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.

Cold event at 5 500 a BP recorded in mud sediments on the inner shelf of the East China Sea

A 700-year record (1.0-1.5 a resolution) of the East Asian winter monsoon (EAWM), based on grain-size analysis and AMS(14)C dating of Core EC2005 from the inner-shelf mud wedge of the East China Sea (ECS), was compared with the Dongge stalagmite delta O-18 record during the mid-Holocene. The upper muddy section of Core EC2005 has been formed mainly by suspended sediments derived from the Changjiang (Yangtze) River mouth since 7.3 ka BP. High precipitation and a strengthened EAWM might have played key roles in the high sedimentation rate (1 324-1 986 cm/ka) between 5.9-5.2 ka BP. The EAWM strengthened when the Asian summer monsoon weakened, especially around 5 500 a BP, which corresponded to a worldwide cold event. The EAWM during the mid-Holocene shows statistically significant solar periodicities at 62 and 11 a. The 5 500 a BP cold event might be resulted from orbital forcing and changes in solar activity.

A broad deglacial delta C-13 minimum event in planktonic foraminiferal records in the Okinawa Trough

The equatorial Pacific upwelling zone has been suspected of playing an important role in the global atmospheric CO2 changes associated with glacial-interglacial cycles. In order to assess the influencing scope of the surface water deglacial delta(13)C minimum in the tropical low-latitude Pacific, the core DGKS9603, collected from the middle Okinawa Trough, was examined for 4513 C records of planktonic foraminifera N. dutertrei and G. ruber. The planktonic foraminiferal delta(13)C records show a clear decreasing event from 20 to 6 cal. kaBP., which is characterized by long duration of about 14 ka and amplitude shift of 0.4 x 10(-3). Its minimum value occurred at 15.7 cal kaBP. The event shows fairly synchrony with the surface water deglacial delta(13)C minimum identified in the tropical Pacific and its marginal seas. Because there is no evidence in planktonic foraminiferal fauna and 45180 records for upwelling and river runoff enhancement, the broad deglacial delta(13)C minimum event in planktonic foraminiferal records revealed in core DGKS9603 might have been the direct influencing result of the deglacial surface water of the tropical Pacific. The identification for the event in the Okinawa Trough provides new evidence that the water evolution in the tropical low-latitude Pacific plays a key role in large regional, even global carbon cycle.

Heinrich event imprints in the Okinawa Trough: evidence from oxygen isotope and planktonic foraminifera

Planktonic foraminiferal faunas, oxygen isotope and modern analog technique sea surface temperature records were obtained in piston core DGKS9603 (28degrees08.869'N, 127degrees16.238'E, water depth 1100 in) collected from the middle Okinawa Trough. During the last glaciation, four cold events were identified and correlate Heinrich events (HE) H2-5 of the last 45 ka. During the last deglaciation, core DGKS9603 has begun to be influenced by the Kuroshio since about 16 cal ka BP. Three weakenings of this warm current occurred at about 2.8-5.3, 11.4 and 15.5 cal ka BP respectively. Among the three fluctuations, the oldest one is synchronous with HE1 and could be a response to the strong cooling observed in the North Atlantic Ocean. The fluctuation occurring at about 11.4 cal ka ago corresponds to the Younger Dryas within the age error bars. Our observations provide new evidence that the HEs documented from Greenland and the northern North Atlantic had a global climatic impact. Changes in the intensity of the East Asian monsoon could be the main mechanism responsible for the paleoccanographic variations observed in the Okinawa Trough. (C) 2001 Elsevier Science B.V. 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.

Dynamics of the cold-water event off the southeast coast of the United States in the summer of 2003

The cold-water event along the southeast coast of the United States in the summer of 2003 is studied using satellite data combined with in situ observations. The analysis suggests that the cooling is produced by wind-driven coastal upwelling, which breaks the thermocline barrier in the summer of 2003. The strong and persistent southwesterly winds in the summer of 2003 play an important role of lifting the bottom isotherms up to the surface and away from the coast, generating persistent surface cooling in July-August 2003. Once the thermocline barrier is broken, the stratification in the nearshore region is weakened substantially, allowing further coastal cooling of large magnitudes by episodic southerly wind bursts or passage of coastally trapped waves at periods of a few days. These short-period winds or waves would otherwise have no effects on the surface temperature because of the strong thermocline barrier in summer if not for the low-frequency cooling produced by the persistent southwesterly winds.

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.

