G-Quadruplex Aptamers with Peroxidase-Like DNAzyme Functions: Which Is the Best and How Does it Work?

Some G-quadruplex DNA aptamers have been found to strongly bind hemin to form DNAzymes with peroxidase-like activity. To help determine the most suitable DNAzymes and to understand how they work, five previously reported G-quadruplex aptamers were compared for their binding affinity and then the potential catalytic mechanism of their corresponding hemin-G-quadruplex DNAzymes was explored. Among these aptamers, a G-quadruplex named AGRO100 was shown to possess the highest hemin-binding affinity and the best DNAzyme function. This means that AGRO100 is the most ideal candidate for DNAzyme-based analysis. Furthermore, we found the peroxidase-like activity of DNAzyme to be primarily dependent on the concentration of H2O2 and independent of that of the peroxidase substrate (that is, 2,2-azino-bis(3-ethytbenzothiazoline-6-sulfonic acid)diammonium salt). Accordingly, a reaction mechanism for DNAzyme-catalyzed peroxidation is proposed. This study provides new insights into the G-quadruplex-based DNAzymes and will help us to further extend their applications in the analytical field.

Applications of generalized torsion angles in studies on quantitative structure-activity relationship

In this article, generalized torsion angles of derivatives of 1-[(2-hydroxyethoxy)methy1]-6(phenylthio)thymine(HEPT) were calculated, which include abundant three dimensional information of molecules. Molecular similarity matrix was built based on the calculated generalized torsion angles. These similarities were taken as the new variables, and the new variables were selected by using Leaps-and-Bounds regression analysis. Multiple regression analysis and neural networks were performed, and the satisfactory results were achieved by using the neural networks.

Discovery of genes involved in defense/immunity functions in a haemocytes cDNA library from Fenneropenaeus chinensis by ESTs annotation

Crustacean haemocytes play important roles in the host immune response including recognition, phagocytosis, melanization, cytotoxicity and inter-cellular signal communication. Expressed sequence tags (ESTs) analysis is proved to be an efficient approach not only for gene discovery, but also for gene expression profiles performance. In order to further understand the innate immune system and defense mechanisms of Chinese shrimp at molecular level, complementary DNA library is constructed from the haemocyte tissue of Fenneropenaeus chinensis. A total of 2371 cDNA clones are successfully sequenced and the average sequence length is 460 bp. About 50% are identified as orthologs of known genes from other organisms by BLASTx and BLASTn program. By sequences comparability and analysis, 34 important genes including 177 ESTs are identified that may be involved in defense or immune functions in shrimp based on the known knowledge. These genes are categorized into five categories according to their putative functions in shrimp immune system: 13 genes are different types of antimicrobial peptides (AMP, penaeidin, antilipopolysaccharide factor, etc.), and their proportion is about 3 8%; 11 genes belong to prophenoloxidase system (prophenoloxidase, serine proteinase, serine proteinase inhibitor, etc.), and their proportion is about 32%; five genes have high homology with clotting protein (lectin, transglutaminase, etc), and their proportion is about 15%; three genes may be involved in inter-cell signal communication (peroxinectin, integrin), and their proportion is about 9%; two genes have been identified to be chaperone proteins (Hsc70, thioredoxin peroxidase), and their proportion is about 6%. These EST sequences enrich our understanding of the immune genes of F chinensis and will help farther experimental research into immune factors and improve our knowledge of the immune mechanisms of shrimp. (c) 2007 Elsevier B.V. All rights reserved.

On SAR wind speed ambiguities and related geophysical model functions

Recent investigations show that normalized radar cross sections for C-band microwave sensors decrease under high wind conditions with certain incident angles instead of increase, as is the case for low to moderate wind speeds. This creates the problem of ambiguities in high wind speed retrievals from synthetic aperture radar (SAR). In the present work, four geophysical model functions (GMFs) are studied, namely the high wind C-band model 4 (CMOD4HW), C-band model 5 (CMOD5), the high wind vertical polarized GMF (HWGMF_VV), and the high wind horizontal polarized GMF (HWGMF_HH). Our focus is on model behaviours relative to wind speed ambiguities. We show that, except for CMOD4HW, the other GMFs exhibit the wind speed ambiguity problem. To consider this problem in high wind speed retrievals from SAR, we focus on hurricanes and propose a method to remove the speed ambiguity using the dominant hurricane wind structure.

