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.

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.

三塘湖盆地牛圈湖区储层特征研究—以齐古组、头屯河组为例

In view of few researches into pore textures and anisotropy characteristics of Qiguzu-toutunhezu reservoir in Niuquanhu block in Santanghu Basin, in order to enhance the hydrocarbon recovery of the region of interest and improve the reservoir development effect, with the employment of the experiments like cast thin slice, scanning electron microscope, conventional high pressure mercury penetration, constant speed mercury penetration and nuclear magnetic resonance, the thesis makes a thorough research into pore texture characteristics and anisotropy characteristics of the sandstone reservoir. The research shows that the microscopic pore textures are complicated, the anisotropy is high and waterflood development water/oil displacement efficiency is low, which are mainly caused by the high microscopic anisotropy of the reservoir. Specially, the research shows that Qiguzu-toutunhezu reservoir belongs to braided delta front intrafacies, the intergranular pore is the main type of pores, which take up 65.50 percent of total pores, intergranular dissolved pores, feldspar dissolved pores and lithic dissolved pores are on the second place, and there are few carbonate dissolved pores. The reservoir belongs to mesopore-fine throat and mesopore-medium throat. The pore distribution of the sandstone reservoir is comparatively centralized. The reservoir inhomogeneity is mainly caused by the throat inhomogeneity. Diagenesis mainly includes compaction, cementation, metasomatism and dissolution. Compared with compaction， cementation exerts more direct impact on the decline of the porosity of the sandstone reservoir ( pore loss factor is 63.75 percent in the cementing process). Based on the classification of diagenetic stages, the reservoir diagenesis is on the stage of the late period of early diagenetic stage to early period of late diagenetic stage. The study area of the small sandstone reservoir layer of the anisotropy of the relatively strong; plane, the anisotropy of the relatively weak. microscopic anisotropy of its relatively strong.

塔里木盆地塔北、塔中地区早古生代白云岩形成机理

In Tarim Basin, extensive carbonates of Lower Paleozoic occur, in which thick Cambrian and Lower Ordovician dolostones are widespread and show a potential perspective in hydrocarbon exploration. So they are viewed as an important target for exploration. Tarim Basin is a poly phase composite basin, which underwent multiphase tectonic modification and volcanic activities; these exerted significant influences on the basin-fills and basin fluid evolution, thereby the diagenetic history, particularly on the deep-buried Lower Paleozoic dolostones. Referring to the classification of dolomite texture proposed by Gregg & Sibley (1984) and Sibley & Gregg (1987). In view of crystal size, crystal shape, crystal surface and contact relation, eight genetic textures of dolomite crystals are identified, based on careful petrographic examinatoins. These textures include: 1) micritic dolomite; 2) relict mimetic dolomite; 3)finely crystalline, planar-e(s), floating dolomite; 4)finely crystalline, planar-e(s) dolomite; 5) finely-coarse crystalline, nonplanar-a dolomite; 6)coarse crystalline, nonplanar saddle dolomite; 7) finely-medium crystalline, planar-e(s) dolomite cement; 8) coarse crystalline, nonplanar saddle dolomite cement, in which the former six textures occurs