Molecular systematics of pikas (genus Ochotona) inferred from mitochondrial DNA sequences

The phylogenetic relationships among worldwide species of genus Ochotona were investigated by sequencing mitochondrial cytochrome b and ND4 genes. Parsimony and neighbor-joining analyses of the sequence data yielded congruent results that strongly indicated three major clusters: the shrub-steppe group, the northern group, and the mountain group. The subgeneric classification of Ochotona species needs to be revised because each of the two subgenera in the present classification contains species from the mountain group. To solve this taxonomic problem so that each taxon is monophyletic, i.e., represents a natural clade, Ochotona could be divided into three subgenera, one for the shrub-steppe species, a second for the northern species, and a third for the mountain species. The inferred tree suggests that the differentiation of this genus in the Palearctic Region was closely related to the gradual uplifting of the Tibet (Qinghai-Xizang) Plateau, as hypothesized previously, and that vicariance might have played a major role in the differentiation of this genus on the Plateau, On the other hand, the North American species, O. princeps, is most likely a dispersal event, which might have happened during the Pliocene through the opening of the Bering Strait. The phylogenetic relationships within the shrub-steppe group are worth noting in that instead of a monophyletic shrub-dwelling group, shrub dwellers and steppe dwellers are intermingled with each other. Moreover, the sequence divergence within the sister tars of one steppe? dweller and one shrub dweller is very low. These findings support the hypothesis that pikes have entered the steppe environment several times and that morphological similarities within steppe dwellers were due to convergent evolution. (C) 2000 Academic Press.