Forms and functions of inorganic carbon in the Jiaozhou Bay sediments

Inorganic carbon forms and their influencing factors, mutual transformation and contribution to carbon cycling in the Jiaozhou Bay sediments were discussed. The results show that inorganic carbon in sediments could be divided into five forms: NaCl form, NH3 center dot H2O form, NaOH form, NH2OH center dot HCl form and HCl form. Thereinto, NH2OH center dot HCl form and HCl form account for more than 70% of total inorganic carbon. There was close relationship among every form of inorganic carbon and their correlativity was clearly different with different sedimentary environment except the similar strong positive correlation among NH2OH center dot HCl form, HCl form and total inorganic carbon in all regions of the Jiaozhou Bay. All forms of inorganic carbon were influenced by organic carbon, pH, Eh, Es, nitrogen and phosphorus in sediments, but their influence had different characteristics in different regions. Every farm of inorganic carbon transformed into each other continuously during early diagenesis of sediments and the common phenomenon was that NaCl form, NH3 center dot H2O form, NaOH form and NH2OH center dot HCl form might transform into steady HCl form. NaCl form, NH3 center dot H2O form, NaOH form and NH2OH center dot HCl form could participate in carbon recycle and they are potential carbon source; HCl form may be buried for a long time in sediments, and it may be one of the final resting places of atmospheric CO2. Inorganic carbon which entered into sediments was about 4.98 x 10(10) g in the Jiaozhou Bay every year, in which about 1.47x10(10) g of inorganic carbon might be buried for a long time and about 3.51. x 10(10) g of inorganic carbon might return into seawater and take part in carbon recycling.

多波多分量地震资料走时近似方法的研究与应用

Compared with the conventional P wave, multi-component seismic data can markedly provide more information, thus improve the quality of reservoir evaluation like formation evaluation etc. With PS wave, better imaging result can be obtained especially in areas involved with gas chimney and high velocity formation. However, the signal-to-noise of multi-component seismic data is normally lower than that of the conventional P wave seismic data, while the frequency range of converted wave is always close to that of the surface wave which adds to the difficulty of removing surface wave. To realize common reflection point data stacking from extracted common conversion point data is a hard nut to crack. The s wave static correction of common receiver point PS wave data is not easy neither. In a word, the processing of multi-component seismic data is more complicated than P wave data. This paper shows some work that has been done, addressing those problems mentioned above. (1) Based on the AVO feature of converted wave, this paper has realized the velocity spectrum of converted waves by using Sarkar’s generalized semblance method taking into account of AVO factor in velocity analysis. (2)We achieve a method of smoothly offset division normal method.Firstly we scan the stacking velocities in different offset divisions for a t0, secondly obtain some hyperbolas using these stacking velocities, then get the travel time for every trace using these hyperbolas; in the end we interpolate the normal move out between two t0 for every trace. (3) Here realize a method of stepwise offset division normal moveout.It is similar to the method of smoothly offset division normal moveout.The main difference is using quadratic curve, sixth order curve or fraction curve to fit these hyperbolas. (4)In this paper, 4 types of travel time versus distance functions in inhomogeneous media whose velocity or slowness varies with depth and vertical travel time have been discussed and used to approximate reflection travel time. The errors of ray path and travel time based on those functions in four layered models were analyzed, and it has shown that effective results of NMO in synthetic or real data can be obtained. (5) The velocity model of converted PS-wave can be considered as that of P -wave based on the ghost source theory, thus the converted wave travel time can be approximated by calculation from 4 equivalent velocity functions: velocity or slowness vary linearly with depth or vertical travel time. Then combining with P wave velocity analysis, the converted wave data can be corrected directly to the P-wave vertical travel time. The improvements were shown in Normal Move out of converted waves with numerical examples and real data. (6) This paper introduces the methods to compute conversion point location in vertical inhomogeneous media based on linear functions of velocity or slowness versus depth or vertical travel time, and introduce three ways to choose appropriate equivalent velocity methods, which are velocity fitting, travel time approximation and semblance coefficient methods.

