Molecular docking and 3D-QSAR study of pyranmycin derivatives against 16S rRNA A site

To understand pharmacophore properties of pyranmycin derivatives and to design novel inhibitors of 16S rRNA A site, comparative molecular field analysis (CoMFA) approach was applied to analyze three-dimensional quantitative structure-activity relationship (3D-QSAR) of 17 compounds. AutoDock 3.0.5 program was employed to locate the orientations and conformations of the inhibitors interacting with 16S rRNA A site. The interaction mode was demonstrated in the aspects of inhibitor conformation, hydrogen bonding and electrostatic interaction. Similar binding conformations of these inhibitors and good correlations between the calculated binding free energies and experimental biological activities suggest that the binding conformations of these inhibitors derived from docking procedure were reasonable. Robust and predictive 3D-QSAR model was obtained by CoMFA with q(2) values of 0.723 and 0.993 for cross-validated and noncross-validated, respectively. The 3D-QSAR model built here will provide clear guidelines for novel inhibitors design based on the Pyranmycin derivatives against 16S rRNA A site. (c) 2005 Elsevier B.V. All rights reserved.

Forecasting Daily Chlorophyll a Concentration during the Spring Phytoplankton Bloom Period in Xiangxi Bay of the Three-Gorges Reservoir by Means of a Recurrent Artificial Neural Network

A recurrent artificial neural network was used for 0-and 7-days-ahead forecasting of daily spring phytoplankton bloom dynamics in Xiangxi Bay of Three-Gorges Reservoir with meteorological, hydrological, and limnological parameters as input variables. Daily data from the depth of 0.5 m was used to train the model, and data from the depth of 2.0 m was used to validate the calibrated model. The trained model achieved reasonable accuracy in predicting the daily dynamics of chlorophyll a both in 0-and 7-days-ahead forecasting. In 0-day-ahead forecasting, the R-2 values of observed and predicted data were 0.85 for training and 0.89 for validating. In 7-days-ahead forecasting, the R-2 values of training and validating were 0.68 and 0.66, respectively. Sensitivity analysis indicated that most ecological relationships between chlorophyll a and input environmental variables in 0-and 7-days-ahead models were reasonable. In the 0-day model, Secchi depth, water temperature, and dissolved silicate were the most important factors influencing the daily dynamics of chlorophyll a. And in 7-days-ahead predicting model, chlorophyll a was sensitive to most environmental variables except water level, DO, and NH3N.

Nonylphenol and octylphenol in urban eutrophic lakes of the subtropical China

The paper studied two estrogenic pollutants, 4-nonylphenol (NP) and 4-tert-octylphenol (OP) in water, suspended particle (SP) and sediments in urban eutrophic lakes. The concentrations of NP ranged from 1.94 to 32.85 mu g/l, 0.876 to 31.13 mu g/l and 3.54 to 32.43 mu g/g dry weight (dw) in water, suspended particle (SP) and sediments, respectively, and that of OP from 0.027 to 1.44 mu g/l, 0.008 to 1.777 mu g/l and 0.058 to 1.245 mu g/g dw in water, suspended particle (SP) and sediments, respectively. An increasing trend in the concentration was noticed in all matrices close to the sewage inlets, which was found to be the major factor affecting the spatial distribution of alkylphenols (APs) in the lakes. Due to restoration of submerged macrophytes, which might accumulate APs, the contaminations of APs in the Little Moon Lake (LML) and the Little Lotus Lake (LLL) were lower than those in the Big, Moon Lake (BML) and the Bier Lotus Lake (BLL). A reasonable correlation of NP and OP was obtained among water, suspended particle and sediment. The possible environmental stress of APs concentration on aquatic organisms in Wuhan urban lakes was also discussed.

Genetic structure and low-genetic diversity suggesting the necessity for conservation of the Chinese Longsnout catfish, Leiocassis longirostris (Pisces : Bagriidae)

Genetic variation and phylogenetic relationship of Leiocassis longirostris populations from the Yangtze River were investigated at mitochondrial DNA level. The samples were collected from the upstream and mid-downstream of the Yangtze River. Three mitochondrial DNA fragments, ND5/6, cytochrome b (Cyt b) and control region (D-loop), were amplified and then digested by 10 restriction endonucleases. Twenty-three D-loop fragments randomly selected were sequenced. Digestion patterns of ND5/6 by AluI and HaeIII, D-loop by HinfI and RsaI, and Cyt b by HaeIII were polymorphic. Ten and eighteen haplotypes were obtained from RFLP data and sequence data, respectively. The individuals from upstream and mid-downstream of the Yangtze River were apparently divided into two groups. The average genetic distance was 0.008 and 0.010 according to the two data. Low diversities and decreasing abundance indicated that Leiocassis longirostris may be in severe danger and reasonable measures of fishery management should be taken.

