HLA-DRB1 allele polymorphisms in genetic susceptibility to esophageal carcinoma

AIM: To probe into the genetic susceptibility of HLA-DRB1 alleles to esophageal carcinoma in Han Chinese in Hubei Province. METHODS: HLA-DRB1 allele polymorphisms were typed by polymerase chain reaction with sequence-specific primers (PCR-SSP) in 42 unrelated patients with esophageal cancer and 136 unrelated normal control subjects and the associated HLA-DRB1 allele was measured by nucleotide sequence analysis with PCR.SAS software was used in statistics. RESULTS: Allele frequency (AF) of HLA-DRB1*0901 was significantly higher in esophageal carcinoma patients than that in the normal controls (0.2500 vs0.1397, P=0.028, the odds ratio 2.053, etiologic fraction 0.1282). After analyzed the allele nucleotide sequence of HLA-DRB1*0901 which approachs to the corresponded exon 2 sequence of the allele in genebank. There was no association between patients and controls in the rested HLA-DRB1 alleles. CONCLUSION: HLA-DRB1*0901 allele is more common in the patients with esophageal carcinoma than in the healthy controls, which is positively associated with the patients of Hubei Han Chinese. Individuals carrying HLA-DRB1*0901 may be susceptible to esophageal carcinoma.

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.

Characterization of 12 single nucleotide polymorphisms (SNPs) in Pacific abalone, Haliotis discus hannai

We report here for the first time 12 polymorphic single nucleotide polymorphisms (SNPs) in a commercially important gastropod, Pacific abalone (Haliotis discus hannai) that were identified by searching expressed sequence tag database. These SNP loci (seven nuclear and five mitochondrial SNPs) were polymorphic among 37 wild abalone individuals, based on a four-primer allele-specific polymerase chain reaction analysis. All loci had two alleles and the minor allele frequency ranged from 0.027 to 0.473. For the seven nuclear SNPs, the expected and observed heterozygosities ranged from 0.053 to 0.499 and from 0.054 to 0.811, respectively.

反假频重建理论及其在储层预测中的应用

To extend the cross-hole seismic 2D data to outside 3D seismic data, reconstructing the low frequency data to high frequency data is necessary. Blind deconvolution method is a key technology. In this paper, an implementation of Blind deconvolution is introduced. And optimized precondition conjugate gradient method is used to improve the stability of the algorithm and reduce the computation. Then high-frequency retrieved Seismic data and the cross-hole seismic data is combined for constraint inversion. Real data processing proved the method is effective. To solve the problem that the seismic data resolution can’t meet the request of reservoir prediction in the river face thin-layers in Chinese eastern oil fields, a high frequency data reconstruction method is proposed. The extrema of the seismic data are used to get the modulation function which operated with the original seismic data to get the high frequency part of the reconstruction data to rebuild the wide band data. This method greatly saves the computation, and easy to adjust the parameters. In the output profile, the original features of the seismic events are kept, the common feint that breaking the events and adding new zeros to produce alias is avoided. And the interbeded details are enhanced compared to the original profiles. The effective band of seismic data is expended and the method is approved by the processing of the field data. Aim to the problem in the exploration and development of Chinese eastern oil field that the high frequency log data and the relative low frequency seismic data can’t be merged, a workflow of log data extrapolation constrained by time-phase model based on local wave decomposition is raised. The seismic instantaneous phase is resolved by local wave decomposition to build time-phase model, the layers beside the well is matched to build the relation of log and seismic data, multiple log info is extrapolated constrained by seismic equiphase map, high precision attributes inverse sections are produced. In the course of resolve the instantaneous phase, a new method of local wave decomposition --Hilbert transform mean mode decomposition(HMMD) is raised to improve the computation speed and noise immunity. The method is applied in the high resolution reservoir prediction in Mao2 survey of Daqing oil field, Multiple attributes profiles of wave impedance, gamma-ray, electrical resistivity, sand membership degree are produced, of which the resolution is high and the horizontal continuous is good. It’s proved to be a effective method for reservoir prediction and estimation.

