Neural networks for nonlinear discriminant analysis in continuous speech recognition

In this paper neural networks for Nonlinear Discriminant Analysis in continuous speech recognition are presented. Multilayer Perceptrons are used to estimate a-posteriori probabilities for Hidden-Markov Model states, which are the optimal discriminant features for the separation of the HMM states. The a-posteriori probabilities are transformed by a principal component analysis to calculate the new features for semicontinuous HMMs, which are trained by the known Maximum-Likelihood training. The nonlinear discriminant transformation is used in speaker-independent phoneme recognition experiments and compared to the standard Linear Discriminant Analysis technique

Deep Sequencing of MYC DNA-Binding Sites in Burkitt Lymphoma

BACKGROUND: MYC is a key transcription factor involved in central cellular processes such as regulation of the cell cycle, histone acetylation and ribosomal biogenesis. It is overexpressed in the majority of human tumors including aggressive B-cell lymphoma. Especially Burkitt lymphoma (BL) is a highlight example for MYC overexpression due to a chromosomal translocation involving the c-MYC gene. However, no genome-wide analysis of MYC-binding sites by chromatin immunoprecipitation (ChIP) followed by next generation sequencing (ChIP-Seq) has been conducted in BL so far. METHODOLOGY/PRINCIPAL FINDINGS: ChIP-Seq was performed on 5 BL cell lines with a MYC-specific antibody giving rise to 7,054 MYC-binding sites after bioinformatics analysis of a total of approx. 19 million sequence reads. In line with previous findings, binding sites accumulate in gene sets known to be involved in the cell cycle, ribosomal biogenesis, histone acetyltransferase and methyltransferase complexes demonstrating a regulatory role of MYC in these processes. Unexpectedly, MYC-binding sites also accumulate in many B-cell relevant genes. To assess the functional consequences of MYC binding, the ChIP-Seq data were supplemented with siRNA- mediated knock-downs of MYC in BL cell lines followed by gene expression profiling. Interestingly, amongst others, genes involved in the B-cell function were up-regulated in response to MYC silencing. CONCLUSION/SIGNIFICANCE: The 7,054 MYC-binding sites identified by our ChIP-Seq approach greatly extend the knowledge regarding MYC binding in BL and shed further light on the enormous complexity of the MYC regulatory network. Especially our observations that (i) many B-cell relevant genes are targeted by MYC and (ii) that MYC down-regulation leads to an up-regulation of B-cell genes highlight an interesting aspect of BL biology

Sunshape Measurements with Conventional Rotating Shadowband Irradiometers

Because of forward scattered radiation in the atmosphere, the circumsolar region closely surrounding the solar disk looks very bright. The radiation coming from this region, the circumsolar radiation, is in large part included in direct normal irradiance (DNI) measurements at the usual 2.5° pyrheliometer opening half angle, but only partially intercepted by the receivers of focusing solar collectors. Therefore, circumsolar radiation measurements are recommended to be included in solar resource assessment. Circumsolar radiation can be characterized using the radial angular distribution of the radiance around the center of the sun – the so-called sunshape. Several sunshape measurement methods have been developed recently. Most approaches use cameras or pyrheliometers with different apertures which require daily maintenance. The Rotating Shadowband Irradiometer (RSI) based method discussed here uses a conventional RSI without any hardware modification to enable sunshape measurements without affecting the RSI’s fundamental function as a DNI measurement device. Thus, it allows to measure circumsolar radiation without any additional hardware and with significantly lower maintenance requirements. The presented RSI-based sunshape measurement algorithm has been validated with four RSIs and more than two years of data. After a short description of the method to derive the circumsolar contribution, the validation results are shown. Then the required calibration method is discussed, followed by the results from the measurement campaigns at four sites in Spain, India and Morocco. It was found that no individual calibration is required per instrument and the algorithm can be used for automatic data processing so that common RSI stations can measure the sunshape with comparably low extra effort. Furthermore, we explain how to derive sunshapes from the RSI measurements

Fruit Distribution in the Canadian West

Transcription factors, by binding to particular DNA sequences termed transcription factor-binding sites, play an important role in regulating gene expression in both prokaryotic and eukaryotic organisms. These binding sites lie within promoters (which are located just upstream of a gene and promote transcription of that gene) and enhancers (short DNA elements enhancing transcription levels of genes in a gene cluster, and which need not be particularly close to the genes they act on, or even located on the same chromosome). Binding of transcription factors in these genomic regulatory regions can influence gene transcription rates either positively or negatively. The binding may also be dependant on the interaction with co-activators and co-repressors, in addition to context (e.g. particular histone modifications in the vicinity of the regulatory element). Identifying all transcription factors and their respective binding sites would be an important step towards a more thorough understanding of gene regulation. Regular expression type patterns, as well as nucleotide distribution matrices, have both been used for describing transcription factor-binding sites, e.g. (Bucher 1990; Ghosh 1990; Chen et al. 1995; Wingender et al. 1996). Here we will discuss some of the computational approaches that are used in binding site identification.SCOPUS: ch.binfo:eu-repo/semantics/publishe