Haplotype frequency distribution and linkage disequilibrium analysis of single nucleotide polymorphisms at the human FMO3 gene locus

We analyzed flavin-containing monooxygenase 3 (FMO3) polymorphisms, haplotype structure, and linkage disequilibrium (LD) in 256 Han Chinese and 50 African-American individuals to compare their haplotype frequencies and LD with other world populations. For

Identification of Nonlinear Systems Through Time-Frequency Filtering Technique

In the previous paper, a class of nonlinear system is mapped to a so-called skeleton linear model (SLM) based on the joint time-frequency analysis method. Behavior of the nonlinear system may be indicated quantitatively by the variance of the coefficients of SLM versus its response. Using this model we propose an identification method for nonlinear systems based on nonstationary vibration data in this paper. The key technique in the identification procedure is a time-frequency filtering method by which solution of the SLM is extracted from the response data of the corresponding nonlinear system. Two time-frequency filtering methods are discussed here. One is based on the quadratic time-frequency distribution and its inverse transform, the other is based on the quadratic time-frequency distribution and the wavelet transform. Both numerical examples and an experimental application are given to illustrate the validity of the technique.

Distribution of CCR2-64I and SDF1-3 ' A alleles and HIV status in 7 ethnic populations of Cameroon

Limited information is available on the prevalence among rural Africans of host genetic polymorphisms conferring resistance to HIV-1 infection or slowing HIV disease progression.We report the allelic frequencies of the AIDS-related polymorphisms CCR2-64I, SDF1-3#A, and CCR5-D32 in 321 volunteers from 7 ethnic groups in Cameroon. Allelic frequencies differed among the 7 ethnic groups, ranging from 10.8% to 31.3% for CCR2-64I and 0.0% to 7.1% for SDF1-3#A. No CCR5-D32 alleles were found. HIV seroprevalence was 6.9% in the total population and peaked at younger ages in girls and women than in boys and men. Among 15- to 54-year-olds, HIV seroprevalence varied from 2.0% to 11.1% among the village populations. Conditional logistic regression analysis using data from boys and men aged 15 to 54 years showed the number of CCR2-64I alleles to be a significant risk factor for HIV seropositivity (odds ratio per allele adjusted for age and matched on ethnic group = 6.3, 95% confidence interval: 1.3–30.3); this association was not found in women. The findings are consistent with the hypothesis that CCR2-64I alleles may delay HIV disease progression without affecting susceptibility to infection among men. We did not observe this relation among women, and other factors, such as multiple pregnancies or maternal stressors (eg, breastfeeding), may have masked any protective effect of CCR2-64I alleles. Further study of this issue among women is warranted. SDF1-3#A did not differ between HIV-seropositive and HIV-seronegative individuals but wasassociated with increasing age among HIV-seronegative women, suggesting a protective effect against HIV-1 infection.

Seasonal dynamics and distribution of the digenean Phyllodistomum pawlovskii (Trematoda : Gorgoderidae) in the bullhead catfish, Pseudobagrus fulvidraco, in a lake of China

Seasonal population dynamics of the digenean Phyllodistomum pawlovskii in the urinary bladder of the bullhead catfish, Pseudobagrus fulvidraco, were investigated in Liangzi Lake in the flood plain of the Yangtze River in China from February 2001 to July 2002. The overall prevalence of the parasite was high, 41.5% (n = 1,476), while the mean abundance was relatively low, 1.24 +/- 2.11. The parasite exhibited evident seasonality in changes of prevalence and abundance. In brief, prevalence and abundance were very low in midwinter (January), but increased and remained relatively high in other seasons and months. The distribution pattern of this parasite in the fish was overdispersed, with a variance to mean ratio > 1, but its frequency distribution could not be described by the negative binomial model. There were positive correlations between the number of the parasites per fish and the age and length of the fish; a peaked age-parasite abundance curve was not detected in the parasite-host association. It is suggested that the parasite P. pawlovskii has little effect on the population structure of the bullhead catfish.

Characteristics in frequency domain by inductively coupled plasma atomic emission spectrometry with charge injection detection

The charactesistics of two-dimension spectra obtained by inductively coupled plasma atomic emission spectrometry (ICP-AES) with charge injection detection (CID) in frequency domain were studied in the present paper. The measurement spectra were Fourier transformed and the frequency distribution of the spectra was obtained. Results showed that the spectra in frequency domain could he divided into two parts:high frequency and low frequency signals. The later stood for measurement spectra and the former for background and noises. However, the high frequecny signals could not be smoothed simply to reduce noises because the background was deteriorated even though the spectral signal did not change significantly.