小波域地震资料的处理方法（WSSP）研究

The modeling formula based on seismic wavelet can well simulate zero - phase wavelet and hybrid-phase wavelet, and approximate maximal - phase and minimal - phase wavelet in a certain sense. The modeling wavelet can be used as wavelet function after suitable modification item added to meet some conditions. On the basis of the modified Morlet wavelet, the derivative wavelet function has been derived. As a basic wavelet, it can be sued for high resolution frequency - division processing and instantaneous feature extraction, in acoordance with the signal expanding characters in time and scale domains by each wavelet structured. Finally, an application example proves the effectiveness and reasonability of the method. Based on the analysis of SVD (Singular Value Decomposition) filter, by taking wavelet as basic wavelet and combining SVD filter and wavelet transform, a new de - noising method, which is Based on multi - dimension and multi-space de - noising method, is proposed. The implementation of this method is discussed the detail. Theoretical analysis and modeling show that the method has strong capacity of de - noising and keeping attributes of effective wave. It is a good tool for de - noising when the S/N ratio is poor. To give prominence to high frequency information of reflection event of important layer and to take account of other frequency information under processing seismic data, it is difficult for deconvolution filter to realize this goal. A filter from Fourier Transform has some problems for realizing the goal. In this paper, a new method is put forward, that is a method of processing seismic data in frequency division from wavelet transform and reconstruction. In ordinary seismic processing methods for resolution improvement, deconvolution operator has poor part characteristics, thus influencing the operator frequency. In wavelet transform, wavelet function has very good part characteristics. Frequency - division data processing in wavelet transform also brings quite good high resolution data, but it needs more time than deconvolution method does. On the basis of frequency - division processing method in wavelet domain, a new technique is put forward, which involves 1) designing filter operators equivalent to deconvolution operator in time and frequency domains in wavelet transform, 2) obtaining derivative wavelet function that is suitable to high - resolution seismic data processing, and 3) processing high resolution seismic data by deconvolution method in time domain. In the method of producing some instantaneous characteristic signals by using Hilbert transform, Hilbert transform is very sensitive to high - frequency random noise. As a result, even though there exist weak high - frequency noises in seismic signals, the obtained instantaneous characteristics of seismic signals may be still submerged by the noises. One method for having instantaneous characteristics of seismic signals in wavelet domain is put forward, which obtains directly the instantaneous characteristics of seismic signals by taking the characteristics of both the real part (real signals, namely seismic signals) and the imaginary part (the Hilbert transfom of real signals) of wavelet transform. The method has the functions of frequency division and noise removal. What is more, the weak wave whose frequency is lower than that of high - frequency random noise is retained in the obtained instantaneous characteristics of seismic signals, and the weak wave may be seen in instantaneous characteristic sections (such as instantaneous frequency, instantaneous phase and instantaneous amplitude). Impedance inversion is one of tools in the description of oil reservoir. one of methods in impedance inversion is Generalized Linear Inversion. This method has higher precision of inversion. But, this method is sensitive to noise of seismic data, so that error results are got. The description of oil reservoir in researching important geological layer, in order to give prominence to geological characteristics of the important layer, not only high frequency impedance to research thin sand layer, but other frequency impedance are needed. It is difficult for some impedance inversion method to realize the goal. Wavelet transform is very good in denoising and processing in frequency division. Therefore, in the paper, a method of impedance inversion is put forward based on wavelet transform, that is impedance inversion in frequency division from wavelet transform and reconstruction. in this paper, based on wavelet transform, methods of time - frequency analysis is given. Fanally, methods above are in application on real oil field - Sansan oil field.

