Comprehensive analysis of epigenetic signatures of human transcription control†

Advances in sequencing technologies have enabled exploration of epigenetic and transcription profiles at a genome-wide level. The epigenetic and transcriptional landscape is now available in hundreds of mammalian cell and tissue contexts. Many studies have performed multi-omics analyses using these datasets to enhance our understanding of relationships between epigenetic modifications and transcription regulation. Nevertheless, most studies so far have focused on the promoters/enhancers and transcription start sites, and other features of transcription control including exons, introns and transcription termination remain under explored. We investigated interplay between epigenetic modifications and diverse transcription features using the data generated by the Roadmap Epigenomics project. A comprehensive analysis of histone modifications, DNA methylation, and RNA-seq data of about thirty human cell lines and tissue types, allowed us to confirm the generality of previously described relations, as well as to generate new hypotheses about the interplay between epigenetic modifications and transcript features. Importantly, our analysis included previously under-explored features of transcription control namely, transcription termination sites, exon-intron boundaries, middle exons and exon inclusion ratio. We have made the analyses freely available to the scientific community at joshiapps.cbu.uib.no/perepigenomics_app/ for easy exploration, validation and hypotheses generation.

DETECTION OF TEXTURE-LESS OBJECTS BY LINE-BASED APPROACH

This paper proposes a method for tackling the problem of scalable object instance detection in the presence of clutter and occlusions. It gathers together advantages in respect of the state-of-the-art object detection approaches, being at the same time able to scale favorably with the number of models, computationally efficient and suited to texture-less objects as well. The proposed method has the following advantages: a) generality – it works for both texture-less and textured objects, b) scalability – it scales sub-linearly with the number of objects stored in the object database, and c) computational efficiency – it runs in near real-time. In contrast to the traditional affine-invariant detectors/descriptors which are local and not discriminative for texture-less objects, our method is based on line segments around which it computes semi-global descriptor by encoding gradient information in scale and rotation invariant manner. It relies on both texture and shape information and is, therefore, suited for both textured and texture-less objects. The descriptor is integrated into efficient object detection procedure which exploits the fact that the line segment determines scale, orientation and position of an object, by its two endpoints. This is used to construct several effective techniques for object hypotheses generation, scoring and multiple object reasoning; which are integrated in the proposed object detection procedure. Thanks to its ability to detect objects even if only one correct line match is found, our method allows detection of the objects under heavy clutter and occlusions. Extensive evaluation on several public benchmark datasets for texture-less and textured object detection, demonstrates its scalability and high effectiveness.

An Analytical Survey on Diagnosis Algorithm in Generic Defect Large-Scale Failures in Computer Networks

We present a framework and a set of algorithms for determining faults in networks when large scale outages occur. The design principles of our algorithm, netCSI, are motivated by the fact that failures are geographically clustered in such cases. We address the challenge of determining faults with incomplete symptom information due to a limited number of reporting nodes. netCSI consists of two parts: a hypotheses generation algorithm, and a ranking algorithm. When constructing the hypothesis list of potential causes, we make novel use of positive and negative symptoms to improve the precision of the results. In addition, we propose pruning and thresholding along with a dynamic threshold value selector, to reduce the complexity of our algorithm. The ranking algorithm is based on conditional failure probability models that account for the geographic correlation of the network objects in clustered failures. We evaluate the performance of netCSI for networks with both random and realistic topologies. We compare the performance of netCSI with an existing fault diagnosis algorithm, MAX-COVERAGE, and demonstrate an average gain of 128 percent in accuracy for realistic topologies.

An Advanced Automatic Electronic Diagnosis System

Every complex system is liable to faults and failures. In the most general terms, a fault is any change in a system that prevents it from operating in the proper manner. Here, the diagnosis of catastrophic defects in complex digital circuits. In fact, today the technical diagnosis is great challenge for design engineers because diagnostic problems are generally under determinate. It is also a deductive process with one set of data creating, in general, unlimited number of hypotheses among which one should try to get the solution. So the diagnosis methods are based on proprietary knowledge and personal experience, although they were built into integrated diagnostic equipment. The approach proposed here is an alternative to existing solutions, and it is expected to encompass all phases of the diagnostic process: symptom detection, hypotheses generation, and hypotheses discrimination.