as in matrix, the latter two in the cements. Detailed geochemistry analysis is carried out on the basis of genetic textures of dolomite and related minerals such as quartz and calcite. The result showed that the calcite has the highest average content in Sr, which can be sorted into two groups; micritic dolomite has the highest average content in Sr among all kinds of dolomites; the REE patterns of all kinds of dolomites is similar to those of marine limestone samples. Saddle dolomite cement has δ13C values from -2.44‰ to 1.27‰ PDB, and δ18O values from -13.01‰ to -5.12‰ PDB, which partially overlap with those of matrix dolomite (δ13C values from -2.83‰ to 2.01‰ PDB, δ18O values from -10.63‰ to -0.85‰ PDB). Saddle dolomite cement has 87Sr/86Sr ratios from 0.7086 to 0.7104, which totally overlap with those of matrix dolomite (0.7084 ~ 0.7116). Compared with saddle dolomite derived from other basins all over the world, the saddle dolomites of Tarim Basin have similar δ13C, δ18O and 87Sr/86Sr ratios values with those of matrix dolomite. This scenario reflects the unusual geological setting and special dolomitizing liquid of Tarim Basin. The values of δ18O, δ13C and 87Sr/86Sr ratios of calcite also can be sorted out two groups, which may been resulted from the one stage of extensive uplift of Tarim Basin from Mesozoic to Cenozoic. Fluid inclusion microthermometry data of the diagenetic mineral indicates that matrix dolomite has relatively low homogenization temperatures (Th) of 80～105oC and salinities of 12.3％ (wt% NaCl equivalent); saddle dolomite has highest Th values, which concentrate in 120～160oC and salinities of 13.5～23.7％ (wt% NaCl equivalent); quartz has relatively low Th of 135～155oC and salinities of 17.8～22.5％ (wt% NaCl equivalent); calcite has relatively low Th of 121～159.5oC and salinities of 1.4～17.5％ (wt% NaCl equivalent). These data suggest that the saddle dolomites could have formed in thermal brine fluids. Based on comprehensive petrographical study, detailed geochemistry and fluid inclusion microthermometry analysis on Lower Paleozoic dolomite of Tarim Basin, three types of dolomitisation mechanism are proposed: Penecontemporaneous dolomitisation (Sabkha dolomitisation & Reflux dolomitisation); Burial dolomitisation (shallow-intermediate burial dolomitisation & Deep burial dolomitisation ); Hydrothermal cannibalized dolomitisation. In view of host-specified occurrences of hydrothermal dolomite, the low abundance of saddle dolomite and high geochemical similarities between saddle dolomite and host dolomite, as well as highest Th and high salinities , the hydrothermal dolomite in Tarim Basin is thus unique, which could have been precipitated in modified fluid in the host dolomite through intraformational thermal fluid cannibalization of Mg ions from the host. This scenario is different from the cases that large scale dolomitizing fluid migration took place along the fluid pathways where abundant saddle dolomite precipitated. Detailed observations on 180 petrographic and 60 casting thin sections show original pores in Lower Paleozoic dolomite were almost died out by complicated diagenetic process after a long time geologic evolution. On the other hand, deep-buried dolomite reservoirs is formed by tectonic and hydrothermal reforming on initial dolomites. Therefore, the distribution of structure-controlled hydrothermal dolomite reservoirs is predicted in Tabei and Tazhong Area of Tarim Basin based on the geophysical data.

