PenBase, the shrimp antimicrobial peptide penaeidin database: Sequence-based classification and recommended nomenclature

Antimicrobial peptides play a major role in innate immunity. The penaeidins, initially characterized from the shrimp Litopenaeus vannamei, are a family of antimicrobial peptides that appear to be expressed in all penaeid shrimps. As of recent, a large number of penaeid nucleotide sequences have been identified from a variety of penaeid shrimp species and these sequences currently reside in several databases under unique identifiers with no nomenclatural continuity. To facilitate research in this field and avoid potential confusion due to a diverse number of nomenclatural designations, we have made a systematic effort to collect, analyse, and classify all the penaeidin sequences available in every database. We have identified a common penaeidin signature and subsequently established a classification based on amino acid sequences. In order to clarify the naming process, we have introduced a 'penaeidin nomenclature' that can be applied to all extant and future penaeidins. A specialized database, PenBase, which is freely available at http://www.penbase.immunaqua.com, has been developed for the penaeidin family of antimicrobial peptides, to provide comprehensive information about their properties, diversity and nomenclature. (c) 2005 Elsevier Ltd. All rights reserved.

Evaluation of a combined wavelet and a combined principal component analysis classification system for BCG diagnostic problem

Heart disease is one of the main factor causing death in the developed countries. Over several decades, variety of electronic and computer technology have been developed to assist clinical practices for cardiac performance monitoring and heart disease diagnosis. Among these methods, Ballistocardiography (BCG) has an interesting feature that no electrodes are needed to be attached to the body during the measurement. Thus, it is provides a potential application to asses the patients heart condition in the home. In this paper, a comparison is made for two neural networks based BCG signal classification models. One system uses a principal component analysis (PCA) method, and the other a discrete wavelet transform, to reduce the input dimensionality. It is indicated that the combined wavelet transform and neural network has a more reliable performance than the combined PCA and neural network system. Moreover, the wavelet transform requires no prior knowledge of the statistical distribution of data samples and the computation complexity and training time are reduced.

A unified criterion for initiation of sediment motion and inception of sheet flow under water waves

A unified criterion is developed for initiation of non-cohesive sediment motion and inception of sheet flow under water waves over a horizontal bed of sediment based on presently available experimental data. The unified threshold criterion is of the single form, U-o = 2 pi C[1 + 5(T-R/T)(2)](-1/4), where U-o is the onset velocity of sediment motion or sheet flow, T is wave period, and C and T-R are the coefficients. It is found that for a given sediment, U-o initially increases sharply with wave period, then gradually approaches the maximum onset velocity U-o = 2 pi C and becomes independent of T when T is larger. The unified criterion can also be extended to define sediment initial motion and sheet flow under irregular waves provided the significant wave orbital velocity and period of irregular waves are introduced in this unified criterion.

Classification of jinjiang oysters Crassostrea rivularis (Gould, 1861) from China, based on morphology and phylogenetic analysis

The jinjiang oyster Crassostrea rivularis [Gould, 1861. Descriptions of Shells collected in the North Pacific Exploring Expedition under Captains Ringgold and Rodgers. Proc. Boston Soc. Nat. Hist. 8 (April) 33-40] is one of the most important and best-known oysters in China. Based on the color of its flesh, two forms of C rivularis are recognized and referred to as the "white meat" and 11 red meat" oysters. The classification of white and red forms of this species has been a subject of confusion and debate in China. To clarify the taxonomic status of the two forms of C. rivularis, we collected and analyzed oysters from five locations along China's coast using both morphological characters and DNA sequences from mitochondrial 16S rRNA and cytochrome oxidase 1, and the nuclear 28S rRNA genes. Oysters were classified as white or red forms according to their morphological characteristics and then subjected to DNA sequencing. Both morphological and DNA sequence data suggest that the red and white oysters are two separate species. Phylogenetic analysis of DNA sequences obtained in this study and existing sequences of reference species show that the red oyster is the same species as C. ariakensis Wakiya [1929. Japanese food oysters. Jpn. J. Zool. 2, 359-367.], albeit the red oysters from north and south China are genetically distinctive. The white oyster is the same species as a newly described species from Hong Kong, C. hongkongensis Lam and Morton [2003. Mitochondrial DNA and identification of a new species of Crassostrea (Bivalvia: Ostreidae) cultured for centuries in the Pearl River Delta, Hong Kong, China. Aqua. 228, 1-13]. Although the name C. rivularis has seniority over C. ariakensis and C. hongkongensis, the original description of Ostrea rivularis by Gould [1861] does not fit shell characteristics of either the red or the white oysters. We propose that the name of C. rivularis Gould [1861] should be suspended, the red oyster should take the name C. ariakensis, and the white oyster should take the name C. hongkongensis. (C) 2004 Elsevier B.V. All rights reserved.