用宽频带远震体波波形研究中国及邻近地区地壳构造及地质意义初探

The theory and approach of the broadband teleseismic body waveform inversion are expatiated in this paper, and the defining the crust structure's methods are developed. Based on the teleseismic P-wave data, the theoretic image of the P-wave radical component is calculated via the convolution of the teleseismic P-wave vertical component and the transform function, and thereby a P-wavefrom inversion method is built. The applied results show the approach effective, stable and its resolution high. The exact and reliable teleseismic P waveforms recorded by CDSN and IRIS and its geodynamics are utilized to obtain China and its vicinage lithospheric transfer functions, this region ithospheric structure is inverted through the inversion of reliable transfer functions, the new knowledge about the deep structure of China and its vicinage is obtained, and the reliable seismological evidence is provided to reveal the geodynamic evolution processes and set up the continental collisional theory. The major studies are as follows: Two important methods to study crustal and upper mantle structure -- body wave travel-time inversion and waveform modeling are reviewed systematically. Based on ray theory, travel-time inversion is characterized by simplicity, crustal and upper mantle velocity model can be obtained by using 1-D travel-time inversion preliminary, which introduces the reference model for studying focal location, focal mechanism, and fine structure of crustal and upper mantle. The large-scale lateral inhomogeneity of crustal and upper mantle can be obtained by three-dimensional t ravel-time seismic tomography. Based on elastic dynamics, through the fitting between theoretical seismogram and observed seismogram, waveform modeling can interpret the detail waveform and further uncover one-dimensional fine structure and lateral variation of crustal and upper mantle, especially the media characteristics of singular zones of ray. Whatever travel-time inversion and waveform modeling is supposed under certain approximate conditions, with respective advantages and disadvantages, and provide convincing structure information for elucidating physical and chemical features and geodynamic processes of crustal and upper mantle. Because the direct wave, surface wave, and refraction wave have lower resolution in investigating seismic velocity transitional zone, which is inadequate to study seismic discontinuities. On the contrary, both the converse and reflected wave, which sample the discontinuities directly, must be carefully picked up from seismogram to constrain the velocity transitional zones. Not only can the converse wave and reflected wave study the crustal structure, but also investigate the upper mantle discontinuities. There are a number of global and regional seismic discontinuities in the crustal and upper mantle, which plays a significant role in understanding physical and chemical properties and geodynamic processes of crustal and upper mantle. The broadband teleseismic P waveform inversion is studied particularly. The teleseismic P waveforms contain a lot of information related to source time function, near-source structure, propagation effect through the mantle, receiver structure, and instrument response, receiver function is isolated form teleseismic P waveform through the vector rotation of horizontal components into ray direction and the deconvolution of vertical component from the radial and tangential components of ground motion, the resulting time series is dominated by local receiver structure effect, and is hardly irrelevant to source and deep mantle effects. Receiver function is horizontal response, which eliminate multiple P wave reflection and retain direct wave and P-S converted waves, and is sensitive to the vertical variation of S wave velocity. Velocity structure beneath a seismic station has different response to radial and vertical component of an accident teleseismic P wave. To avoid the limits caused by a simplified assumption on the vertical response, the receiver function method is mended. In the frequency domain, the transfer function is showed by the ratio of radical response and vertical response of the media to P wave. In the time domain, the radial synthetic waveform can be obtained by the convolution of the transfer function with the vertical wave. In order to overcome the numerical instability, generalized reflection and transmission coefficient matrix method is applied to calculate the synthetic waveform so that all multi-reflection and phase conversion response can be included. A new inversion method, VFSA-LM method, is used in this study, which successfully combines very fast simulated annealing method (VFSA) with damped least square inversion method (LM). Synthetic waveform inversion test confirms its effectiveness and efficiency. Broadband teleseismic P waveform inversion is applied in lithospheric velocity study of China and its vicinage. According to the data of high quality CDSN and IRIS, we obtained an outline map showing the distribution of Asian continental crustal thickness. Based on these results gained, the features of distribution of the crustal thickness and outline of crustal structure under the Asian continent have been analyzed and studied. Finally, this paper advances the principal characteristics of the Asian continental crust. There exist four vast areas of relatively minor variations in the crustal thickness, namely, northern, eastern southern and central areas of Asian crust. As a byproduct, the earthquake location is discussed, Which is a basic issue in seismology. Because of the strong trade-off between the assumed initial time and focal depth and the nonlinear of the inversion problems, this issue is not settled at all. Aimed at the problem, a new earthquake location method named SAMS method is presented, In which, the objective function is the absolute value of the remnants of travel times together with the arrival times and use the Fast Simulated Annealing method is used to inverse. Applied in the Chi-Chi event relocation of Taiwan occurred on Sep 21, 2000, the results show that the SAMS method not only can reduce the effects of the trade-off between the initial time and focal depth, but can get better stability and resolving power. At the end of the paper, the inverse Q filtering method for compensating attenuation and frequency dispersion used in the seismic section of depth domain is discussed. According to the forward and inverse results of synthesized seismic records, our Q filtrating operator of the depth domain is consistent with the seismic laws in the absorbing media, which not only considers the effect of the media absorbing of the waves, but also fits the deformation laws, namely the frequency dispersion of the body wave. Two post stacked profiles about 60KM, a neritic area of China processed, the result shows that after the forward Q filtering of the depth domain, the wide of the wavelet of the middle and deep layers is compressed, the resolution and signal noise ratio are enhanced, and the primary sharp and energy distribution of the profile are retained.

