Novel Markov model of induced pluripotency predicts gene expression changes in reprogramming

<p>Abstract</p> <p>Background</p> <p>Somatic cells can be reprogrammed to induced-pluripotent stem cells (iPSCs) by introducing few reprogramming factors, which challenges the long held view that cell differentiation is irreversible. However, the mechanism of induced pluripotency is still unknown.</p> <p>Methods</p> <p>Inspired by the phenomenological reprogramming model of Artyomov et al (2010), we proposed a novel Markov model, stepwise reprogramming Markov (SRM) model, with simpler gene regulation rules and explored various properties of the model with Monte Carlo simulation. We calculated the reprogramming rate and showed that it would increase in the condition of knockdown of somatic transcription factors or inhibition of DNA methylation globally, consistent with the real reprogramming experiments. Furthermore, we demonstrated the utility of our model by testing it with the real dynamic gene expression data spanning across different intermediate stages in the iPS reprogramming process.</p> <p>Results</p> <p>The gene expression data at several stages in reprogramming and the reprogramming rate under several typically experiment conditions coincided with our simulation results. The function of reprogramming factors and gene expression change during reprogramming could be partly explained by our model reasonably well.</p> <p>Conclusions</p> <p>This lands further support on our general rules of gene regulation network in iPSC reprogramming. This model may help uncover the basic mechanism of reprogramming and improve the efficiency of converting somatic cells to iPSCs.</p

COMPUTER SIMULATION OF "SPLASH CONTROL IN COMPETITIVE DIVING

The purpose of the study was to examine the relationship between the hand pattern and the water splash height during a diver's entry using a computer simulation method. A physical and mathematical model of the impact of a wedged solid object with an ideal fluid was developed. The motion equation (interaction function of solid and fluid) of the solid was established with satisfaction of control functions and initial boundary conditions of the fluid. A finite element method was used to simulate the impact process, with the wedge angle changed from 4" to 80- during the impact. The results suggested that the fluid splash height is inversely proportional to the wedge angle. The "splash control" technique derived from the simulation was also applied in training professional divers and positive results were obtained

Influence of fluid temperature gradient on the flow within the shaft gap of a PLR pump

In nuclear power plants the primary-loop recirculation (PLR) pump circulates the high temperature/high-pressure coolant in order to remove the thermal energy generated within the reactor. The pump is sealed using the cold purge flow in the shaft seal gap between the rotating shaft and stationary casing, where different forms of Taylor–Couette flow instabilities develop. Due to the temperature difference between the hot recirculating water and the cold purge water (of order of 200 °C), the flow instabilities in the gap cause temperature fluctuations, which can lead to shaft or casing thermal fatigue cracks. The present work numerically investigated the influence of temperature difference and rotating speed on the structure and dynamics of the Taylor–Couette flow instabilities. The CFD solver used in this study was extensively validated against the experimental data published in the open literature. Influence of temperature difference on the fluid dynamics of Taylor vortices was investigated in this study. With large temperature difference, the structure of the Taylor vortices is greatly stretched at the interface region between the annulus gap and the lower recirculating cavity. Higher temperature difference and rotating speed induce lower fluctuating frequency and smaller circumferential wave number of Taylor vortices. However, the azimuthal wave speed remains unchanged with all the cases tested. The predicted axial location of the maximum temperature fluctuation on the shaft is in a good agreement with the experimental data, identifying the region potentially affected by the thermal fatigue. The physical understandings of such flow instabilities presented in this paper would be useful for future PLR pump design optimization

Biological Nitrogen Removal through Nitritation Coupled with Thiosulfate-Driven Denitritation.

A novel biological nitrogen removal system based on nitritation coupled with thiosulfate-driven denitritation (Nitritation-TDD) was developed to achieve a high nitrogen removal rate and low sludge production. A nitritation sequential batch reactor (nitritation SBR) and an anoxic up-flow sludge bed (AnUSB) reactor were applied for effective nitritation and denitritation, respectively. Above 75% nitrite was accumulated in the nitritation SBR with an influent ammonia loading rate of 0.43 kg N/d/m(3). During Nitritation-TDD operation, particle sizes (d50) of the sludge decreased from 406 to 225 um in nitritation SBR and from 327-183 um in AnUSB reactor. Pyrosequencing tests revealed that ammonium-oxidizing bacteria (AOB) population was stabilized at approximately 7.0% (calculated as population of AOB-related genus divided by the total microbial population) in the nitritation SBR. In contrast, nitrite-oxidizing bacteria (NOB) population decreased from 6.5-0.6% over the same time, indicating the effective nitrite accumulation in the nitritation SBR. Thiobacillus, accounting for 34.2% in the AnUSB reactor, was mainly responsible for nitrogen removal via autotrophic denitritation, using an external source of thiosulfate as electron donor. Also, it was found that free nitrous acid could directly affect the denitritation activity