Evidence for Positive Selection on the Osteogenin (BMP3) Gene in Human Populations

Background: Human skeletal system has evolved rapidly since the dispersal of modern humans from Africa, potentially driven by selection and adaptation. Osteogenin (BMP3) plays an important role in skeletal development and bone osteogenesis as an antagonist of the osteogenic bone morphogenetic proteins, and negatively regulates bone mineral density. Methodology/Principal Findings: Here, we resequenced the BMP3 gene from individuals in four geographically separated modern human populations. Features supportive of positive selection in the BMP3 gene were found including the presence of an excess of nonsynonymous mutations in modern humans, and a significantly lower genetic diversity that deviates from neutrality. The prevalent haplotypes of the first exon region in Europeans demonstrated features of long-range haplotype homogeneity. In contrast with findings in European, the derived allele SNP Arg192Gln shows higher extended haplotype homozygosity in East Asian. The worldwide allele frequency distribution of SNP shows not only a high-derived allele frequency in Asians, but also in Americans, which is suggestive of functional adaptation. Conclusions/Significance: In conclusion, we provide evidence for recent positive selection operating upon a crucial gene in skeletal development, which may provide new insight into the evolution of the skeletal system and bone development.

Population dynamics and maturation cycle of Camallanus cotti (Nematoda : Camallanidae) in the Chinese hooksnout carp Opsariichthys bidens (Osteichthyes : Cyprinidae) from a reservoir in China

The seasonal population dynamics and maturation cycle of the nematode Camallanus cotti in the posterior intestine of Chinese hooksnout carp Opsariichthys bidens have been studied in the Danjiangkou Reservoir of the Hubei Province in central China from September 2004 to November, 2005. The overall prevalence, mean abundance and intensity of C cotti among fish sampled (n = 700 fish) were 47%, 2.29 +/- 12.38 ( +/- S.D.) and 1-307 (average 4.89 +/- 17.74), respectively. The overall sexual ratio of female to male nematodes (excluding L3 and L4 juveniles) was 1.17:1. Statistical results showed weakly positive correlations betweerl fish length and the number of nematodes per host. The dynamics of infection of the nematode exhibited significant seasonal pattern in changes in mean abundance. A similar pattern was found for changes in nematode prevalence, although this was not statistically significant. Higher levels of infection were observed among fish sampled in summer months and the lower in the winter. Neither the prevalence nor the abundance of the parasite was significantly different between male and female hosts. The pattern of frequency distribution of the parasite in the host was found to be over-dispersed throughout the sampling period. In addition, studies on the development and maturation of the parasite in O. bidens revealed that development (maturation), recruitment of the next generation, and reproduction may be continuous year-round, although reproduction may peak during the winter. (c) 2007 Elsevier B.V. All rights reserved.

Mortalities induced by the copepod Sinergasilus polycolpus in farmed silver and bighead carp in a reservoir

The frequency distributions of the parasitic copepod Sinergasilus polycolpus were examined in silver carp Hypophthalmichthys molitrix and bighead carp Aristichthys nobilis during a disease outbreak of the 2 species of fish in a reservoir in China. The mean abundance of the copepod was positively related with host length and age, and the overdispersion of the copepod in both silver and bighead carp was fitted well with negative binomial distribution. Although parasite-induced host mortality was observed, a peaked age-parasite abundance curve was not detected in the present parasite-host system. It is also proposed that this peaked age-abundance curve is unlikely to be observed in its natural host populations.

Seasonal population dynamics of parasitic copepods, Sinergasilus spp. on farmed fish in China

Seasonal population dynamics of parasitic copepods in the genus Sinergasilus on fanned silver carp Hypophthalmichthys molitrix, farmed bighead carp Aristichthys nobilis, and grass carp Ctenopharyngodon idellus were investigated in China. Changes in prevalence and abundance were seasonal with higher levels observed in summer. Reproduction of the copepods occurs from spring to early autumn as indicated by the higher ratio of gravid copepods. The frequency distribution of Sinergasilus polycolpus and S. major in their host populations can be fitted well with negative binomial distribution. (C) 2000 Elsevier Science B.V. All rights reserved.

Urban functional structure characteristics and transformation in China

The paper analyzes urban functional structure characteristics of Chinese cities in 1996 using the Nelson method. The manufacturing employment percentage is much higher in metropolitan areas but is decreasing from 1989 to 1996. On the other hand, the weight of science, education, culture, hygiene, finance, insurance and real estate increases. The employment structure changes dramatically. Although the urbanization level of China is lower than that of the USA in 1955, the frequency distribution curve of urban functions is similar. The construction, transportation, commerce, finance, insurance, real estate, science, education, culture, hygiene and administration curves are normal. The mining employment converges on minor cities and the distribution is not normal. The urban function has changed with urban scale. The bigger the cities are, the smaller the manufacture, mining and construction employment weights, and the larger are the science, education, finance, insurance, real estate and administration weights. Commerce and transportation are distributed evenly and the difference is less. From the comparison in three zones of China, the employment percentage of manufacture, finance, insurance and real estate is higher in eastern coastal areas, while the employment percentage of science, education, administration is higher in western areas. (C) 2002 Elsevier Science Ltd. All rights reserved.