A Theory of Networks for Appxoimation and Learning

Learning an input-output mapping from a set of examples, of the type that many neural networks have been constructed to perform, can be regarded as synthesizing an approximation of a multi-dimensional function, that is solving the problem of hypersurface reconstruction. From this point of view, this form of learning is closely related to classical approximation techniques, such as generalized splines and regularization theory. This paper considers the problems of an exact representation and, in more detail, of the approximation of linear and nolinear mappings in terms of simpler functions of fewer variables. Kolmogorov's theorem concerning the representation of functions of several variables in terms of functions of one variable turns out to be almost irrelevant in the context of networks for learning. We develop a theoretical framework for approximation based on regularization techniques that leads to a class of three-layer networks that we call Generalized Radial Basis Functions (GRBF), since they are mathematically related to the well-known Radial Basis Functions, mainly used for strict interpolation tasks. GRBF networks are not only equivalent to generalized splines, but are also closely related to pattern recognition methods such as Parzen windows and potential functions and to several neural network algorithms, such as Kanerva's associative memory, backpropagation and Kohonen's topology preserving map. They also have an interesting interpretation in terms of prototypes that are synthesized and optimally combined during the learning stage. The paper introduces several extensions and applications of the technique and discusses intriguing analogies with neurobiological data.

A Connection Between GRBF and MLP

Both multilayer perceptrons (MLP) and Generalized Radial Basis Functions (GRBF) have good approximation properties, theoretically and experimentally. Are they related? The main point of this paper is to show that for normalized inputs, multilayer perceptron networks are radial function networks (albeit with a non-standard radial function). This provides an interpretation of the weights w as centers t of the radial function network, and therefore as equivalent to templates. This insight may be useful for practical applications, including better initialization procedures for MLP. In the remainder of the paper, we discuss the relation between the radial functions that correspond to the sigmoid for normalized inputs and well-behaved radial basis functions, such as the Gaussian. In particular, we observe that the radial function associated with the sigmoid is an activation function that is good approximation to Gaussian basis functions for a range of values of the bias parameter. The implication is that a MLP network can always simulate a Gaussian GRBF network (with the same number of units but less parameters); the converse is true only for certain values of the bias parameter. Numerical experiments indicate that this constraint is not always satisfied in practice by MLP networks trained with backpropagation. Multiscale GRBF networks, on the other hand, can approximate MLP networks with a similar number of parameters.

Algebraic Functions For Recognition

In the general case, a trilinear relationship between three perspective views is shown to exist. The trilinearity result is shown to be of much practical use in visual recognition by alignment --- yielding a direct method that cuts through the computations of camera transformation, scene structure and epipolar geometry. The proof of the central result may be of further interest as it demonstrates certain regularities across homographies of the plane and introduces new view invariants. Experiments on simulated and real image data were conducted, including a comparative analysis with epipolar intersection and the linear combination methods, with results indicating a greater degree of robustness in practice and a higher level of performance in re-projection tasks.

On the Relationship Between Generalization Error, Hypothesis Complexity, and Sample Complexity for Radial Basis Functions

In this paper, we bound the generalization error of a class of Radial Basis Function networks, for certain well defined function learning tasks, in terms of the number of parameters and number of examples. We show that the total generalization error is partly due to the insufficient representational capacity of the network (because of its finite size) and partly due to insufficient information about the target function (because of finite number of samples). We make several observations about generalization error which are valid irrespective of the approximation scheme. Our result also sheds light on ways to choose an appropriate network architecture for a particular problem.

Generalized Low-Rank Approximations

We study the frequent problem of approximating a target matrix with a matrix of lower rank. We provide a simple and efficient (EM) algorithm for solving {\\em weighted} low rank approximation problems, which, unlike simple matrix factorization problems, do not admit a closed form solution in general. We analyze, in addition, the nature of locally optimal solutions that arise in this context, demonstrate the utility of accommodating the weights in reconstructing the underlying low rank representation, and extend the formulation to non-Gaussian noise models such as classification (collaborative filtering).