Comparing the biological coherence of network clusters identified by different detection algorithms

Protein-protein interaction networks serve to carry out basic molecular activity in the cell. Detecting the modular structures from the protein-protein interaction network is important for understanding the organization, function and dynamics of a biological system. In order to identify functional neighbor- hoods based on network topology, many network cluster identification algorithms have been devel- oped. However, each algorithm might dissect a network from a different aspect and may provide dif- ferent insight on the network partition. In order to objectively evaluate the performance of four com- monly used cluster detection algorithms: molecular complex detection (MCODE), NetworkBlast, shortest-distance clustering (SDC) and Girvan-Newman (G-N) algorithm, we compared the biological coherence of the network clusters found by these algorithms through a uniform evaluation framework. Each algorithm was utilized to find network clusters in two different protein-protein interaction net- works with various parameters. Comparison of the resulting network clusters indicates that clusters found by MCODE and SDC are of higher biological coherence than those by NetworkBlast and G-N algorithm.     

Research on the Bit Computation Model for Time Variable Channel Bandwidth

For the encoding bit-rate problem in H.264 wireless video communication,this paper analyzes the bit-rate computation model and the Mean Square Error distortion model,establishes the relation between the quantization parameter of the encoding bit-rate and the intra frame refresh rate of the macro block,and put forward a new ideal about the coding rate on the basis of general binomial computation model theory. Furthermore,this method not only can adaptively adjust the bit allocation and quantization parameter and prevents buffer from overflowing downward or upward under given network bandwidth,but also can apply the rate-distortion to optimize the solution method,control the encoding bits accurately and optimizes the allocation between the intra and inter frame encoding macro block.     

The Response of Debris-Flow Events to Solar Proton Flares （Ⅰ）

By analyzing the observation data from Dongchuan Debris Flow Observation and Research Station and historical data from year 1965 to 1990 gotten from National Astronomical Ob-servatories/Yunnan Observatory,the responding of debris flow in Jiangjia Ravine to Solar Proton Flare is studied. The following conclusion can be drawn. Solar Proton Flare,as one of most im-portant astronomical factors,affects the activity of debris flow in Yunnan. Generally,from 1965 to1990,the more active Solar Pro-ton Flare is,the greater the probability of high frequency and large runoff of debris flow is. On the contrary,the less active Solar Pro-ton Flare is,the greater the probability of low frequency,small runoff,and low sediment transport of debris flow is.     

Investigation of Highly Designable Dented Structures in HP Model with Hydrogen Bond Energy

Some highly designable protein structures have dented on the surface of their native structures, and are not full compactly folded. According to hydrophobic-polar （HP） model the most designable structures are full compactly folded. To investigate the designability of the dented structures, we introduce the hydrogen bond energy in the secondary structures by using the secondary-structure-favored HP model proposed by Ou-yang etc. The result shows that the average designability increases with the strength of the hydrogen bond. The designabilities of the structures with same dented shape increase exponentially with the number of secondary structure sites. The dented structures can have the highest designabilities for a certain value of hydrogen bond energy density.     

Density functional theory study on the insertion reaction mechanism of dibromocarbene with formaldehyde

The insertion reaction mechanism of CBr2 with CH3CH2O has been studied by using the B3LYP/6-311G(d) and CCSD(T)/6-311G(d) at single point. The geometries of reactions,transition state and products were completely optimized. All the transition state is verified by the vibrational analysis and the internal re-action coordinate (IRC) calculations. The results show that reaction (1) is the dominant reaction path,which proceeds via two steps: i) two reactants form an intermediate (IM1),which is an exothermal re-action of 8.62 kJ·mol?1 without energy barrier; ii) P1 is obtained via the TS1 and the H-shift,in which the energy barrier is 44.53 kJ·mol?1. The statistical thermodynamics and Eyring transition state theory with Wigner correction are used to study the thermodynamic and kinetic characters of this reaction in temperature range from 100 to 2200 K. The results show that the appropriate reaction temperature ranges from 200 to 1900 K at 1.0 atm,in which the reaction has a bigger spontaneity capability,equi-librium constant (K) and higher rate constant (k).     

