Genome-Wide Survey of MicroRNA - Transcription Factor Feed-Forward Regulatory Circuits in Human

In this work, we describe a computational framework for the genome-wide identification and characterization of mixed transcriptional/post-transcriptional regulatory circuits in humans. We concentrated in particular on feed-forward loops (FFL), in which a master transcription factor regulates a microRNA, and together with it, a set of joint target protein coding genes. The circuits were assembled with a two step procedure. We first constructed separately the transcriptional and post-transcriptional components of the human regulatory network by looking for conserved over-represented motifs in human and mouse promoters, and 3'-UTRs. Then, we combined the two subnetworks looking for mixed feed-forward regulatory interactions, finding a total of 638 putative (merged) FFLs. In order to investigate their biological relevance, we filtered these circuits using three selection criteria: (I) GeneOntology enrichment among the joint targets of the FFL, (II) independent computational evidence for the regulatory interactions of the FFL, extracted from external databases, and (III) relevance of the FFL in cancer. Most of the selected FFLs seem to be involved in various aspects of organism development and differentiation. We finally discuss a few of the most interesting cases in detail.Comment: 51 pages, 5 figures, 4 tables. Supporting information included. Accepted for publication in Molecular BioSystem

Automatic programming methodologies for electronic hardware fault monitoring

This paper presents three variants of Genetic Programming (GP) approaches for intelligent online performance monitoring of electronic circuits and systems. Reliability modeling of electronic circuits can be best performed by the Stressor - susceptibility interaction model. A circuit or a system is considered to be failed once the stressor has exceeded the susceptibility limits. For on-line prediction, validated stressor vectors may be obtained by direct measurements or sensors, which after pre-processing and standardization are fed into the GP models. Empirical results are compared with artificial neural networks trained using backpropagation algorithm and classification and regression trees. The performance of the proposed method is evaluated by comparing the experiment results with the actual failure model values. The developed model reveals that GP could play an important role for future fault monitoring systems.This research was supported by the International Joint Research Grant of the IITA (Institute of Information Technology Assessment) foreign professor invitation program of the MIC (Ministry of Information and Communication), Korea

Programmable photonics : an opportunity for an accessible large-volume PIC ecosystem

We look at the opportunities presented by the new concepts of generic programmable photonic integrated circuits (PIC) to deploy photonics on a larger scale. Programmable PICs consist of waveguide meshes of tunable couplers and phase shifters that can be reconfigured in software to define diverse functions and arbitrary connectivity between the input and output ports. Off-the-shelf programmable PICs can dramatically shorten the development time and deployment costs of new photonic products, as they bypass the design-fabrication cycle of a custom PIC. These chips, which actually consist of an entire technology stack of photonics, electronics packaging and software, can potentially be manufactured cheaper and in larger volumes than application-specific PICs. We look into the technology requirements of these generic programmable PICs and discuss the economy of scale. Finally, we make a qualitative analysis of the possible application spaces where generic programmable PICs can play an enabling role, especially to companies who do not have an in-depth background in PIC technology

Design Synthesis of Adaptive Mesoscopic Cellular Structures with Unit Truss Approach and Particle Swarm Optimization Algorithm

Cellular material structures have been engineered at the mesoscopic scale for high performance and multifunctional capabilities. However, the design of adaptive cellular structures - structures with cellular configurations, sizes, and shapes designed for a specific geometric and loading context - has not been sufficiently investigated. In this paper, the authors present a design synthesis method with the use of unit truss approach and particle swarm optimization algorithm to design adaptive cellular structures. A critical review is presented to show the pros and cons of the new design synthesis method and an existing homogenization method. The research extends the application of additive manufacturing in the design of new materials for high performances and benefits its long-term growth.Mechanical Engineerin

Using genetic algorithms to generate test sequences for complex timed systems

The generation of test data for state based specifications is a computationally expensive process. This problem is magnified if we consider that time con- straints have to be taken into account to govern the transitions of the studied system. The main goal of this paper is to introduce a complete methodology, sup- ported by tools, that addresses this issue by represent- ing the test data generation problem as an optimisa- tion problem. We use heuristics to generate test cases. In order to assess the suitability of our approach we consider two different case studies: a communication protocol and the scientific application BIPS3D. We give details concerning how the test case generation problem can be presented as a search problem and automated. Genetic algorithms (GAs) and random search are used to generate test data and evaluate the approach. GAs outperform random search and seem to scale well as the problem size increases. It is worth to mention that we use a very simple fitness function that can be eas- ily adapted to be used with other evolutionary search techniques

A Survey of Prediction and Classification Techniques in Multicore Processor Systems

In multicore processor systems, being able to accurately predict the future provides new optimization opportunities, which otherwise could not be exploited. For example, an oracle able to predict a certain application\u27s behavior running on a smart phone could direct the power manager to switch to appropriate dynamic voltage and frequency scaling modes that would guarantee minimum levels of desired performance while saving energy consumption and thereby prolonging battery life. Using predictions enables systems to become proactive rather than continue to operate in a reactive manner. This prediction-based proactive approach has become increasingly popular in the design and optimization of integrated circuits and of multicore processor systems. Prediction transforms from simple forecasting to sophisticated machine learning based prediction and classification that learns from existing data, employs data mining, and predicts future behavior. This can be exploited by novel optimization techniques that can span across all layers of the computing stack. In this survey paper, we present a discussion of the most popular techniques on prediction and classification in the general context of computing systems with emphasis on multicore processors. The paper is far from comprehensive, but, it will help the reader interested in employing prediction in optimization of multicore processor systems

Hardware simulation of KU-band spacecraft receiver and bit synchronizer, phase 2, volume 1

The acquisition behavior of the PN subsystem of an automatically acquiring spacecraft receiver was studied. A symbol synchronizer subsystem was constructed and integrated into the composite simulation of the receiver. The overall performance of the receiver when subjected to anomalies such as signal fades was evaluated. Potential problems associated with PN/carrier sweep interactions were investigated