Gene-network inference by message passing

The inference of gene-regulatory processes from gene-expression data belongs to the major challenges of computational systems biology. Here we address the problem from a statistical-physics perspective and develop a message-passing algorithm which is able to infer sparse, directed and combinatorial regulatory mechanisms. Using the replica technique, the algorithmic performance can be characterized analytically for artificially generated data. The algorithm is applied to genome-wide expression data of baker's yeast under various environmental conditions. We find clear cases of combinatorial control, and enrichment in common functional annotations of regulated genes and their regulators.Comment: Proc. of International Workshop on Statistical-Mechanical Informatics 2007, Kyot

Gene-network inference by message passing

The inference of gene-regulatory processes from gene-expression data belongs to the major challenges of computational systems biology. Here we address the problem from a statistical-physics perspective and develop a message-passing algorithm which is able to infer sparse, directed and combinatorial regulatory mechanisms. Using the replica technique, the algorithmic performance can be characterized analytically for artificially generated data. The algorithm is applied to genome-wide expression data of baker's yeast under various environmental conditions. We find clear cases of combinatorial control, and enrichment in common functional annotations of regulated genes and their regulators.Comment: Proc. of International Workshop on Statistical-Mechanical Informatics 2007, Kyot

Gene-network inference by message passing

The inference of gene-regulatory processes from gene-expression data belongs to the major challenges of computational systems biology. Here we address the problem from a statistical-physics perspective and develop a message-passing algorithm which is able to infer sparse, directed and combinatorial regulatory mechanisms. Using the replica technique, the algorithmic performance can be characterized analytically for artificially generated data. The algorithm is applied to genome-wide expression data of baker's yeast under various environmental conditions. We find clear cases of combinatorial control, and enrichment in common functional annotations of regulated genes and their regulators.Comment: Proc. of International Workshop on Statistical-Mechanical Informatics 2007, Kyot

Resection Cavity Contraction Effects in the Use of Radioactive Sources (1-25 versus Cs-131) for Intra-Operative Brain Implants.

Background and Objectives Intra-parenchymal brain surgical resection cavities usually contract in volume following low dose rate (LDR) brachytherapy implants. In this study, we systematically modeled and assessed dose variability resulting from such changes for I-125 versus Cs-131 radioactive sources. Methods Resection cavity contraction was modeled based on 95 consecutive patient cases, using surveillance magnetic resonance (MR) images. The model was derived for single point source geometry and then fully simulated in 3D where I-125 or Cs-131 seeds were placed on the surface of an ellipsoidal resection cavity. Dose distribution estimated via TG-43 calculations and biological effective dose (BED) calculations were compared for both I-125 and Cs-131, accounting for resection cavity contractions. Results Resection cavity volumes were found to contract with an effective half-life of approximately 3.4 months (time to reach 50% of maximum volume contraction). As a result, significant differences in dose distributions were noted between I-125 and Cs-131 radioactive sources. For example, when comparing with static volume, assuming no contraction effect, I-125 exhibited a 31.8% and 30.5% increase in D90 and D10 values (i.e., the minimal dose to 90% and 10% of the volume respectively) in the peripheral target areas over the follow-up period of 20.5 months. In contrast, Cs-131 seeds only exhibited a 1.44% and 0.64% increase in D90 and D10 values respectively. Such discrepancy is likewise similar for BED calculations. Conclusion Resection cavity contractions affects Cs-131 dose distribution significantly less than that of I-125 for permanent brain implants. Care must be taken to account for cavity contractions when prescribing accumulative doses of a radioactive source in performing the brain implant procedures

Universal cloning of continuous quantum variables

The cloning of quantum variables with continuous spectra is analyzed. A universal - or Gaussian - quantum cloning machine is exhibited that copies equally well the states of two conjugate variables such as position and momentum. It also duplicates all coherent states with a fidelity of 2/3. More generally, the copies are shown to obey a no-cloning Heisenberg-like uncertainty relation.Comment: 4 pages, RevTex. Minor revisions, added explicit cloning transformation, added reference

Jamming in complex networks with degree correlation

We study the effects of the degree-degree correlations on the pressure congestion J when we apply a dynamical process on scale free complex networks using the gradient network approach. We find that the pressure congestion for disassortative (assortative) networks is lower (bigger) than the one for uncorrelated networks which allow us to affirm that disassortative networks enhance transport through them. This result agree with the fact that many real world transportation networks naturally evolve to this kind of correlation. We explain our results showing that for the disassortative case the clusters in the gradient network turn out to be as much elongated as possible, reducing the pressure congestion J and observing the opposite behavior for the assortative case. Finally we apply our model to real world networks, and the results agree with our theoretical model

Multipartite entanglement for continuous variables: A quantum teleportation network

We show that {\it one} single-mode squeezed state distributed among $N$ parties using linear optics suffices to produce a truly $N$-partite entangled state for any nonzero squeezing and arbitrarily many parties. From this $N$-partite entangled state, via quadrature measurements of $N-2$ modes, bipartite entanglement between any two of the $N$ parties can be `distilled', which enables quantum teleportation with an experimentally determinable fidelity better than could be achieved in any classical scheme.Comment: 4 pages, 2 figures, published version, paper shorter, title longe

Entangling two distant nanocavities via a waveguide

In this paper, we investigate the generation of continuous variable entanglement between two spatially-separate nanocavities mediated by a coupled resonator optical waveguide in photonic crystals. By solving the exact dynamics of the cavity system coupled to the waveguide, the entanglement and purity of the two-mode cavity state are discussed in detail for the initially separated squeezing inputs. It is found that the stable and pure entangled state of the two distant nanocavities can be achieved with the requirement of only a weak cavity-waveguide coupling when the cavities are resonant with the band center of the waveguide. The strong couplings between the cavities and the waveguide lead to the entanglement sudden death and sudden birth. When the frequencies of the cavities lie outside the band of the waveguide, the waveguide-induced cross frequency shift between the cavities can optimize the achievable entanglement. It is also shown that the entanglement can be easily manipulated through the changes of the cavity frequencies within the waveguide band.Comment: 8 pages, 8 figure