Stocking models of Chinese mitten crab (Eriocheir japonica sinensis) in Yangtze lakes

The fanning of Chinese mitten crab, a quality aquatic product in China and neighbouring Asian countries, has been developing rapidly in China since last decade. It reached a total yield of 3.4 X 10(5) tonnes in 2002. Due to the successive over-stocking year after year, many lakes in the mid-lower Yangtze Basin, the main farming area, are under deterioration, leading to a reduction of crab yield and quality, and, subsequently, a loss of fanning profits. Aiming at a normal development of crab culture and the sustainable use of lakes, an annual investigation dealing with lake environmental factors in relation to stocked crab populations was carried out at 20 farms in 4 lakes. The results show that the submersed macrophyte biomass (B-Mac) is the key factor affecting annual crab yield (CY). Using the ratio of Secchi depth to mean depth (Z(SD)/Z(M)), an easily measured parameter closely correlated to BMac, as driving variable, 10 regression models of maximal crab yields were generated (r(2) ranging 0.49-0.81). Based on the theory of MSY (Maximum Sustainable Yield), in combination with body-weight (BW) and recapture rate (RR) of adult crabs, a general optimal stocking model was eventually formulated. All models are simple and easy to operate. Comments on their applications and prospects are given in brief. (c) 2006 Elsevier B.V. All rights reserved.

Discharges and sediments as sources of extracellular alkaline phosphatase in a shallow Chinese eutrophic lake

Total alkaline phosphatase activity (APA) and soluble reactive phosphorus (SRP) concentrations were measured in municipal wastewater, and a shallow Chinese freshwater lake receiving it. Activities of Dissolved alkaline phosphatase ( ADAP) in overlying and interstitial water were also analyzed monthly at three sites for several years. The lake was enriched with SRP and alkaline phosphatase by discharge of the wastewater, indicating that the inclusion of APA for estimating water pollution was reasonable. Annual data showed that APA in coarser fraction was significantly higher at the site receiving more wastewaters, both in surface and overlying water, suggesting that resuspension of enzyme most likely occurred in the basin heavily discharged. ADAP was an order of magnitude higher in the wastewater than those in lake waters, and was generally higher in interstitial water, a feature more striking at the site receiving more discharges. Besides, it was irrespectively inhibited by Na2WO4, L-cysteine and EDTA-Na, but stimulated by Cu2+, Zn2+, CTAB and Triton X-100 in interstitial, overlying and surface waters. This similarity of responding patterns to the stressors indicated an analogy between dissolved alkaline phosphatase in water column and that in interstitial water, supporting the hypothesis that the polluted sediments act as source of dissolved alkaline phosphatase in eutrophic lakes.

Gut contents of silver carp, Hypophthalmichthys molitrix, and the disruption of a centric diatom, Cyclotella, on passage through the esophagus and intestine

The digestibility of algae by stomachless filter-feeding fish has been debated for decades. Results from gut contents and digestive enzyme analysis suggest poor utilization, while the measurement of food assimilation using radiolabeled isotope techniques indicate reasonable assimilation efficiency. Phytoplankton in the gut contents of the planktivorous filter-feeding silver carp were studied during March-May. The fish were cultured in a large net cage in a shallow, hypertrophic subtropical Chinese lake, Lake Donghu. In terms of biomass, the dominant phytoplankton in the fore-gut contents were Cyclotella (average 77.8%, range 69.7-93.5%) and Cryptomonas (average 9.57%, range 0-20.4%). The Ivlev's electivity index E of silver carp was much higher for Cyclotella (1.54) than for Cryptomonas (0.56). The majority of the phytoplankton found in the intestines of silver carp were 8-20 mu m, but they were also able to collect particles as small as 4.5-10 mu m, smaller than their filtering net meshes, suggesting that the secretion of mucus may play an important role in collecting such small particles. We conclude that disruption of cell walls is principally by the pharyngeal teeth, explaining previous contradictory conclusions. (C) 1999 Elsevier Science B.V. All rights reserved.

Investigation of responsivity decreasing with rising bias voltage in a GaN Schottky barrier photodetector

The unexpected decrease in measured responsivity observed in a specific GaN Schottky barrier photodetector (PD) at high reverse bias voltage was investigated and explained. Device equivalent transforms and small signal analysis were performed to analyse the test circuit. On this basis, a model was built which explained the responsivity decrease quantitatively. After being revised by this model, responsivity curves varying with bias voltage turned out to be reasonable. It is proved that the decrease is related to the dynamic parallel resistance of the photodiode. The results indicate that with a GaN Schottky PD, the choice of load resistance is restricted according to the dynamic parallel resistance of the device to avoid responsivity decay at high bias voltage.