Classification of common oysters from North China

Oysters are commonly found on rocky shores along China's northern coast, although there is considerable confusion as to what species they are. To determine the taxonomic status of these oysters, we collected specimens from nine locations north of the Yangtze River and conducted genetic identification using DNA sequences. Fragments from three genes, mitochondrial 165 rRNA, mitochondria! cytochrome oxidase I (COI), and nuclear 285 rRNA, were sequenced in six oysters from each of the nine sites. Phylogenetic analysis of all three gene fragments clearly demonstrated that the small oysters commonly found on intertidal rocks in north China are Crassostrea gigas (Thunberg, 1793), not C. plicatula (the zhe oyster) as widely assumed. Their small size and irregular shell characteristics are reflections of the stressful intertidal environment they live in and not reliable characters for classification. Our study confirms that the oysters from Weifang, referred to as Jinjiang oysters or C. rivularis (Gould, 1861), are C. ariakensis (Wakiya, 1929). We found no evidence for the existence of C. talienwhanensis (Crosse, 1862) and other Crassostrea species in north China. Our study highlights the need for reclassifying oysters of China with molecular data.

岩体力学参数及稳定性能量判据研究

There are two major problems that have been concerned all the times, which are the mechanics characters of joint rock mass and the criterion for stability of engineering rock. Aim at the two problems, several works were conducted as follow: (1) Firstly, the mechanics characters of rock mass was studied by means of the Distinct Element Code. Subsequently, it was studied that the sensibility of joint surface roughness, strength of joint wall, joint stiffness ( i.e. tangential and normal stiffness) on the rock mass strength. (2) Based on the experimental rock mass classification methods of RMR and GSI, the program of “Parameters Calculation of the Rock Mass ” was developed. It has realized the rapid choice of rock mass parameters. (3) The concept of Representive Element Volume was induced based on the study of dimensional effect of rock mass. The Representive Element Volume of the horizontal and vertical pillar (ab. Two Pillars ) in the 2nd zone of Jinchuan mine were gained by the Geology Statistic Method and the Distinct Element Code. And then, the strength and deformatiom parameters of rock mass of the Two Pillars were obtained through numerical experiment. (4) From the confining depressure after thriaxial compression test of rock sample, it was concluded that the failure of rock is caused mainly by the lateral deformation and energy release happened during the confining depressure processure. The criterion of plastic energy catastrophe of rock engineering failure was proposed and validated. Subsquently, the stability of the horizontal pillar and Qianjiangping landslide in Three Gorges was judged by means of above-mentioned method. (5) Based on the fact there is a phenomenon of increasing energy concentration while the rock mass was compressed, rock information entropy (i.e. energy distribution entropy) was proposed. And it was revealed that there was change of energy distribution entropy while the rock mass was compressed to failure.