东天山红山高硫型浅成低温铜-金矿床氧化带的形成机理和硫酸盐矿物的系列发现及意义

Located in the Paleozoic uplift along the southern margin of Tu-Ha basin in eastern Xinjiang, the newly discovered Hongshan Cu-Au deposit occurs in the superimposed Mesozoic volcanic basin upon the north section of later Paleozoic Dananhu-Tousuquan accretionary arc. Kalatage Cu-Au orebelt is controlled by NWW-trend faults, and includes Hongshan and Meiling Cu-Au deposits. The host rocks of Hongshan ore district are mainly rhyolitic-dacitic ignimbrites, whereas Cu-Au mineralization is closely related to quartz porphyry, rhyolitic porphyry and granitic porphyry. Mineralization styles are dominantly veinlet-disseminated and veinlet, occasionally stockwork. The mineral association is chalcopyrite, pyrite, bornite, chalcocite and sphalerite. The hydrothermal alteration consists of silicfication, sericitization, alunitization, pyrophylitization, illitization, hydromuscovitization, and chloritization. Hongshan Cu-Au deposit, on the edge of the desert, is one of the driest areas in eastrn Tianshan. Moreover， the highest temperature has been up to 60℃, and the average rainfall receives only 34.1mm/y. The light rainfall and rapid evaporation in the vicinity of this deposit have allowed the formation of a great variety of water-soluble sulfates. Oxidization zone of this deposit lies on the upper part of primary sulfide orebodies appearing with a depth of 50-60m, which is dominant in sulfate minerals. 1. Based on the field observation, the volcanic and sub-volcanic rock composition, hydrothermal alteration, ore structure and mineralization characteristics, this paper proposed that the Hongshan Cu-Au deposit belongs to a transitional type from high-sulfide epithermal to porphyry Cu-Au deposit, which corresponds with the typical HS-epithermal deposit such as Zijinshan Au-Cu deposit in Fujian Province, SE-China. 2. The Hongshan copper-gold deposit was controlled by the tectonic, stratum, magma activity and volcanic apparatus, whereas Au mineralization is closely related to quartz porphyry, rhyolitic porphyry and fine grained pyritization in hydrothermal activity, and Cu mineralization is closely related to quartz porphyry and hydrothermal explosive breccia. 3. Oxidation zone of Hongshan Cu-Au deposit lies on the upper part of primary sulfide orebodies deposit. 23 sulfate minerals were identified in this work. The results of samples XRD and chemical analysis were furthermore confirmed through thermal, infrared spectrum and mössbauer spectrum analysis. Among those, nine minerals as Ferricopiapite, Cuprocopiapite, Rhomboclase, Parabutlerite, Krausite, Yavapaiite, Metasideronatrite Kroehnkite and Paracoquimbite were founded in China for the first time. And Paracoquimbite was secondly reported in the world (first case reported at 1938 in Chile). 4. EPMA analysis shows that Al impurity in crystal lattice is important to polytype formation of paracoquimbite and coquimbite besides stack fault. 5. Compared with Meiling Cu-Au deposit in the same Kalatage ore belt from the characteristics of δ34S of barite, lithofacies, hydrothermal alteration and homogeneous temperature, Hongshan Cu-Au deposit belongs to the same metallogenic system of HS-epithermal type as Meiling Cu-Au deposit. But Hongshan Cu-Au deposit has less extensive alteration and shallower denudation. 6. Sulfur isotope analyses show that δ34S values of pyrites vary in the range of +1.86‰~+5.69‰, with an average of 3.70‰, mostly in the range of +1.86‰~+3.20‰, and δ34Scp<δ34Spy. Therefore ore-forming fluid of porphyry comes from mantle and was contaminated by the earth’s crust. Sulfur isotope has reached balance in ore-forming process. 7. Sulfur isotope analyses show that δ34S values of sulfates vary in the range of +2.15‰~+6.73‰, with an average of +3.74‰, mostly equals as δ34S values of primary sulfides in Hongshan Cu-Au deposit. So supergene sulfates inherit sulfur of primary sulfide. δ34S values are mostly same in different sulfates. As well as pyrite and chalcopyrite, volcanic hot spring and associated native sulfur underground also provide water medium and sulfur during the formation process of sulfate. 8. According to the EPMA of sample chalcopyrite and pyrite in Hongshan Cu-Au, the value of Cu/Ni is 0.98-34.72, mostly close to the value of 5, which shows that Hongshan deposit is a typical volcanogenic magmaic hypothermal deposit. Au and Ag, Zn, Te and Bi are positive correlation, Cu and Hg, Se, Sb are positive correlation, indicates Au and Cu don’t locate in the factor of mineralization of same mineralization groups. The reasons of gold concentration in the oxidation zone are: 1). Change of redox potential (Eh) makes gold to deposit from the liquid of mineralization zone; 2). PH is one of the most factors of gold’s deposition; 3). Soluble complex and colloid of gold can be adsorbed easily. 9. The biotite and hornblende K-Ar isotopic ages from the wall rock－quartz diorite, biotite granite and monzonite granite are 231.99±3.45Ma, 237.97±2.36Ma and 296.53±6.69Ma respectively. The ore-bearing rhyolitic breccia lava contains breccia of the biotite granite which indicates the volcanism and related Cu-Au mineralization occurred later than the granite, possibly in Mesozoic. K-Ar ages of granitoids in Sanya, Baishiquan and Hongliugou area and Molybdenite Re-Os age of Baishan Mo deposit all are in Triassic. Besides late Paleozoic magmatism, igneous magmatic event of Mesozoic was widespread in eastern Tianshan. 10. The K-Ar age dating indicates that the K-Ar age of Voltaite occurred below surface 1m is 56.02±3.98Ma, K-Ar age of Ferricopiapite occurred below surface 1.5m is 8.62±1.12Ma, K-Ar age of Yavapaiite occurred below surface 14 m is 4.07±0.39Ma, and K-Ar age of Voltaite occurred below surface 10 m is 14.73±1.73Ma. So the age interval of oxidation zone of Hongshan copper-golden bed is between 60 -3.38Ma. Oxidization occurred at Caenozoic era (from 65Ma), which can be identified through comparing with different deposits oxidation zone in other countries. The coupling between global tectonic event and climatic change event which occur from Caenozoic era has some effect on epigeosphere system, which can act on the surface of bed oxidation zone similarly. It induces that the age mentioned above coincide with collision of India-Asia and multistage uplifting of Qinhai-Tibet Plateau happened subsequently. Bed oxidation zone is the effect and record of collision and uplifting of Tibet Plateau. The strong chemical weathering of surface accumulation to which was leaded by PETM event occurred Paleocene and Eocene is the reason of Voltaite sharply rises. On the contrary, Ferricopiapite formed due to the global cold weather. The predecessor did much research through biota, isotopes, susceptibility, but this paper try to use different sulfate mineral instead of climatic change. So the research of sulfate minerals not only indicates a great deal of oxidized zone feature, but also the intergrowth of sulfate minerals may be used to trace paleoenviroment and paleoclimate of oxidation zone. 11. Analysis of the information of alteration and mineralization features of four bore cores, induced activity polarization well logging and Eh-4 geophysical section, deep mineralization anomaly objects of Hongshan ore districts shows low resistance, middle and high polarization, measurements of Eh-4 consecutive conductance section show the existing of concealed porphyry ore body deeper than 450m, on the top of and around rock body there are low resistance body ranged from 100-300Ω•m, this area may be the ore-bearing part. In a word, Hongshan Cu-Au deposit deposit is a combine of upper HS-style epithermal Au deposit and deeper porphyry mineralization system. It has great potential to find large HS-style epithermal-porphyry Au-Cu deposits. This paper consists of seven chapters and twenty seven sections. The geological character of deposit is basic condition in this work. Constitute of oxidation zone, research of sulfate mineral, relation between oxidation and primary zone, K-Ar ages of potassic sulfate are key parts of thesis. Genesis of ore deposit is the further expansion of this research. Analysis of ore-controlling factors is the penetration above basic. Analysis of potential is application of exploration.