粘弹性介质中的地震波传播与波形反演研究

The real earth is far away from an ideal elastic ball. The movement of structures or fluid and scattering of thin-layer would inevitably affect seismic wave propagation, which is demonstrated mainly as energy nongeometrical attenuation. Today, most of theoretical researches and applications take the assumption that all media studied are fully elastic. Ignoring the viscoelastic property would, in some circumstances, lead to amplitude and phase distortion, which will indirectly affect extraction of traveltime and waveform we use in imaging and inversion. In order to investigate the response of seismic wave propagation and improve the imaging and inversion quality in complex media, we need not only consider into attenuation of the real media but also implement it by means of efficient numerical methods and imaging techniques. As for numerical modeling, most widely used methods, such as finite difference, finite element and pseudospectral algorithms, have difficulty in dealing with problem of simultaneously improving accuracy and efficiency in computation. To partially overcome this difficulty, this paper devises a matrix differentiator method and an optimal convolutional differentiator method based on staggered-grid Fourier pseudospectral differentiation, and a staggered-grid optimal Shannon singular kernel convolutional differentiator by function distribution theory, which then are used to study seismic wave propagation in viscoelastic media. Results through comparisons and accuracy analysis demonstrate that optimal convolutional differentiator methods can solve well the incompatibility between accuracy and efficiency, and are almost twice more accurate than the same-length finite difference. They can efficiently reduce dispersion and provide high-precision waveform data. On the basis of frequency-domain wavefield modeling, we discuss how to directly solve linear equations and point out that when compared to the time-domain methods, frequency-domain methods would be more convenient to handle the multi-source problem and be much easier to incorporate medium attenuation. We also prove the equivalence of the time- and frequency-domain methods by using numerical tests when assumptions with non-relaxation modulus and quality factor are made, and analyze the reason that causes waveform difference. In frequency-domain waveform inversion, experiments have been conducted with transmission, crosshole and reflection data. By using the relation between media scales and characteristic frequencies, we analyze the capacity of the frequency-domain sequential inversion method in anti-noising and dealing with non-uniqueness of nonlinear optimization. In crosshole experiments, we find the main sources of inversion error and figure out how incorrect quality factor would affect inverted results. When dealing with surface reflection data, several frequencies have been chosen with optimal frequency selection strategy, with which we use to carry out sequential and simultaneous inversions to verify how important low frequency data are to the inverted results and the functionality of simultaneous inversion in anti-noising. Finally, I come with some conclusions about the whole work I have done in this dissertation and discuss detailly the existing and would-be problems in it. I also point out the possible directions and theories we should go and deepen, which, to some extent, would provide a helpful reference to researchers who are interested in seismic wave propagation and imaging in complex media.

