Selection of thermodynamic models for combinatorial control of multiple transcription factors in early differentiation of embryonic stem cells

<p>Abstract</p> <p>Background</p> <p>Transcription factors (TFs) have multiple combinatorial forms to regulate the transcription of a target gene. For example, one TF can help another TF to stabilize onto regulatory DNA sequence and the other TF may attract RNA polymerase (RNAP) to start transcription; alternatively, two TFs may both interact with both the DNA sequence and the RNAP. The different forms of TF-TF interaction have different effects on the probability of RNAP's binding onto the promoter sequence and therefore confer different transcriptional efficiencies.</p> <p>Results</p> <p>We have developed an analytical method to identify the thermodynamic model that best describes the form of TF-TF interaction among a set of TF interactions for every target gene. In this method, time-course microarray data are used to estimate the steady state concentration of the transcript of a target gene, as well as the relative changes of the active concentration for each TF. These estimated concentrations and changes of concentrations are fed into an inference scheme to identify the most compatible thermodynamic model. Such a model represents a particular way of combinatorial control by multiple TFs on a target gene.</p> <p>Conclusions</p> <p>Applying this approach to a time-course microarray dataset of embryonic stem cells, we have inferred five interaction patterns among three regulators, Oct4, Sox2 and Nanog, on ten target genes.</p

An hourglass model for the flare of HST-1 in M87

To explain the multi-wavelength light curves (from radio to X-ray) of HST-1 in the M87 jet, we propose an hourglass model that is a modified two-zone system of Tavecchio & Ghisellini (hereafter TG08): a slow hourglass-shaped or Laval nozzle-shaped layer connected by two revolving exponential surfaces surrounding a fast spine, through which plasma blobs flow. Based on the conservation of magnetic flux, the magnetic field changes along the axis of the hourglass. We adopt the result of TG08---the high-energy emission from GeV to TeV can be produced through inverse Compton by the two-zone system, and the photons from radio to X-ray are mainly radiated by the fast inner zone system. Here, we only discuss the light curves of the fast inner blob from radio to X-ray. When a compressible blob travels down the axis of the first bulb in the hourglass, because of magnetic flux conservation, its cross section experiences an adiabatic compression process, which results in particle acceleration and the brightening of HST-1. When the blob moves into the second bulb of the hourglass, because of magnetic flux conservation, the dimming of the knot occurs along with an adiabatic expansion of its cross section. A similar broken exponential function could fit the TeV peaks in M87, which may imply a correlation between the TeV flares of M87 and the light curves from radio to X-ray in HST-1. The Very Large Array (VLA) 22 GHz radio light curve of HST-1 verifies our prediction based on the model fit to the main peak of the VLA 15 GHz radio light curve.Comment: 14 pages, 2 figures, accepted for publication in A

Measurement-device-independent QKD with Modified Coherent State

The measurement-device-independent quantum key distribution (MDI-QKD) protocol has been proposed for the purpose of removing the detector side channel attacks. Due to the multi-photon events of coherent states sources, real-life implementations of MDI-QKD protocol must employ decoy states to beat the photon-number-splitting attack. Decoy states for MDI-QKD based on the weak coherent states have been studied recently. In this paper, we propose to perform MDI-QKD protocol with modified coherent states (MCS) sources. We simulate the performance of MDI-QKD with the decoy states based on MCS sources. And our simulation indicates that both the secure-key rate and transmission distance can be improved evidently with MCS sources.The physics behind this improvement is that the probability of multi-photon events of the MCS is lower than that of weak coherent states while at the same time the probability of single-photon is higher

Influence of oil film stiffness on natural characteristics of single-rotor three-input helicopter main gearbox

The elastohydrodynamic lubrication (EHL) contact model is established, the oil film stiffness is calculated based on Dowson-Higginson empirical minimum thickness equation. The vibration model of single-rotor three-input helicopter main reducer is proposed by lumped mass method, and nonlinear factors like oil film stiffness, dynamic meshing force are taken into account. The influence of oil film stiffness on system natural frequency is analyzed as well. The results show that oil film stiffness of the internal and external meshing pairs in the planetary gear system have greater impact on the natural frequency, which tends to destabilize the system. Therefore, the planetary gear train is the most crucial branch regarding the system splash lubrication. When all the oil film stiffness in the system are greater than 4×109 N/m, the natural frequencies tend to be stable. This study can provide the theoretical reference for the lubrication characteristics in the single-rotor multi-input helicopter

Factors Influencing the Perception of Seller Credibility in Online Reputation System: an Eye-Movement Approach

The current online reputation systems for online sellers face great challenges from bad-faith behavior such as malicious negative reviews, click farming, mismatch between images and commodities, and forged commodities. To optimize the design of online reputation systems, explore the consumer utilization of credit clues, and describe the law of mutual trust, this paper puts forth three hypotheses about the influencing factors of consumer perception of online seller credibility and integrates various research methods such as an eye-movement experiment, questionnaire survey, econometric analysis, and empirical research. To evaluate the three hypotheses, the display modes of commodities on a current e-commerce platform were optimized, and eye-movement experiments were conducted on original and optimized webpages. Results show that the display of sales growth, the refinement and tagging of review content significantly impacted consumer perception of seller credibility. Further, designers of online reputation systems were advised to display sales trends, provide personalized sales queries, and tag a variety of reviews for consumers to easily ascertain credible sellers. This advice helped curb bad-faith behavior