水-岩土反应的力学与环境效应研究

The research on mechanical effects of water-rock and soil interaction on deformation and failure of rocks and soils involves three aspects of mechanics, physics and chemistry. It is the cross between geochemistry and rock mechanics and soil mechanics. To sum up, the mechanical effects of water-rock and soil interaction is related to many complex processes. Research in this respect has been being an important forward field and has broad prospects. In connection with the mechanism of the effects of the chemical action of water-rock on deformation and failure of rocks and soils, the research significance, the present state, the developments in this research domain are summarized. Author prospects the future of this research. The research of the subject should be possessed of important position in studying engineering geology and will lead directly to a new understand on geological hazard and control research. In order to investigation the macroscopic mechanics effects of chemical kinetics of water-rock interaction on the deformation and failure, calcic rock, red sandstone and grey granite reacting chemically with different aqueous solution at atmospheric temperature and atmospheric pressure are uniaxially compressed. The quantitative results concerning the changes of uniaxially compressive strength and elastic modulus under different conditions are obtained. It is found that the mechanical effects of water on rock is closely related to the chemical action of water-rock or the chemical damage in rock, and the intensity of chemical damage is direct ratio to the intensity of chemical action in water-rock system. It is also found that the hydrochemical action on rock is time-dependent through the test. The mechanism of permeation and hydrochemical action resulting in failure of loaded rock mass or propagation of fractures in rocks would be a key question in rock fracture mechanics. In this paper, the fracture mechanical effects of chemical action of water-rock and their time- and chemical environment-dependent behavior in grey granite, green granite, grey sandstone and red sandstone are analyzed by testing K_(IC) and COD of rock under different conditions. It is found that: ①the fracture mechanical effect of chemical action of water-rock is outstanding and time-dependent, and high differences exist in the influence of different aqueous solution, different rocks, different immersion ways and different velocity of cycle flow on the fracture mechanical effects in rock. ②the mechanical effects of water-rock interaction on propagation of fractures is consistent with the mechanical effects on the peak strength of rock. ③the intensity of the mechanical fracture effects increases as the intensity of chemical action of water-rock increases. ④iron and calcium ion bearing mineral or cement in rock are some key ion or chemical composition, and especially iron ion-bearing mineral resulting in chemical action of water-rock to be provided with both positive and negative mechanical effects on rock. Through the above two tests, we suggest that primary factors influencing chemical damage in rock consist of the chemical property of rock and aqueous solution, the structure or homogeneity of rocks, the flow velocity of aqueous solution passing through rock, and cause of formation or evolution of rock. The paper explores the mechanism on the mechanical effects of water-rock interaction on rock by using the theory of chemistry and rock fracture mechanics with chemical damage proposed by author, the modeling method and the energy point of view. In this paper, the concept of absorbed suction between soil grains caused by capillary response is given and expounded, and the relation and basic distinction among this absorbed suction, surface tension and capillary pressure of the soil are analyzed and established. The law of absorbed suction change and the primary factors affecting it are approached. We hold that the structure suction are changeable along with the change of the saturation state in unsaturated soils. In view of this, the concept of intrinsic structure suction and variable structure suction are given and expounded, and this paper points out: What we should study is variable structure suction when studying the effective stress. By IIIy κHH's theory of structure strength of soils, the computer method for variable structure suction is analyzed, the measure method for variable structure suction is discussed, and it reach the conclusions: ①Besides saturation state, variable structure suction is affected by grain composition and packing patter of grains. ②The internal relations are present between structure parameter N in computing structure suction and structure parameter D in computing absorbed suction. We think that some problems exit in available principle of effective stress and shear strength theory for unsaturated soil. Based on the variable structure suction and absorbed suction, the classification of saturation in soil and a principle of narrow sense effective stress are proposed for unsaturated soils. Based on generalized suction, the generalized effective stress formula and a principle of generalized effective stress are proposed for unsaturated soils. The experience parameter χ in Bishop's effective stress formula is defined, and the principal factors influencing effective stress or χ. The primary factor affecting the effective stress in unsaturated soils, and the principle classifying unsaturated soils and its mechanics methods analyzing unsaturated soils are discussed, and this paper points out: The theory on studying unsaturated soil mechanics should adopt the micromechanics method, then raise it to macromechanics and to applying. Researching the mechanical effects of chemical action of water-soil on soil is of great importance to geoenvironmental hazard control. The texture of soil and the fabric of soil mass are set forth. The tests on physical and mechanical property are performed to investigate the mechanism of the positive and negative mechanical effects of different chemical property of aqueous solution. The test results make clear that the plastic limit, liquid limit and plasticity index are changed, and there exists both positive and negative effects on specimens in this test. Based on analyzing the mechanism of the mechanical effects of water-soil interaction on soil, author thinks that hydrochemical actions being provided with mechanical effects on soil comprise three kinds of dissolution, sedimentation or crystallization. The significance of these tests lie in which it is recognized for us that we may improve, adjust and control the quality of soils, and may achieve the goal geological hazard control and prevention.The present and the significance of the research on environmental effects of water-rock and soil interaction. Various living example on geoenvironmental hazard in this field are enumerated. Following above thinking, we have approached such ideals that: ①changing the intensity and distribution of source and sink in groundwater flow system can be used to control the water-rock and soil interaction. ②the chemical action of water-rock and soil can be used to ameliorate the physical and mechanical property of rocks and soils. Lastly, the research thinking and the research methods on mechanical effects and environmental effects of water-rock and soil interaction are put forward and detailed.

