14367958
A new measure of the robustness of biochemical networks
MOTIVATION
The robustness of a biochemical network is defined as the tolerance of variations in kinetic parameters with respect to the maintenance of steady state. Robustness also plays an important role in the fail-safe mechanism in the evolutionary process of biochemical networks. The purposes of this paper are to use the synergism and saturation system (S-system) representation to describe a biochemical network and to develop a robustness measure of a biochemical network subject to variations in kinetic parameters. Since most biochemical networks in nature operate close to the steady state, we consider only the robustness measurement of a biochemical network at the steady state.


RESULTS
We show that the upper bound of the tolerated parameter variations is related to the system matrix of a biochemical network at the steady state. Using this upper bound, we can calculate the tolerance (robustness) of a biochemical network without testing many parametric perturbations. We find that a biochemical network with a large tolerance can also better attenuate the effects of variations in rate parameters and environments. Compensatory parameter variations and network redundancy are found to be important mechanisms for the robustness of biochemical networks. Finally, four biochemical networks, such as a cascaded biochemical network, the glycolytic-glycogenolytic pathway in a perfused rat liver, the tricarboxylic acid cycle in Dictyostelium discoideum and the cAMP oscillation network in bacterial chemotaxis, are used to illustrate the usefulness of the proposed robustness measure.
5294188
Method for identifying transcription factor binding sites in yeast
MOTIVATION
Identifying transcription factor binding sites (TFBSs) is helpful for understanding the mechanism of transcriptional regulation. The abundance and the diversity of genomic data provide an excellent opportunity for identifying TFBSs. Developing methods to integrate various types of data has become a major trend in this pursuit.


RESULTS
We develop a TFBS identification method, TFBSfinder, which utilizes several data sources, including DNA sequences, phylogenetic information, microarray data and ChIP-chip data. For a TF, TFBSfinder rigorously selects a set of reliable target genes and a set of non-target genes (as a background set) to find overrepresented and conserved motifs in target genes. A new metric for measuring the degree of conservation at a binding site across species and methods for clustering motifs and for inferring position weight matrices are proposed. For synthetic data and yeast cell cycle TFs, TFBSfinder identifies motifs that are highly similar to known consensuses. Moreover, TFBSfinder outperforms well-known methods.


AVAILABILITY
http://cg1.iis.sinica.edu.tw/~TFBSfinder/.
5910842
Quantitative characterization of the transcriptional regulatory network in the yeast cell cycle
MOTIVATION
Genome-wide gene expression programs have been monitored and analyzed in the yeast Saccharomyces cerevisiae, but how cells regulate global gene expression programs in response to environmental changes is still far from being understood. We present a systematic approach to quantitatively characterize the transcriptional regulatory network of the yeast cell cycle. For the interpretative purpose, 20 target genes were selected because their expression patterns fluctuated in a periodic manner concurrent with the cell cycle and peaked at different phases. In addition to the most significant five possible regulators of each specific target gene, the expression pattern of each target gene affected by synergy of the regulators during the cell cycle was characterized. Our first step includes modeling the dynamics of gene expression and extracting the transcription rate from a time-course microarray data. The second step embraces finding the regulators that possess a high correlation with the transcription rate of the target gene, and quantifying the regulatory abilities of the identified regulators.


RESULTS
Our network discerns not only the role of the activator or repressor for each specific regulator, but also the regulatory ability of the regulator to the transcription rate of the target gene. The highly coordinated regulatory network has identified a group of significant regulators responsible for the gene expression program through the cell cycle progress. This approach may be useful for computing the regulatory ability of the transcriptional regulatory networks in more diverse conditions and in more complex eukaryotes.


SUPPLEMENTARY INFORMATION
Matlab code and test data are available at http://www.ee.nthu.edu.tw/~bschen/quantitative/regulatory_network.htm
6073358
Non-photorealistic virtual environments
We describe a system for non-photorealistic rendering (NPR) of virtual environments. In real time, it synthesizes imagery of architectural interiors using stroke-based textures. We address the four main challenges of such a system — interactivity, visual detail, controlled stroke size, and frame-to-frame coherence — through image based rendering (IBR) methods. In a preprocessing stage, we capture photos of a real or synthetic environment, map the photos to a coarse model of the environment, and run a series of NPR filters to generate textures. At runtime, the system re-renders the NPR textures over the geometry of the coarse model, and it adds dark lines that emphasize creases and silhouettes. We provide a method for constructing non-photorealistic textures from photographs that largely avoids seams in the resulting imagery. We also offer a new construction, art-maps, to control stroke size across the images. Finally, we show a working system that provides an immersive experience rendered in a variety of NPR styles.
32428574
Actual holding times for calls in a PCS network
The explicit distribution function of the actual holding time of a new call in a PCS network, with general cell residence time and general requested call holding time, is obtained. The effective call holding time of an incompleted and of completed calls are shown to be the conditional actual holding time of an incompleted call and of a completed call, respectively. If the holding time is of Erlang or if both the residence and requested call holding times belong to the class of new better than used (NBU), we proved that the mean effective call holding time of an incompleted call is less than the mean requested call holding time of a call. For any kind of random variables of the residence time and requested call holding time, we proved that the mean effective call holding time of a completed call is always less than the mean requested call holding time of a call.
18767466
Spectra of Regular Graphs and Hypergraphs and Orthogonal Polynomials
Abstract In this paper we study the distribution of eigenvalues of regular graphs, regular hypergraphs, and biregular bipartite graphs of given girth by considering the polynomials orthogonal with respect to the measures attached to the spectra of such graphs and to the continuous spectra of their ‘universal covers’. Our estimates are tight for Biggs graphs and generalized polygons. We also give an application to the distribution of eigenvalues of Hecke operators acting on weight 2 cusp forms for certain congruence subgroups.
18531635
A generalized model for network survivability
The high expectation of network to be available and perform at all time has created growing concerns between network operators and engineers all over the globe. Network should be available to users whenever they want to use them. In the wake of an attack, network should be also able to recover as soon as possible. A survivable network is one that can provide services in the presence of an attack or failure and be able to recover fully in a timely manner. Designing a model for network survivability basically involves the understanding of three key issues, i.e, how the system will function in the wake of failures, what will be the impact of failures on the user, and how to overcome these failures. To achieve these goals, this paper proposes a quantitative approach to evaluate the network survivability in terms of using a generalized model; we consider a more complex system with several faults to study the survivability of a network using Markov chain. In presenting a better survivability performance, some numerical comparisons for the network availability, failure frequency and survivability is also developed.
34801552
Profile-based event tracking
In this research, we focus on tracking topics that originate and evolve from a specific event. Intuitively, a few key elements of a target event, such as date, location, and persons involved, would be enough for making a decision on whether a test story is on-topic. Consequently, a profile-based event tracking method is proposed. We attempt to build an event profile from the given on-topic stories by robust information retrieval technologies. A feature selection metric and a recognized event clause are utilized to determine most (if not all) key semantic elements of the target event. Preliminary experiments on the TDT2 mandarin corpus show that this profile-based event tracking method is promising.