Determining method and conditional factors of electrochemical fingerprint of Chinese traditional medicine

The thermodynamic systems and kinetic model suitable for the electrochemical token of the compo-nent throng in Chinese traditional medicines have been analyzed. It has been indicated that the damp oscillatory reactions in the non-equilibrium close system and open system without the supplement of dissipative substance have important significance for the throng token and analysis of chemical com-ponents in Chinese traditional medicines. Various factors influencing the electrochemical fingerprint,such as reactant species and their concentrations,electrode types,temperature,stir rate,the kind,dosage and granularity of Chinese traditional medicines,have amply been researched by the B-Z os-cillatory reaction which used malonic acid as a main dissipative substance. In addition,the quantitative information about the chemical components in Chinese traditional medicines has been discussed in detail. The method and its conditions for determining the electrochemical fingerprint used in scientifi-cally distinguishing and evaluating Chinese traditional medicines have successfully been put forward.     

IL-1β regulates the mouse Fas ligand expression in corneal endothelial cells

Constitutively expressed Fas ligand (FasL) in several distinct epithelial cell types appears to protect tissues by inducing apoptosis of Fas immune cells during inflammatory reactions. To study the rela-tionship of FasL and inflammation process in cornea,we examined the effects of inflammatory cytokine IL-1β on the FasL production,expression and cytotoxic function in corneal endothelial cells. In this paper,we demonstrate that IL-1β inhibits the FasL production and expression in corneal endothelial cells. The promoter activities of FasL in these cells are reduced by IL-1β in a dose-dependent manner. Finally,we also find that IL-1β block the cytotoxic effects of FasL derived from corneal endothelial cells to the Fas target cells. These data support the view that FasL derived from corneal endothelial cells modulate inflammation within cornea.     

Analysis of fragrance composition in three cultivars of <Emphasis Type="Italic">Osmanthus fragrans</Emphasis> Albus group flower by gas chromatography-mass spectrometry

With supercritical CO2 fluid extraction(SCFE), essential oil was extracted from three cultivars of Xianning osmanthus. The fresh osmanthus flower was processed with a petroleum ether digestion method to produce the extractum. The yields of essential oil and extractum were 0.19 % and 0.13 % (m/m) respectively. The essential oil and fragrance composition and content extracted were analyzed with gas chromatography-mass spectrometer (GC-MS). The result showed that essential oil contained 36.99%(area/total area) of ionone, ionol and 13.11% of linalool; ionone and ionol contained in extractum were as high as up to 33.33%, while linalool up to 21.92%. Whether essential oil or extractum contains only about 40% fat acid and other ester matters. None of environmental estrogen (phthalic ester) was found in fragrance ingredients. The result also showed that the quality of O. fragrans Albus group fragrance in Xianning is better than that produced in Hangzhou and Anhui districts.     

Normalized transfer function for characterizing conversion efficiency and harmonic distortion of all-optical sampling

A novel method for characterizing the nonlinearity of all-optical sampling is proposed based on the normalized transfer function.Simulation results demonstrate the effectiveness of our method.Furthermore,an all-optical sampling experiment is performed to verify our method.Both simulation and experiment show consistency between our method and the measurements.The method only requires normalization and polynomial fitting of the transfer curve,and enables direct expression of the nonlinearity with the coefficients of the normalized transfer function.     

A venomous arthropod in the Early Cambrian Sea

A number of recently evolved animals possess poison glands for feeding and/or defense.However,examples of such animals are rare in the fossil record.We report a fossil arthropod Isoxys curvirostratus from the Early Cambrian Chengjiang biota of China.This species is regarded as the oldest known venomous arthropod based on the presence of venomous glands in its head region.The adult animal is 2-5 cm long and the body is covered entirely with a carapace.The presence of large stalk eyes and a pair of stout grasping appendages with a terminal spine suggest it was raptorial.Interestingly,the two pear-shaped,three-dimensionally preserved objects that are present in the head region and at the base of the grasping appendages closely resemble the venom glands of some living arthropods in size,shape,and position.These features indicate that the presence of venomous predators could date back 520 million years.Furthermore,our observations suggest that the feeding strategies and organs adapted for this purpose had already reached a high level of diversity and anatomical sophistication in the Early Cambrian ecosystems.