沾化凹陷火成岩油气藏形成条件和分布规律研究

As a kind of special lithologic ones, Igneous rock oil and gas pool is more and more paid attention, and it has different forming condition and distribution from conventional ones, such as various terrane distribution types, serious reservoir anisotropy, complicated hydrocarbon-bearing, so there is not successful experience to follow for exploration and development of this complex subtle oil and gas pool at present. For an example of Igneous oil and gas pool of Luo151 area in Zhanhua seg, Eastern China, this article study the difficult problem, including petrologic nd lithofacies analysis, Origin, invasion age and times of Igneous rock, reservoir anisotropy, Geological Modeling, Igneous reservoir synthesis evaluation. forming condition and distribution are studied synthetically, and an integrated method to predict igneous rock oil and gas pool is formed, which is evaluated by using development data. The Igneous rock is mainly diabase construction in Luo151 area of Zhanhua Sag, and petrologic types include carbonaceous slate, hornfels, and diabases. Based on analyzing synthetically petrologic component, texture and construct, 4 lithofacies zones, such as carbonaceous slate subfacies, hornfels subfacies containing cordierite and grammite, border subfacies and central subfacies, are divided in the diabase and wall rock. By studying on isotopic chronology, terrane configuration and imaging logging data, the diabase intrusion in Zhanhua Sag is formed by tholeiite magma emplacing in Shahejie formation stratum on the rift tension background Lower Tertiary in North China. The diabase intrusion of Luo151 is composed possibly of three periods magma emplacement. There is serious anisotropy in the diabase reservoirs of Luo151 in Zhanhua Sag. Fracture is primary reservoir space, which dominated by tensile fracture in high obliquity, and the fracture zones are mainly developed round joint belt of igneous rock and wall rock and position of terrane thickness changing rapidly. The generation materials of the reservoirs in Luo151 igneous oil pools consist of Intergranular micropore hornfels, condensate blowhole-solution void diabase condensate edge, the edge and center of the condensate seam diabase, of which are divided into horizontal, vertical and reticulated cracks according fracture occurrence. Based on the above research, a conceptual model of igneous rock reservoir is generated, which is vertically divided into 4 belts and horizontally 3 areas. It is built for the first time that classification evaluation pattern of igneous rock reservoir in this area, and 3 key wells are evaluated. The diabase construction is divided into grammite hornfels micropore type and diabase porous-fracture type reservoirs. The heavy mudstone layers in Third Member of Shahejie formation (Es3) provide favorable hydrocarbon source rock and cap formation, diabase and hornfels belts serve as reservoirs, faults and microcracks in the wall rocks as type pathways for oil and gas migration. The time of diabase invasion was about in the later deposition period of Dongying Formation and the middle of that of Guantao Formation, the oil generated from oil source rock of Es3 in the period of the Minghuazhen formation and is earlier more than the period of diabase oil trap and porous space forming. Based on geological and seismic data, the horizon of igneous rocks is demarcated accurately by using VSP and synthetic seismogram, and the shape distribution and continuity of igneous rocks are determined by using cross-hole seismic technology. The reservoir capability is predicted by using logging constraining inversion and neural network technology. An integrated method to predict igneous rock oil and gas pool is formed. The study is appraised by using development data. The result show the reservoir conceptual model can guide the exploration and development of oil pool, and the integrated method yielded marked results in the production.

东南极格罗夫山地区的陨石回收与研究

Chinese National Antarctic Research Expedition (CHTNARE) has collected 4480 meteorite specimens in the Grove Mountains, East Antarctica, from 1998 to 2003. According to the location characteristics and the diversity of the classification, the paper concludes that the Grove Mountains is another important meteorite concentration area in the Antarctica. The Concentration mechanisms at the site could be related to the last glacier activity and katabatic wind. An empirical model was proposed: 1) Probably during the Last Glacial Maximum, ice flow overrided the Gale Escarpment range in the area. Formerly concentrated meteorites were carried by the new glacier and stayed in the terminal moraine when the glacier retreated. 2) Blown by strong katabatic wind, Newly exposed meteorites on the ablation zone were scattered on the blue ice at the lee side of the Gale escarpment. Some of them would be buried when they were moved further onto the firn snow zone. Many floating meteorites stopped and mustered at the fringe of the moraine. The chemical-petrographic of 31 meteorites were assigned based on electron probe microanalyses, petrography and mineralogy, including 1 martian lherzolitic shergottite, 1 eucrite, 1 extreme fine grain octahedron iron meteorite, and 28 ordinary chondrites (the chemical groups: 7 H-group, 13 L-group, 6 LL-group, 2 L/LL group; the petrographic types: 6 unequilibrated type 3 and 22 equilibrated type 4-6). GRV99028 meteorite has the komatiite-like spinifex texture consisting of acicular olivine crystals and some hornblende-family minerals in the interstitial region. Possibly it has crystallized from a supercooled, impact-generated, ultramafic melt of the host chondrite, then experienced the retrogressive metamorphism. Four typical chondrule textures were studied: porphyritic texture, radiative texture, barred texture and glass texture. The minerals are characteristically enriched in MgO content.