Inferring gene regulatory networks from gene expression data by a dynamic Bayesian network-based model

Enabled by recent advances in bioinformatics, the inference of gene regulatory networks (GRNs) from gene expression data has garnered much interest from researchers. This is due to the need of researchers to understand the dynamic behavior and uncover the vast information lay hidden within the networks. In this regard, dynamic Bayesian network (DBN) is extensively used to infer GRNs due to its ability to handle time-series microarray data and modeling feedback loops. However, the efficiency of DBN in inferring GRNs is often hampered by missing values in expression data, and excessive computation time due to the large search space whereby DBN treats all genes as potential regulators for a target gene. In this paper, we proposed a DBN-based model with missing values imputation to improve inference efficiency, and potential regulators detection which aims to lessen computation time by limiting potential regulators based on expression changes. The performance of the proposed model is assessed by using time-series expression data of yeast cell cycle. The experimental results showed reduced computation time and improved efficiency in detecting gene-gene relationships

Exploring the Way to Approach the Efficiency Limit of Perovskite Solar Cells by Drift-Diffusion Model

Drift-diffusion model is an indispensable modeling tool to understand the carrier dynamics (transport, recombination, and collection) and simulate practical-efficiency of solar cells (SCs) through taking into account various carrier recombination losses existing in multilayered device structures. Exploring the way to predict and approach the SC efficiency limit by using the drift-diffusion model will enable us to gain more physical insights and design guidelines for emerging photovoltaics, particularly perovskite solar cells. Our work finds out that two procedures are the prerequisites for predicting and approaching the SC efficiency limit. Firstly, the intrinsic radiative recombination needs to be corrected after adopting optical designs which will significantly affect the open-circuit voltage at its Shockley-Queisser limit. Through considering a detailed balance between emission and absorption of semiconductor materials at the thermal equilibrium, and the Boltzmann statistics at the non-equilibrium, we offer a different approach to derive the accurate expression of intrinsic radiative recombination with the optical corrections for semiconductor materials. The new expression captures light trapping of the absorbed photons and angular restriction of the emitted photons simultaneously, which are ignored in the traditional Roosbroeck-Shockley expression. Secondly, the contact characteristics of the electrodes need to be carefully engineered to eliminate the charge accumulation and surface recombination at the electrodes. The selective contact or blocking layer incorporated nonselective contact that inhibits the surface recombination at the electrode is another important prerequisite. With the two procedures, the accurate prediction of efficiency limit and precise evaluation of efficiency degradation for perovskite solar cells are attainable by the drift-diffusion model.Comment: 32 pages, 11 figure

Energy Extraction From Gravitational Collapse to Static Black Holes

The mass--energy formula of black holes implies that up to 50% of the energy can be extracted from a static black hole. Such a result is reexamined using the recently established analytic formulas for the collapse of a shell and expression for the irreducible mass of a static black hole. It is shown that the efficiency of energy extraction process during the formation of the black hole is linked in an essential way to the gravitational binding energy, the formation of the horizon and the reduction of the kinetic energy of implosion. Here a maximum efficiency of 50% in the extraction of the mass energy is shown to be generally attainable in the collapse of a spherically symmetric shell: surprisingly this result holds as well in the two limiting cases of the Schwarzschild and extreme Reissner-Nordstr\"{o}m space-times. Moreover, the analytic expression recently found for the implosion of a spherical shell onto an already formed black hole leads to a new exact analytic expression for the energy extraction which results in an efficiency strictly less than 100% for any physical implementable process. There appears to be no incompatibility between General Relativity and Thermodynamics at this classical level.Comment: 7 pages, 2 figures, to appear on Int. Journ. Mod. Phys.

Efficiency at maximum power: An analytically solvable model for stochastic heat engines

We study a class of cyclic Brownian heat engines in the framework of finite-time thermodynamics. For infinitely long cycle times, the engine works at the Carnot efficiency limit producing, however, zero power. For the efficiency at maximum power, we find a universal expression, different from the endoreversible Curzon-Ahlborn efficiency. Our results are illustrated with a simple one-dimensional engine working in and with a time-dependent harmonic potential.Comment: 6 pages, 3 figure

Polarization-independent wavelength conversion at 2.5 Gb/s by dual-pump four-wave mixing in a strained semiconductor optical amplifier

We give a general expression for the polarization dependence of the four-wave mixing (FWM) efficiency in the dual-pump configuration. This expression, along with some general properties of the FWM susceptibility tensor, is used to propose a simple scheme to generate a nearly (1.5-dB variation) polarization independent FWM converted signal. The viability of this scheme is verified in a wavelength conversion experiment at 2.5 Gb/s

Effect of genotype on duodenal expression of nutrient transporter genes in dairy cows

peer-reviewedBackground Studies have shown clear differences between dairy breeds in their feed intake and production efficiencies. The duodenum is critical in the coordination of digestion and absorption of nutrients. This study examined gene transcript abundance of important classes of nutrient transporters in the duodenum of non lactating dairy cows of different feed efficiency potential, namely Holstein-Friesian (HF), Jersey (JE) and their F1 hybrid. Duodenal epithelial tissue was collected at slaughter and stored at -80°C. Total RNA was extracted from tissue and reverse transcribed to generate cDNA. Gene expression of the following transporters, namely nucleoside; amino acid; sugar; mineral; and lipid transporters was measured using quantitative real-time RT-PCR. Data were statistically analysed using mixed models ANOVA in SAS. Orthogonal contrasts were used to test for potential heterotic effects and spearman correlation coefficients calculated to determine potential associations amongst gene expression values and production efficiency variables. Results While there were no direct effects of genotype on expression values for any of the genes examined, there was evidence for a heterotic effect (P < 0.05) on ABCG8, in the form of increased expression in the F1 genotype compared to either of the two parent breeds. Additionally, a tendency for increased expression of the amino acid transporters, SLC3A1 (P = 0.072), SLC3A2 (P = 0.081) and SLC6A14 (P = 0.072) was also evident in the F1 genotype. A negative (P < 0.05) association was identified between the expression of the glucose transporter gene SLC5A1 and total lactational milk solids yield, corrected for body weight. Positive correlations (P < 0.05) were also observed between the expression values of genes involved in common transporter roles. Conclusion This study suggests that differences in the expression of sterol and amino acid transporters in the duodenum could contribute towards the documented differences in feed efficiency between HF, JE and their F1 hybrid. Furthermore, positive associations between the expression of genes involved in common transporter roles suggest that these may be co-regulated. The study identifies potential candidates for investigation of genetic variants regulating nutrient transport and absorption in the duodenum in dairy cows, which may be incorporated into future breeding programmes

Quantum efficiency of single-photon sources in the cavity-QED strong-coupling regime

We calculate the integrated-pulse quantum efficiency of single-photon sources in the cavity quantum electrodynamics (QED) strong-coupling regime. An analytical expression for the quantum efficiency is obtained in the Weisskopf-Wigner approximation. Optimal conditions for a high quantum efficiency and a temporally localized photon emission rate are examined. We show the condition under which the earlier result of Law and Kimble [J. Mod. Opt. 44, 2067 (1997)] can be used as the first approximation to our result.Comment: 8 pages, 3 figures, final version, tex file uploade