锦屏电站地下厂房卸荷岩体参数研究

It is a basic work to ascertain the parameters of rock mass for evaluation about stability of the engineering. Anisotropism、inhomogeneity and discontinuity characters of the rock mass arise from the existing of the structural plane. Subjected to water、weathering effect、off-loading, mechanical characters of the rock mass are greatly different from rock itself, Determining mechanical parameters of the rock mass becomes so difficult because of structure effect、dimension effect、rheological character, ‘Can’t give a proper parameter’ becomes one of big problems for theoretic analysis and numerical simulation. With the increment of project scale, appraising the project rock mass and ascertaining the parameters of rock mass becomes more and more important and strict. Consequently, researching the parameters of rock mass has important theoretical significance and actual meaning. The Jin-ping hydroelectric station is the first highest hyperbolic arch dam in the world under construction, the height of the dam is about 305m, it is the biggest hydroelectric station at lower reaches of Yalong river. The length of underground factory building is 204.52m, the total height of it is 68.83m, the maximum of span clearance is 28.90m. Large-scale excavation in the underground factory of Jin-ping hydroelectric station has brought many kinds of destructive phenomenon, such as relaxation、spilling, providing a precious chance for study of unloading parameter about rock mass. As we all know, Southwest is the most important hydroelectric power base in China, the construction of the hydroelectric station mostly concentrate at high mountain and gorge area, basically and importantly, we must be familiar with the physical and mechanical character of the rock mass to guarantee to exploit safely、efficiently、quickly, in other words, we must understand the strength and deformation character of the rock mass. Based on enough fieldwork of geological investigation, we study the parameter of unloading rock mass on condition that we obtain abundant information, which is not only important for the construction of Jin-ping hydroelectric station, but also for the construction of other big hydroelectric station similar with Jin-ping. This paper adopt geological analysis、test data analysis、experience analysis、theory research and Artificial Neural Networks （ANN） brainpower analysis to evaluate the mechanical parameter, the major production is as follows: (1)Through the excavation of upper 5-layer of the underground powerhouse and the statistical classification of the main joints fractures exposed, We believe that there are three sets of joints, the first group is lay fracture, the second group and the fourth group are steep fracture. These provide a strong foundation for the following calculation of and analysis; (2)According to the in-situ measurement about sound wave velocity、displacement and anchor stress, we analyses the effects of rock unloading effect，the results show a obvious time-related character and localization features of rock deformation. We determine the depth of excavation unloading of underground factory wall based on this. Determining the rock mass parameters according to the measurement about sound wave velocity with characters of low- disturbing、dynamic on the spot, the result can really reflect the original state, this chapter approximately the mechanical parameters about rock mass at each unloading area; (3)Based on Hoek-Brown experienced formula with geological strength index GSI and RMR method to evaluate the mechanical parameters of different degree weathering and unloading rock mass about underground factory, Both of evaluation result are more satisfied; (4)From the perspective of far-field stress, based on the stress field distribution ideas of two-crack at any load conditions proposed by Fazil Erdogan (1962)，using the strain energy density factor criterion (S criterion) proposed by Xue changming(1972)，we establish the corresponding relationship between far-field stress and crack tip stress field, derive the integrated intensity criterion formula under the conditions of pure tensile stress among two line coplanar intermittent jointed rock，and establish the corresponding intensity criterion for the exploratory attempt; (5)With artificial neural network, the paper focuses on the mechanical parameters of rock mass that we concerned about and the whole process of prediction of deformation parameters, discusses the prospect of applying in assessment about the parameters of rock mass，and rely on the catalog information of underground powerhouse of Jinping I Hydropower Station, identifying the rock mechanics parameters intellectually，discusses the sample selection, network design, values of basic parameters and error analysis comprehensively. There is a certain significance for us to set up a set of parameters evaluation system，which is in construction of large-scale hydropower among a group of marble mass.

改造型盆地油气成藏机理与油气预测－以银根－额济纳旗盆地为例

Reformed basin is a basin that underwent multiple immense reformation after the sedimentary stage, the major geologic elements of the petroleum system in the prototyped basin are destroyed to a certain extent, and their petroleum system has been reconstructed. This type of basin is frequently found in the course of exploration both home and abroad. In China, especially in the western and southern part of China, the basins in which oil explorations have been conducted are mostly reformed basins. The reformed basins from Paleozoic, Late Mesozoic to Cenozoic are widely distributed in West and South China. They are, and moreover, will be a challenge for oil and gas exploration. The conventional investigation and exploration techniques used in the slightly reconstructed basin just don't work well when facing the reformed basin. Therefore, the study on the reformed basin, especially the study on the pool-forming mechanism and reservoir prediction becomes a focus and one of difficulties for the geologists overseas and domestic. Yingen-Ejinaqi Basin is a typical case of the Late Mesozoic and Cenozoic reformed basins in China. It locates in West China and is a exploration frontier with difficulties and no break through is made for years. A comprehensive research on it will be of significance for oil and gas exploration in similar basins of China. The late research for reformed basin in China now is mainly concentrated on basin classification, formation mechanism, geologic features, and survey technique, distribution regularity of oil accumulation and its dominating factors, assessment of oil exploration prospect and target zones, etc. On the other hand, the study on the pool-forming mechanism and reservoir prediction seems insufficient in systematization, and the research is deficient in methodology and combination of qualitative and quantitative studies, as well as the application of the new theory and techniques. The current efforts are mainly directed to structures (faults), sedimentation, the relationship between reservoir evolution and oil accumulation, and some other relevant fields. However, the application of the new theory and techniques seems to be insufficient such as petroleum system, pool-forming dynamics, fluid pressure compartment, and basin simulation, etc. So is the dynamic and integrated research. As a result, incomplete knowledge and understandings derived from the research on pool-forming mechanism and reservoir prediction often do not accord with rea-lity of the basin. The study and exploration under the guidance of this knowledge will inevitably lead to errors and failure. This paper, based on the previous study of the other geologists on reformed basins, with emphasis on "wholeness or systematic, dynamic and integrated" research, presents a reverse thinking of beginning from conserved units in the basin and the combination of qualitative and quantitative study with new theory and technique by building a geological model. The paper also puts forward a new thought for studying the oil & gas accumulation and reservoir prediction , and establishes a new research system for reformed basin. It is verified by the known reservoir and oil accumulation area in the basin and has a practical value for use and reference. The new ideas and achievements in this research are as following: 1.This is the first time that the system for studying the reformed basin and its pool-forming mechanism and reservoir prediction is presented. A reverse thinking and combination of qualitative & quantitative are applied here with emphasis on "wholeness or systematic, dynamic and integrated" research, new theory, techniques & methods comprehensive use and geologic models building. 2. Identifying criterion and methods, classifying schemes, and denominating principles for the conserved units of reformed basins are presented in this paper. The geologic model of conserved units of Yingen-Ejinaqi Basin has been built. It is a practical method when combined with the traditional way for basin survey and the conserved units study. 3.The dynamic sources of basin deformation are believed to be stress, gravity and thermodynamics. The stress and gravity are key factors in basin deformation and pool forming, especially stress. Scientific proof is provided by classifying the functional type, style and range of the stress, gravity and thermodynamics. 4.The pool forming and reservoir distribution of Yingen-Ejinaqi Basin are controlled by multiple factors or geologic conditions or/and co-controlled by both of them. The qualitative and quantitative research on petroleum system and basin modeling will help us understand and determine the pool-forming period of the conserved unit (timing), the oil migrating direction (orientation), the oil accumulating region (location), the oil distributing border (bordering) and the size of oil accumulation (quantification). Thus the pool-forming and distribution zones can be predicted. 5.Three generating modes (reform-succession type, reform-destroyed type and reform-regenerating type or reform-newborn type) of pool forming for reformed basins are presented here, together with the inner relationships between basin deformation type, overlapping style and pool-forming modes. The pool-forming modes are determined by deformation type and overlapping style. Reservoir distribution will be predicted based on the modes and other concrete pool-forming conditions. 6.The evaluation methods of the conserved units and zones and the parameter selection are reliable in optimal selecting of target zones. The technical terms, new ideas and methods for the study of reformed basins, the pool-forming mechanism and reservoir prediction are presented in this paper. The concepts and terms, the identifying criterion, the denominating principles, the generating modes for pool forming, the methods of reservoir prediction, and the evaluation techniques for conserved units and zones can be used for reference in studies on the petroleum exploration of reformed basins in China and abroad. It serves as a typical example for further research of the reformed basins and the geologic regulations of oil accumulation. It has a practical value of use and reference. The future research in the field of pool-forming mechanism of the reformed basins may well be on the process simulation of pool-forming dynamics of the reformed basins. Experimental work has been conducted to simulate the processes by using quantitative and qualitative methods combined. The further study in this field calls for more efforts.