Electronic structures and mechanical properties of uranium monocarbide from first-principles LDA plus U and GGA plus U calculations

The electronic structure, elastic constants, Poisson's ratio, and phonon dispersion curves of UC have been systematically investigated from the first-principles calculations by the projector-augmented-wave (PAW) method. In order to describe precisely the strong on-site Coulomb repulsion among the localized U 5f electrons, we adopt the local density approximation (LDA) + U and generalized gradient approximation (GGA) + U formalisms for the exchange correlation term. We systematically study how the electronic properties and elastic constants of UC are affected by the different choice of U as well as the exchange-correlation potential. We show that by choosing an appropriate Hubbard U parameter within the GGA + U approach, most of our calculated results are in good agreement with the experimental data. Therefore. the results obtained by the GGA + U with effective Hubbard parameter U chosen around 3 eV for UC are considered to be reasonable. (C) 2009 Elsevier B.V. All rights reserved.

Fine structural splitting and exciton spin relaxation in single InAs quantum dots

We have studied the exciton spin dynamics in single InAs quantum dots (QDs) with different exciton fine structural splitting (FSS) by transient luminescence measurements. We have established the correlation between exciton spin relaxation rate and the energy splitting of the FSS when FSS is nonzero and found that the spin relaxation rate in QD increases with a slope of 8.8x10(-4) ns(-1) mu eV(-1). Theoretical analyses based on the phonon-assisted relaxations via the deformation potential give a reasonable interpretation of the experimental results.

Study on Closed-set Speaker Identification Based on Biomimetic Pattern Recognition

In this paper, a new classifier of speaker identification has been proposed, which is based on Biomimetic pattern recognition (BPR). Distinguished from traditional speaker recognition methods, such as DWT, HMM, GMM, SVM and so on, the proposed classifier is constructed by some finite sub-space which is reasonable covering of the points in high dimensional space according to distributing characteristic of speech feature points. It has been used in the system of speaker identification. Experiment results show that better effect could be obtained especially with lesser samples. Furthermore, the proposed classifier employs a much simpler modeling structure as compared to the GMM. In addition, the basic idea "cognition" of Biomimetic pattern recognition (BPR) results in no requirement of retraining the old system for enrolling new speakers.

Mode quality factor based on far-field emission for square resonators

The quality factors of modes in square resonators are calculated based on the far-field emission of the analytical field distribution. The obtained quality factors are in reasonable agreement with those calculated by the finite-difference time-domain (FDTD) technique and Pade approximation method. The emission power in the square diagonal directions for whispering-gallery-like modes in square resonators is zero due to the interference cancellation caused by the odd field distributions relative to the diagonal mirror planes, so they have larger quality factors than the modes with even field distribution.

Electrical and optical coupling in an electroabsorption modulator integrated with a DFB laser

Electrical and optical coupling in an electroabsorption (EA) modulator integrated with a distributed feedback (DFB) laser have been investigated. The integrated device is treated as a three-port optoelectronic device with two electrical ports and one optical output port. The scattering parameters of this three-port device have been measured in the designed experiment. The measured results indicate that there exists the electrical coupling between the DFB laser and EA modulator of the integrated light source whenever the current applied to the laser section is below or above the threshold current, and the optical coupling will have stronger influence on the frequency responses than the electrical coupling when the bias current is above the threshold. A small-signal equivalent circuit model for the integrated device is established considering both the electrical and internal optical coupling. Experiments show that the equivalent circuit model is reasonable and the determined element values are correct. Based on the measurement and modeling, the influences of the electrical and optical coupling on the high-frequency responses are investigated and the effective measure to eliminate the additional modulation in the DFB laser are discussed.

Correlation effects for semiconducting single-wall carbon nanotubes: A density matrix renormalization group study

In this paper we report the applicability of the density matrix renormalization group (DMRG) approach to the cylindrical single wall carbon nanotube (SWCN) for the purpose of its correlation effect. By applying the DMRG approach to the t+U+V model, with t and V being the hopping and Coulomb energies between the nearest neighboring sites, respectively, and U the on-site Coulomb energy, we calculate the phase diagram for the SWCN with chiral numbers (n(1)=3, n(2)=2), which reflects the competition between the correlation energy U and V. Within reasonable parameter ranges, we investigate possible correlated ground states, the lowest excitations, and the corresponding correlation functions in which the connection with the excitonic insulator is particularly addressed.

Observation of quantum-confined Stark shifts in SiGe/Si type-I multiple quantum wells

Quantum-confined Stark shifts in SiGe/Si type-I multiple quantum wells are suggested by the bias dependence of the photocurrent spectra of p-i-n photodiodes. Both Stark redshift and blueshift have been observed for the same sample in the different ranges of electric fields applied to the quantum wells. The turnaround point corresponds to a certain electric field (named "critical" field). This phenomenon was generally predicted by Austin in 1985 [Phys. Rev. B 31, 5569 (1985)] and calculated in detail for SiGe quantum structure by Kim recently [Thin Solid Films 321, 215 (1998)]. The critical electric field obtained from the photocurrent spectra is in reasonable agreement with the theoretical prediction. (C) 2000 American Institute of Physics. [S0021-8979(00)03711-7].