31293594
Integrating mRNA Decay Information into Co-Regulation Study
Absolute or relative transcript amounts measured through high-throughput technologies (e.g., microarrays) are now commonly used in bioinformatics analysis, such as gene clustering and DNA binding motif finding. However, transcription rates that represent mRNA synthesis may be more relevant in these analyses. Because transcription rates are not equivalent to transcript amounts unless the mRNA degradation rates as well as other factors that affect transcript amount are identical across different genes, the use of transcription rates in bioinformatics analysis may lead to a better description of the relationships among genes and better identification of genomic signals. In this article, we propose to use experimentally measured mRNA decay rates and mRNA transcript amounts to jointly infer transcription rates, and then use the inferred transcription rates in downstream analyses. For gene expression similarity analysis, we find that there tends to be higher correlations among co-regulated genes when transcription-rate-based correlations are used compared to those based on transcript amounts. In the context of identifying DNA binding motifs, using inferred transcription rates leads to more significant findings than those based on transcript amounts. These analyses suggest that the incorporation of mRNA decay rates and the use of the inferred transcription rates can facilitate the study of gene regulations and the reconstruction of transcriptional regulatory networks.
16818834
Negative correlation between compositional symmetries and local recombination rates
Although still not much understood, the universal reverse complement symmetry in genomes may contain much information about the genome. In this article, under the hypothesis that recombination rate variations may be related to the high order DNA structure, we studied the association between local recombination rates and local symmetry levels in mouse, rat and human. We found significant negative correlations between recombination rates and reverse complement compositional symmetries in these three organisms. This negative correlation pattern also held at individual chromosome levels when data only from each individual chromosome was analyzed.
2603707
Evaluating Critiquing-based Recommender Agents
We describe a user study evaluating two critiquing-based recommender agents based on three criteria: decision accuracy. decision effort, and user confidence. Results show that user-motivated critiques were more frequently applied and the example critiquing system employing only this type of critiques achieved the best results. In particular, the example critiquing agent significantly improves users' decision accuracy with less cognitive effort consumed than the dynamic critiquing recommender with system-proposed critiques. Additionally, the former is more likely to inspire users' confidence of their choice and promote their intention to purchase and return to the agent for future use.
17619661
Your way your missions: from location-based to route-based pervasive gaming
In this paper, we describe the design and implementation of a route-based pervasive game named Your Way Your Missions (YWYM). Since the game obtains the planned routes of players and returns missions in the routes, players can play the game in a casual way, without changing their routes to respond to picked up missions. A self-reporting method is proposed to obtain the planned routes of players, and a corresponding route defining tool is developed upon Google Maps. Two approaches to realize route-based mission adaptation with spatial databases are presented.
22490692
Aligning Multiple Protein Structures by Deterministic Annealing
Protein structure alignment plays a key role in protein structure prediction and fold family classification. An efficient method for multiple protein structure alignment in a mathematical manner is presented, based on deterministic annealing technique. The alignment problem is mapped onto a nonlinear continuous optimization problem (NCOP) with common consensus chain, matching assignment matrices and atomic coordinates as variables. At each step in the annealing procedure, the NCOP is decomposed into as many sub-problems as the number of protein chains, each of which is actually an independent pairwise structure alignment between a protein chain and the consensus chain and hence can be efficiently solved by the parallel computation technique. The proposed method is robust with respect to choice of iteration parameters for a wide range of proteins, and performs well in both multiple and pairwise structure alignment cases, compared with existing alignment methods.
8972258
Designing oscillators in synthetic gene networks based on multi-scale dynamics
Multistability, oscillations, and switching exist at various levels of biological processes and organizations and have been investigated on the basis of many theoretical models, such as circadian oscillations with the period protein (PER) and the timeless protein (TIM) in Drosophila, and multistable dynamics regulated by transcriptional factors. Considerable experimental evidence suggests that cellular processes are intrinsically rhythmic or periodic. Various periodic oscillations with different time scales ranging from less than a second to more than a year, which may allow for living organisms to adapt their behaviors to a periodically varying environment, have also been observed experimentally. On the other hand, in synthetic gene networks, both toggle switch and repressilator have been theoretically proposed and further confirmed by experiments. All of these works stress the importance of feedback regulation of transcriptional factors, which is a key in giving rise to oscillatory or multistable dynamical behaviors exhibited by biological genetic systems. In addition, it should be noted that many periodic behaviors do not simply oscillate smoothly; rather, they change rapidly or jump at certain states. In gene expression systems, many different time scales characterize the gene regulatory processes. For instance, the transcription and translation processes generally evolve on a time scale that is much slower than that of phosphorylation, dimerization or binding reactions of transcription factors. In genetic networks, the time scale for expression of some genes is much slower than that of others, depending on the length of the genes. We aim to design robust periodic oscillators in synthetic gene-protein systems by simple nonlinear models and to analyze the basic mechanism of limit cycles with jumping behaviors or relaxation oscillations by exploiting multiple time-scale properties [1, 2]. We show that periodic oscillations are mainly generated by nonlinear feedback loops in gene regulatory systems and the jumping dynamics caused by time scale differences among biochemical reactions. Moreover, effects of time delay are also examined. We show that time delay generally enlarges the stability region of oscillations, thereby making the oscillations more sustainable despite parameter changes or noise [1, 2]. The dynamics of the proposed models is robust in terms of stability and period length to the parameter perturbations or environment variations. Although we mainly analyze some specific models, the mechanisms identified in this work are likely to apply to a variety of genetic regulatory systems. These simple models may actually act as basic building block in synthetic gene-protein networks, such as genetic oscillators or switches because the dynamics is robust for parameter perturbations or environment variations. Several examples are also provided to demonstrate implementation of synthetic oscillators by using genes of the /spl lambda/ phage bacteria.
42859429
Hardware verification using symbolic state transition graphs
A new approach for hardware verification using symbolic state transition graphs (implemented in BDDs) is presented. We propose a novel idea, a symbolic state transition graph (STG), which can represent finite state machines FSM in terms of the relations between symbolic input variables, state variables, and output results, rather than the exact input-output bit patterns. Compared to conventional STG methods, the symbolic STG is more concise, higher-level, has fewer states and is easier to specify. Based on the transition relation method and an event-driven scheduling technique to compute the symbolic states, we propose two algorithms to verify the circuit implementation with respect to its symbolic STGs. The algorithms can be used to find out a necessary condition for the implementation to satisfy the specification, which can be used for the allocation of design errors.<<ETX>>