An extended Kalman filtering approach to modeling nonlinear dynamic gene regulatory networks via short gene expression time series

Copyright [2009] IEEE. This material is posted here with permission of the IEEE. Such permission of the IEEE does not in any way imply IEEE endorsement of any of Brunel University's products or services. Internal or personal use of this material is permitted. However, permission to reprint/republish this material for advertising or promotional purposes or for creating new collective works for resale or redistribution must be obtained from the IEEE by writing to [email protected]. By choosing to view this document, you agree to all provisions of the copyright laws protecting it.In this paper, the extended Kalman filter (EKF) algorithm is applied to model the gene regulatory network from gene time series data. The gene regulatory network is considered as a nonlinear dynamic stochastic model that consists of the gene measurement equation and the gene regulation equation. After specifying the model structure, we apply the EKF algorithm for identifying both the model parameters and the actual value of gene expression levels. It is shown that the EKF algorithm is an online estimation algorithm that can identify a large number of parameters (including parameters of nonlinear functions) through iterative procedure by using a small number of observations. Four real-world gene expression data sets are employed to demonstrate the effectiveness of the EKF algorithm, and the obtained models are evaluated from the viewpoint of bioinformatics

Role of Interlayer Coupling on the Evolution of Band Edges in Few-Layer Phosphorene

Using first-principles calculations, we have investigated the evolution of band-edges in few-layer phosphorene as a function of the number of P layers. Our results predict that monolayer phosphorene is an indirect band gap semiconductor and its valence band edge is extremely sensitive to strain. Its band gap could undergo an indirect-to-direct transition under a lattice expansion as small as 1% along zigzag direction. A semi-empirical interlayer coupling model is proposed, which can well reproduce the evolution of valence band-edges obtained by first-principles calculations. We conclude that the interlayer coupling plays a dominated role in the evolution of the band-edges via decreasing both band gap and carrier effective masses with the increase of phosphorene thickness. A scrutiny of the orbital-decomposed band structure provides a better understanding of the upward shift of valence band maximum surpassing that of conduction band minimum.Comment: 25 pages, 9 figure

Enhanced Raman Detection System based on a Hollow-core Fiber Probe design

This paper focus on an enhanced Raman-based detection probe and its performance evaluated. The probe employs a hollow-core fiber design to allow liquid micro-sample to be analyzed. The hollow-core fiber is used both to transmit the light signal used to excite the sample and to collect the Raman scattering signal received from the micro-sample under analysis. In order to maximize the performance of the system, various parameters have been studied experimentally, including the diameter and the height of the liquid sample in the probe. The aim has been optimizing both as a means to enhance the Raman scattering signal received from the liquid sample. As a result, a Raman-based detection probe using a reflector approach was developed and evaluated. This design enabling a greater area for interaction with the sample to be formed and to concentrate the excitation light into it. This then increases the efficiency of the light-liquid interaction and improves the collection efficiently of the forward Raman scattering light signal. With the use of this design, the detected Raman scattering signal was increased by a factor of 103~104 over what otherwise would be achieved. A key feature is that with the use of a hollow-core fiber to collect the liquid sample, only a very small volume is needed, making this well suited to practical applications where limited amounts of material are available e.g. biofluids or high value liquids. The system designed and evaluated thus provides the basis of an effective all-fiber Raman-based detection system, capable of being incorporated into portable analysis equipment for rapid detection and in-the-field use

Multiple and virtual photon processes in radiation-induced magnetoresistance oscillations in two-dimensional electron systems

Recently discovered new structures and zero-resistance states outside the well-known oscillations are demonstrated to arise from multiphoton assisted processes, by a detailed analysis of microwave photoresistance in two-dimensional electron systems under enhanced radiation. The concomitant resistance dropping and peak narrowing observed in the experiments are also reproduced. We show that the radiation-induced suppression of average resistance comes from virtual photon effect and exists throughout the whole magnetic field range.Comment: 4 pages, 2 figures, published versio