基于信息重建技术的地震信号处理方法研究

The dissertation addressed the problems of signals reconstruction and data restoration in seismic data processing, which takes the representation methods of signal as the main clue, and take the seismic information reconstruction (signals separation and trace interpolation) as the core. On the natural bases signal representation, I present the ICA fundamentals, algorithms and its original applications to nature earth quake signals separation and survey seismic signals separation. On determinative bases signal representation, the paper proposed seismic dada reconstruction least square inversion regularization methods, sparseness constraints, pre-conditioned conjugate gradient methods, and their applications to seismic de-convolution, Radon transformation, et. al. The core contents are about de-alias uneven seismic data reconstruction algorithm and its application to seismic interpolation. Although the dissertation discussed two cases of signal representation, they can be integrated into one frame, because they both deal with the signals or information restoration, the former reconstructing original signals from mixed signals, the later reconstructing whole data from sparse or irregular data. The goal of them is same to provide pre-processing methods and post-processing method for seismic pre-stack depth migration. ICA can separate the original signals from mixed signals by them, or abstract the basic structure from analyzed data. I surveyed the fundamental, algorithms and applications of ICA. Compared with KL transformation, I proposed the independent components transformation concept (ICT). On basis of the ne-entropy measurement of independence, I implemented the FastICA and improved it by covariance matrix. By analyzing the characteristics of the seismic signals, I introduced ICA into seismic signal processing firstly in Geophysical community, and implemented the noise separation from seismic signal. Synthetic and real data examples show the usability of ICA to seismic signal processing and initial effects are achieved. The application of ICA to separation quake conversion wave from multiple in sedimentary area is made, which demonstrates good effects, so more reasonable interpretation of underground un-continuity is got. The results show the perspective of application of ICA to Geophysical signal processing. By virtue of the relationship between ICA and Blind Deconvolution , I surveyed the seismic blind deconvolution, and discussed the perspective of applying ICA to seismic blind deconvolution with two possible solutions. The relationship of PC A, ICA and wavelet transform is claimed. It is proved that reconstruction of wavelet prototype functions is Lie group representation. By the way, over-sampled wavelet transform is proposed to enhance the seismic data resolution, which is validated by numerical examples. The key of pre-stack depth migration is the regularization of pre-stack seismic data. As a main procedure, seismic interpolation and missing data reconstruction are necessary. Firstly, I review the seismic imaging methods in order to argue the critical effect of regularization. By review of the seismic interpolation algorithms, I acclaim that de-alias uneven data reconstruction is still a challenge. The fundamental of seismic reconstruction is discussed firstly. Then sparseness constraint on least square inversion and preconditioned conjugate gradient solver are studied and implemented. Choosing constraint item with Cauchy distribution, I programmed PCG algorithm and implement sparse seismic deconvolution, high resolution Radon Transformation by PCG, which is prepared for seismic data reconstruction. About seismic interpolation, dealias even data interpolation and uneven data reconstruction are very good respectively, however they can not be combined each other. In this paper, a novel Fourier transform based method and a algorithm have been proposed, which could reconstruct both uneven and alias seismic data. I formulated band-limited data reconstruction as minimum norm least squares inversion problem where an adaptive DFT-weighted norm regularization term is used. The inverse problem is solved by pre-conditional conjugate gradient method, which makes the solutions stable and convergent quickly. Based on the assumption that seismic data are consisted of finite linear events, from sampling theorem, alias events can be attenuated via LS weight predicted linearly from low frequency. Three application issues are discussed on even gap trace interpolation, uneven gap filling, high frequency trace reconstruction from low frequency data trace constrained by few high frequency traces. Both synthetic and real data numerical examples show the proposed method is valid, efficient and applicable. The research is valuable to seismic data regularization and cross well seismic. To meet 3D shot profile depth migration request for data, schemes must be taken to make the data even and fitting the velocity dataset. The methods of this paper are used to interpolate and extrapolate the shot gathers instead of simply embedding zero traces. So, the aperture of migration is enlarged and the migration effect is improved. The results show the effectiveness and the practicability.

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.

Time-Frequency Analysis of Nonlinear Systems: The Skeleton Linear Model and the Skeleton Curves

The joint time-frequency analysis method is adopted to study the nonlinear behavior varying with the instantaneous response for a class of S.D.O.F nonlinear system. A time-frequency masking operator, together with the conception of effective time-frequency region of the asymptotic signal are defined here. Based on these mathematical foundations, a so-called skeleton linear model (SLM) is constructed which has similar nonlinear characteristics with the nonlinear system. Two skeleton curves are deduced which can indicate the stiffness and damping in the nonlinear system. The relationship between the SLM and the nonlinear system, both parameters and solutions, is clarified. Based on this work a new identification technique of nonlinear systems using the nonstationary vibration data will be proposed through time-frequency filtering technique and wavelet transform in the following paper.

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.

Evolution of the DRD2 gene haplotype and its association with alcoholism in Mexican Americans

The human D2 dopamine receptor gene (DRD2) plays a central role in the neuromodulation of appetitive behaviors and is implicated in having a possible role in susceptibility to alcoholism. We genotyped an SNP in DRD2 Exon 8 in 251 nonalcoholic, unrelated, healthy controls and 200 alcoholic Mexican Americans. The DRD2 haplotypes were analyzed using the Exon 8 genotype in combination with five other SNP genotypes, which were obtained from our previous study. The ancestral origins of the DRD2 polymorphisms have been determined by sequencing the homologous region in other higher primates. Twenty DRD2 haplotypes, defined as H1 to H20 based on their frequency from high to low, were obtained in this major minority population. The ancestral haplotype "I-132-G-C-G-A1" and two one-step mutation haplotypes were absent in our study population. The haplotype H1, "I-B1-T-C-A-A1", with the highest frequency in the population, is a three-step mutation from the ancestral form. The first five or eight major haplotypes make up 87% or 95% of the entire population, respectively. The prevalence of the haplotype H1+ (H1/H1 and H1/Hn genotypes) is significantly higher in alcoholics and alcoholic subgroups, including early onset drinkers and benders, than in their respective control groups. The Promoter -141C allele is in linkage disequilibrium (LD) with five other loci in the nonalcoholic group, but not in the alcoholic group. All of the other five loci are in LD in both the alcoholic and control groups. The DRD2 TaqI B allele is in complete LD with the allele located in intron 6. Five SNPs, Promoter -141C, TaqI B (or Intron 6), Exon 7, Exon 8, and TaqI A, are sufficient to define the DRD2 haplotypes in Mexican Americans. Our data indicate that the DRD2 haplotypes are associated with alcoholism in Mexican Americans. (c) 2005 Elsevier Inc. All rights reserved.