The polymorphism of lysozyme gene in Zhikong scallop (Chlamys farreri) and its association with susceptibility/resistance to Listonella anguillarum

Lysozyme functions as a crucial biodefence effector against the infection of bacterial pathogens in innate immunity. The nucleotide sequence polymorphisms in promoter region of a nuclear goose type lysozyme gene from Zhikong scallop Chlamys farreri (designated as CFLysG) were investigated to explore their association with susceptibility/resistance to Listonella anguillarum infection. Eight sites of single nucleotide polymorphisms (SNPs) and two sites of insert-deletion (ins-del) polymorphisms were identified in the promoter region of CFLysG. Two of them, -753 TATCTCGATCAGG ins-del polymorphism and -391 A-G SNP were selected to analyze their distribution in the susceptible and resistant stocks, which were identified according to the survival time after L. anguillarum challenge. Using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP), two genotypes were found at each site, which were ins/del and ins/ins at locus -753, and A/A and A/G at locus -391, respectively. The -753 ins/del genotype was more prevalent in the resistant stock than that in the susceptible stock, 30% vs 16.67% in frequency, but there was no significant difference in the frequency distribution between these two stocks (P=0.15). In contrast, the frequency of -391A/G genotype in the resistant stock was significantly higher (30%) than that in the susceptible stock (7.14%) (P=0.007), indicating a significant association with the resistance of Zhikong scallop to L anguillarum. To confirm the presumption, another independent challenge experiment was performed, in which the cumulative mortality of scallops with -391 A/A genotype (96.8%) was significantly higher than those with -391 A/G genotype (64.5%) (P=0.001), which further validate the association between -391 A/G genotype and the resistance of Zhikong scallop to L anguillarum. These results suggested that the -391 A/G could be a potential marker applied in future selection of Zhikong scallop with enhanced resistance to L anguillarum. (C) 2008 Elsevier Ltd. All rights reserved.

塔克拉玛干沙漠地球化学研究

The Taklamakan Desert, lying in the center Tarim Basin of sourthern Xinjiang, is the largest sand sea in China and well known in the world as its inclemency. For understanding the formation and evolution of the Taklamakan Desert, it is very important to identify the provenance of aeolian sediments in the extensive dune fields, but the opinions from earlier studies are quite different. In this study, we examined the major- and trace-element compositions, mineral compositions and grain-size distributions of some Quaternary aeolian and nonaeolian sediments collected from the Taklamakan Desert, together with the variation of chemical and mineralogical compositions of different grain-size fraction. At the same time, we also studied the chemistries of some natural water samples (river water and groundwater) with the items of TDS, pH, Alkalinity, conductivity and major cation and anion compositions. Our results of analysis show some significant opinions as follow: Most of the frequency-distribution curves of grain size of dune sand samples are simgle peak, but that of the river and lacustrine sediment are most double peak or multi-peak. The grain-size distribution of dunefield sand changed gradually from north to south with the major wind direction in large scale, but there are many differences in regional scale. The major, REE, trace element compositions and mineral compositions are very different among the coarse, fine fraction and bulk samples due to the influence of grain-size. Most of the fine fractions are geochemically homogenous, but the coarse fractions and bulk samples are heterogenous. All the surface and ground waters are limnetic or sub-salty, their chemical compositions are mainly controlled by rock-weathering and crystallization- evaporation processes, and mainly come from the evaporate, while the contributions of the carbonate and silicate are little, excluding the influence on oasis water by carbonate. The mineral compositions of selected samples are stable, mainly composed of the strongly resistant mineral types. The mineral maturity of them are more immature at whole compared with other sandy sediments in the world, and they have experienced less degree of chemical weathering and recycling, being lying in the early stage of continental weathering. Among these sediments, the river sediments are relatively primitive. The sources of these sediments are maybe mainly terrigenous, silicic and subaluminous/ metalunious rocks, such as the granodiorite and its metamorphic rock. The geochemical compositions of dunefield sand are similar with those of the river sediments and dune sands near the river way; There are not only the resemblances but also the differences on geochemistry and granularity between north and south dunesands; The sediments from same section have different age but same trace-element compositions; The sediments from the south edge of Tarim Basin are all somewhat geochemically similar with the palaeo-river-sediment on the south edge of studying area. The REE data support the idea that the south dunesands are a little older than the north dunesands, and the tectonic settings of source area are mainly active continental margin based on the major-element compositions, so they indicate that the sediment of Taklamakan Desert maybe come mainly from the rock-weathering production of north part of the Kunlun Mountains. Compared with the sands of other dune field in north of China, the sands of the Taklamakan Desert are distinct by REE composition, but similar with the Luochuan loess, center China, and the two sandy dusts of Beijing, eastern China.