大港油田孔南地区孔一段储层流动单元研究

The main reservoir type in the south of Dagang Oilfield is alluvial reservoir. In this paper, the reservoir structure model and the distribution of connected body and flow barrier were built on base of the study of high-resolution sequential stratigraphic skeleton and fine sedimentary microfacies on level of single sandbody. Utilizing the static and dynamic data synthetically and carrying out the comparision of the classification method for reservoir flow unit in different reservoir, the criterion, which can be used to classify the flow unit in first section of Kongdian formation of Kongnan area, was defined. The qualitative method of well-to-well correlation and the quantitative method of conditional simulation using multiple data are adopted to disclose the oil and water moving regulation in different flow unit and the distribution rule of remaining oil by physical simulation measure. A set of flow unit study method was formed that is suit for the Dagang Oilfield on account of the remaining oil production according to the flow unit. Several outstanding progresses was obtained in the following aspects:It is considered that the reservoir structure of Zao V iow oil group- Zao Vup4 layerand are jigsaw-puzzled reservoir, while ZaoVup3-ZaoVupi layers are labyrinth reservoir,which are studied on base of high-resolution sequential stratigraphic skeleton on the levelof single sandbody in first section of Kongdian formation of Kongnan area and accordingto the study of fine sedimentary microfacies and fault sealeing.When classifying the flow unit, only permeability is the basic parameter using thestatic and dynamic data and, and also different parameters should be chose or deleted, suchas porosity, effective thickness, fluid viscosity and so on, because of the weak or stronginterlayer heterogeneous and the difference of interlayer crude oil character.The method of building predicting-model of flow unit was proposed. This methodis according to the theories of reservoir sedimentology and high-resolution sequencestratigraphic and adopts the quantitative method of well-to well correlation and the quantitative method of stochastic simulation using integrateddense well data. Finally the 3-D predicting-model of flow unit and the interlay er distribution model in flow unit were built which are for alluvial fan and fan delta fades in first section of Kongdian formation of Kongnan area, and nine genetic model of flow unit of alluvial environment that spread in the space were proposed.(4) Difference of reservoir microscopic pore configuration in various flow units and difference of flow capability and oil displacement effect were demonstrated through the physical experiments such as nuclear magnetic resonance (NMR), constant rate mercury penetration, flow simulation and so on. The distribution of remaining oil in this area was predicted combining the dynamic data and numerical modeling based on the flow unit. Remaining oil production measure was brought up by the clue of flow unit during the medium and late course of the oilfield development.