Fiber Dispersion and Nonlinearity Influences on Transmissions of AM and FM Data Modulation Signals in Radio-Over-Fiber System

Transmission properties of data amplitude modulation (AM) and frequency modulation (FM) in radio-over-fiber (RoF) system are studied numerically. The influences of fiber dispersion and nonlinearity on different microwave modulation schemes, including double side band (DSB), single side band (SSB) and optical carrier suppression (OCS), are investigated and compared. The power penalties at the base station (BS) and the eye opening penalties of the recovered data at the end users are both calculated and analyzed. Numerical simulation results reveal that the power penalty of FM can be drastically decreased due to the larger modulation depth it can achieve than that of AM. The local spectrum broadening around subcarrier microwave frequency of AM due to fiber nonlinearity can also be eliminated with FM. It is demonstrated for the first time that the eye openings of the FM recovered data can be controlled by its modulation depths and the coding formats. Negative voltage encoding format was used to further decrease the RF frequency thus increase the fluctuation period considering their inverse relationship.

Improved optical heterodyne methods for measuring. frequency responses of photodetectors

An improved optical self-heterodyne method utilizing a distributed Bragg reflector (DBR) tunable laser and an optical fiber ring interferometer is presented in this paper. The interference efficiency can be increased by 7 dB compared with the scheme using the conventional Mach-Zehnder interferometer. The unsteady process that the beating frequency experiences in each tuning period is investigated. According to the measurement results, the wavelength and optical power of the tunable laser will be steady when the square-wave frequency is lower than 300 kHz. It has been shown that when a square-wave voltage is applied to the phase section of the tunable laser, the laser linewidths vary in a wide range, and are much larger than that under dc voltage tuning. The errors caused by the variations in the linewidth of the beat signal and optical power can be eliminated using the proposed calibration procedures, and the measurement accuracy can, therefore, be significantly improved. Experiments show that the frequency responses obtained using our method agree well with the data provided by the manufacturer, and the improved optical self-heterodyne method is as accurate as the intensity noise technique.

A direct digital frequency synthesizer with fourth-order phase domain Delta Sigma noise shaper and 12-bit current-steering DAC

This paper presents a direct digital frequency synthesizer (DDFS) with a 16-bit accumulator, a fourth-order phase domain single-stage Delta Sigma interpolator, and a 300-MS/s 12-bit current-steering DAC based on the Q(2) Random Walk switching scheme. The Delta Sigma interpolator is used to reduce the phase truncation error and the ROM size. The implemented fourth-order single-stage Delta Sigma noise shaper reduces the effective phase bits by four and reduces the ROM size by 16 times. The DDFS prototype is fabricated in a 0.35-mu m CMOS technology with active area of 1.11 mm(2) including a 12-bit DAC. The measured DDFS spurious-free dynamic range (SFDR) is greater than 78 dB using a reduced ROM with 8-bit phase, 12-bit amplitude resolution and a size of 0.09 mm(2). The total power consumption of the DDFS is 200)mW with a 3.3-V power supply.

Frequency limitation in the calibration of microwave test fixtures

The problem of frequency limitation arising from the calibration of asymmetric and symmetric test fixtures has been investigated. For asymmetric test fixtures, a new algorithm based on the thru-short-match (TSM) method is outlined. It is found that the conventional TSM method does not have any inherent frequency limitation, but using the same procedure with an unknown match may lead to the said problem. This limitation can be avoided by using a different algorithm. The various calibration methods for symmetric test fixtures using known standards are also discussed and the origin of the frequency limitation is identified. Several ways in avoiding the problem are proposed. There is good agreement between the theories and experimental data.