基于匹配追踪方法的地震信号时频分析研究

Seismic signal is a typical non-stationary signal, whose frequency is continuously changing with time and is determined by the bandwidth of seismic source and the absorption characteristic of the media underground. The most interesting target of seismic signal’s processing and explaining is to know about the local frequency’s abrupt changing with the time, since this kind of abrupt changing is indicating the changing of the physical attributes of the media underground. As to the seismic signal’s instantaneous attributes taken from time-frequency domain, the key target is to search a effective, non-negative and fast algorithm time-frequency distribution, and transform the seismic signal into this time-frequency domain to get its instantaneous power spectrum density, and then use the process of weighted adding and average etc. to get the instantaneous attributes of seismic signal. Time-frequency analysis as a powerful tool to deal with time variant non-stationary signal is becoming a hot researching spot of modern signal processing, and also is an important method to make seismic signal’s attributes analysis. This kind of method provides joint distribution message about time domain and frequency domain, and it clearly plots the correlation of signal’s frequency changing with the time. The spectrum decomposition technique makes seismic signal’s resolving rate reach its theoretical level, and by the method of all frequency scanning and imaging the three dimensional seismic data in frequency domain, it improves and promotes the resolving abilities of seismic signal vs. geological abnormal objects. Matching pursuits method is an important way to realize signal’s self-adaptive decomposition. Its main thought is that any signal can be expressed by a series of time-frequency atoms’ linear composition. By decomposition the signal within an over completed library, the time-frequency atoms which stand for the signal itself are selected neatly and self-adaptively according to the signal’s characteristics. This method has excellent sparse decomposition characteristics, and is widely used in signal de-noising, signal coding and pattern recognizing processing and is also adaptive to seismic signal’s decomposition and attributes analysis. This paper takes matching pursuits method as the key research object. As introducing the principle and implementation techniques of matching pursuits method systematically, it researches deeply the pivotal problems of atom type’s selection, the atom dictionary’s discrete, and the most matching atom’s searching algorithm, and at the same time, applying this matching pursuits method into seismic signal’s processing by picking-up correlative instantaneous messages from time-frequency analysis and spectrum decomposition to the seismic signal. Based on the research of the theory and its correlative model examination of the adaptively signal decomposition with matching pursuit method, this paper proposes a fast optimal matching time-frequency atom’s searching algorithm aimed at seismic signal’s decomposition by frequency-dominated pursuit method and this makes the MP method pertinence to seismic signal’s processing. Upon the research of optimal Gabor atom’s fast searching and matching algorithm, this paper proposes global optimal searching method using Simulated Annealing Algorithm, Genetic Algorithm and composed Simulated Annealing and Genetic Algorithm, so as to provide another way to implement fast matching pursuit method. At the same time, aimed at the characteristics of seismic signal, this paper proposes a fast matching atom’s searching algorithm by means of designating the max energy points of complex seismic signal, searching for the most optimal atom in the neighbor area of these points according to its instantaneous frequency and instantaneous phase, and this promotes the calculating efficiency of seismic signal’s matching pursuit algorithm. According to these methods proposed above, this paper implements them by programmed calculation, compares them with some open algorithm and proves this paper’s conclusions. It also testifies the active results of various methods by the processing of actual signals. The problems need to be solved further and the aftertime researching targets are as follows: continuously seeking for more efficient fast matching pursuit algorithm and expanding its application range, and also study the actual usage of matching pursuit method.

Self-consistent kinetic modeling of low-pressure inductively coupled radio-frequency discharges

An efficient method for solving the spatially inhomogeneous Boltzmann equation in a two-term approximation for low-pressure inductively coupled plasmas has been developed. The electron distribution function (EDF), a function of total electron energy and two spatial coordinates, is found self-consistently with the static space-charge potential which is computed from a 2D fluid model, and the rf electric field profile which is calculated from the Maxwell equations. The EDF and the spatial distributions of the electron density, potential, temperature, ionization rate, and the inductive electric field are calculated and discussed. (C) 1996 American Institute of Physics.