Hadron-quark phase transition in asymmetric matter with dynamical quark masses

The two-Equation of State (EoS) model is used to describe the hadron-quark phase transition in asymmetric matter formed at high density in heavy-ion collisions. For the quark phase, the three-flavor Nambu--Jona-Lasinio (NJL) effective theory is used to investigate the influence of dynamical quark mass effects on the phase transition. At variance to the MIT-Bag results, with fixed current quark masses, the main important effect of the chiral dynamics is the appearance of an End-Point for the coexistence zone. We show that a first order hadron-quark phase transition may take place in the region T=(50-80)MeV and \rho_B=(2-4)\rho_0, which is possible to be probed in the new planned facilities, such as FAIR at GSI-Darmstadt and NICA at JINR-Dubna. From isospin properties of the mixed phase somepossible signals are suggested. The importance of chiral symmetry and dynamical quark mass on the hadron-quark phase transition is stressed. The difficulty of an exact location of Critical-End-Point comes from its appearance in a region of competition between chiral symmetry breaking and confinement, where our knowledge of effective QCD theories is still rather uncertain.Comment: 13 pages, 16 figures (revtex

Magnetoresistance oscillations in two-dimensional electron systems under monochromatic and bichromatic radiations

The magnetoresistance oscillations in high-mobility two-dimensional electron systems induced by two radiation fields of frequencies 31 GHz and 47 GHz, are analyzed in a wide magnetic-field range down to 100 G, using the balance-equation approach to magnetotransport for high-carrier-density systems. The frequency mixing processes are shown to be important. The predicted peak positions, relative heights, radiation-intensity dependence and their relation with monochromatic resistivities are in good agreement with recent experimental finding [M. A. Zudov {\it et al.} Phys. Rev. Lett. 96, 236804 (2006)].Comment: 4 pages, 3 figure

Fabrication of a high sensitive Ag-nanoparticle substrate and its application to the detection of toxic substances

Surface Enhanced Raman Scattering (SERS) is typically observed with the substrate in a liquid medium and it has been proposed as a promising technique for detecting low levels of pollutants in liquids. A technique is presented for self-assembly to immobilize Ag nanoparticles (Ag-NPs), with diameters ranging from 100 to 800nm on a solid support. Experimental results have been obtained through experiments using Ag-NPs active substrates to detect Rhodamine 6G (R6G) and crystal violet in the deionized water. Further, the SERS spectrum and Raman spectrum of phoxim were also measured, showing the enhancement in the performance of the active substrate as a result

TDLAS Detection of propane and butane gas over the near-infrared wavelength range from 1678nm to 1686nm

It is important in the petrochemical industry that there are high sensitivity, high accuracy, low-power consumption and intrinsically safe methods for the detection of propane, butane and their gas mixtures, to provide early warning of potential explosion hazards during both storage and transportation of oil and gas. This paper proposes a 'proof of principle' method for the detection of propane and butane using a Tunable Diode Laser Absorption Spectroscopy (TDLAS) technique over the near-infrared wavelength range from 1678nm to 1686nm. This method is relatively inexpensive to implement and is thus more practical, compared with detection methods using wavelengths further into the infra-red, near 3.3μm. The minimum detectable concentration was found to be low as 300ppm for propane or butane. Importantly, the relative measurement errors were all below 3% LEL, which meets the requirements from the petrochemical and oil-gas storage and transportation industries for a field-based system for monitoring of combustible gases

A homogeneous analysis of disks around brown dwarfs

We re-analyzed the Herschel/PACS data of a sample of 55 brown dwarfs (BDs) and very low mass stars with spectral types ranging from M5.5 to L0. We investigated the dependence of disk structure on the mass of the central object in the substellar regime based on a homogeneous analysis of Herschel data from flux density measurements to spectral energy distribution (SED) modeling. A systematic comparison between the derived disk properties and those of sun-like stars shows that the disk flaring of BDs and very low mass stars is generally smaller than that of their higher mass counterparts, the disk mass is orders of magnitude lower than the typical value found in T Tauri stars, and the disk scale heights are comparable in both sun-like stars and BDs. We further divided our sample into an early-type brown dwarf (ETBD) group and a late-type brown dwarf (LTBD) group by using spectral type (=M8) as the border criterion. We systematically compared the modeling results from Bayesian analysis between these two groups, and found the trends of flaring index as a function of spectral type also present in the substellar regime. The spectral type independence of the scale height is also seen between high-mass and very low-mass BDs. However, both the ETBD and LTBD groups feature a similar median disk mass of 10^{-5}Msun and no clear trend is visible in the distribution, probably due to the uncertainty in translating the far-IR photometry into disk mass, the detection bias and the age difference among the sample. Unlike previous studies, our analysis is completely homogeneous in Herschel/PACS data reduction and modeling with a statistically significant sample. Therefore, we present evidence of stellar-mass-dependent disk structure down to the substellar mass regime, which is important for planet formation models. (Abridged Version)Comment: Accepted for publication in A&