentinel SNPs p-value <1x10-30). In cells over-expressing human or various mammalian orthologs of SLC22A24, we showed that steroid conjugates and bile acids were substrates of the transporter. Phylogenetic, genomic, and transcriptomic analyses suggested that SLC22A24 has a specialized role in the kidney and appears to function in the reabsorption of organic anions, and in particular, anionic steroids. Phenome-wide analysis showed that functional variants of SLC22A24 are associated with human disease such as cardiovascular diseases and acne, which have been linked to dysregulated steroid metabolism. Collectively, these functional genomic studies reveal a previously uncharacterized protein involved in steroid homeostasis, opening up new possibilities for SLC22A24 as a pharmacological target for regulating steroid levels

Protejá: Programa Proteção da Informação da Embrapa Gado de Corte.

O Protejá (Proteja já o conhecimento), implantado em 2008 pela Embrapa Gado de Corte em parceria com a Agência Brasileira de Informação (ABIN), consiste em uma ação gerencial vinculada à Diretriz Estratégica do V Plano Diretor da Embrapa (PDE) ? de ??promover a gestão e proteção do conhecimento``. Percebida a fragilidade na proteção deficiente das informações/conhecimento sensível a Unidade identificou o Programa Nacional de Proteção do Conhecimento Sensível ? PNPC da ABIN, como instrumento necessário à implantação de programas/processos de gestão e proteção do conhecimento buscando evitar a perda e vazamento de conhecimento relevante.Poster 009

Microscopic image classification using sparsity in a transform domain and Bayesian learning

Some biomedical images show a large quantity of different junctions and sharp corners. It is possible to classify several types of biomedical images in a region covariance approach. Cancer cell line images are divided into small blocks and covariance matrices of image blocks are computed. Eigen-values of the covariance matrices are used as classification parameters in a Bayesian framework using the sparsity of the parameters in a transform domain. The efficiency of the proposed method over classification using standard Support Vector Machines (SVM) is demonstrated on biomedical image data. © 2011 EURASIP

Alterations in long noncoding RNAs in women with and without polycystic ovarian syndrome

Long noncoding RNAs (lncRNAs) are RNA transcripts over 200 nucleotides long that are not translated into protein; however, there is increasing evidence of their regulatory functions. To date, there are few studies measuring lncRNA in control women or women with polycystic ovary syndrome (PCOS). Objective: To determine lncRNA differences between PCOS and control women. Design: Cross sectional study. Patients: Twenty four anovulatory women with all three diagnostic features of PCOS compared to 24 control women in the follicular phase of their menstrual cycle from a PCOS biobank. Results: Women with PCOS were age and weight matched compared to the control women but were significantly insulin resistant and hyperandrogenemic (

Mendelian inheritance of trimodal CpG methylation sites suggests distal cis-acting genetic effects.

Environmentally influenced phenotypes, such as obesity and insulin resistance, can be transmitted over multiple generations. Epigenetic modifications, such as methylation of DNA cytosine-guanine (CpG) pairs, may be carriers of inherited information. At the population level, the methylation state of such "heritable" CpG sites is expected to follow a trimodal distribution, and their mode of inheritance should be Mendelian. Using the Illumina Infinium 450 K DNA methylation array, we determined DNA CpG-methylation in blood cells from a family cohort 123 individuals of Arab ethnicity, including 18 elementary father-mother-child trios, we asked whether Mendelian inheritance of CpG methylation is observed, and most importantly, whether it is independent of any genetic signals. Using 40× whole genome sequencing, we therefore excluded all CpG sites with possibly confounding genetic variants (SNP) within the binding regions of the Illumina probes. We identified a total of 955 CpG sites that displayed a trimodal distribution and confirmed trimodality in a study of 1805 unrelated Caucasians. Of 955 CpG sites, 99.9% observed a strict Mendelian pattern of inheritance and had no SNP within +/-110 nucleotides of the CpG site by design. However, in 97% of these cases a distal cis-acting SNP within a +/-1 Mbp window was found that explained the observed CpG distribution, excluding the hypothesis of epigenetic inheritance for these clear-cut trimodal sites. Using power analysis, we showed that in 46% of all cases, the closest CpG-associated SNP was located more than 1000 bp from the CpG site. Our findings suggest that CpG methylation is maintained over larger genomic distances. Furthermore, nearly half of the SNPs associated with these trimodal sites were also associated with the expression of nearby genes (P = 4.08 × 10(-6)), implying a regulatory effect of these trimodal CpG sites

Metabolic GWAS of elite athletes reveals novel genetically-influenced metabolites associated with athletic performance

Genetic research of elite athletic performance has been hindered by the complex phenotype and the relatively small effect size of the identified genetic variants. The aims of this study were to identify genetic predisposition to elite athletic performance by investigating genetically-influenced metabolites that discriminate elite athletes from non-elite athletes and to identify those associated with endurance sports. By conducting a genome wide association study with high-resolution metabolomics profiling in 490 elite athletes, common variant metabolic quantitative trait loci (mQTLs) were identified and compared with previously identified mQTLs in non-elite athletes. Among the identified mQTLs, those associated with endurance metabolites were determined. Two novel genetic loci in FOLH1 and VNN1 are reported in association with N-acetyl-aspartyl-glutamate and Linoleoyl ethanolamide, respectively. When focusing on endurance metabolites, one novel mQTL linking androstenediol (3alpha, 17alpha) monosulfate and SULT2A1 was identified. Potential interactions between the novel identified mQTLs and exercise are highlighted. This is the first report of common variant mQTLs linked to elite athletic performance and endurance sports with potential applications in biomarker discovery in elite athletic candidates, non-conventional anti-doping analytical approaches and therapeutic strategies