承德公路隧道围岩分级与塌方机理分析

During tunnel constriction the classification of rock mass is widely used in tunnel design and construction. Moreover it offers the base information about tunnel investment and security. The quick classification of rock mass is very important for not delaying tunnel construction. Nowadays the tunnel engineers usually use initial survey files which are obtained by probe drilling to design a tunnel. It brings the problem that initial surrounding rock classification is usually much different from the real condition during the tunnel construction. Because initial surrounding rock lack credibility, it need us to make real time surrounding rock classification during the tunnel construction, and feed back the result to designers and constructors. Therefore, to find a quick wall rock classification method is very important not only for the time limit for a project but also for not delaying tunnel construction. Not all but many tunnels and underground constructions do suffer form collapse during the period of construction. Although accidental collapse in a large project in civil and geotechnical engineering sometimes appears to be a local event, if it occurred, it can bring about casualties, disrupted，production, construction delay, environmental damage, capital cost etc，therefore, it has been a difficult problem ,both in theory and in practice, establishing how to prevent underground structures form collapse and how to handle such an event in case in occurs. It is important to develop effective solutions and technical measures to prevent and control the collapse. According to the tunnel collapse occurred in Cheng De this paper analyze the main collapse mechanism leading to tunnel collapse and summon up the disposal method when collapse happened. It may be useful for tunnel construction in Cheng De in future. This paper is base on tunnel surrounding rock classification and tunnel support tasks during the tunnel construction in Cheng De area. It aims at solving 4 important problems in tunnel design and construction. 1) The relationship between rock rebound strength and rock single axle compression strength. First we go to the face wall and do rebound test on the tunnel face, then we chose some pieces of rock and do point loading test. Form the tests record we try to find the relationship between rock rebound strength and rock single axle compression strength. 2) The relationship between the value [BQ] and the value Q. First in order to obtain the information of rock character, rock strength, degree of weathering, the structure of rock mass, the joint condition, underground water condition and so on, we go to the tunnel face to do field investigation. And then we use two kinds of rock classification method to make surrounding rock classification. Base on the works above, finally we analyze the relationship between the value [BQ] and the value Q. 3) Sum up the mechanism leading to tunnel collapse and it disposal method in Cheng De area According to the tunnel collapse occurred in Cheng De this paper analyze the main reasons leading to the tunnel collapse and sum up the disposal method when collapse happened. 4) Obtain the properties of steel frame grid by numerical simulation. First we establish the 3D numeral model of steel frame grid by ADINA, and then find the mechanics properties by numerical simulation in ADINA. Second Based on the rock mass geological structure model, we established steel frame grid numeral model which is installed in the tunnel by FLAC3D and simulated the progress of tunnel construction. We hope that the support effect in tunnel can be evaluated from the numerical simulation.

三峡库区堆积层斜坡稳定性分级与应用研究

Considering the lacking of standard for the classification of Accumulative slopes so far, research working was conducted based on the results of geological investigation, data analysis and experiment carried out in Wanzhou. By mean of statistical method and grey system, the author studied in detail inflationary factors to Accumulative slopes. In order to study the mechanism of Rock-Soil Aggregate (RSA), numerical testing method was used. Coordinates in the two and three dimensional space and its corresponding rock fragments in the sample were generated randomly by VB and Particle flow code. After being built the models of RSA with different rock content, uniaxial and triaxial numerical simulation tests were carried out respectively. In order to study the effect of rainfall in Accumulative slopes, in situ infiltration testing had been conducted on site in Wanzhou, Three Gorges Area. Relationship between the infiltration rate and amount of precipitation has been obtained. Eleven factors are considered in the classification of Accumulative slopes in this paper.(1)On the basis of four basic factors and four inducing factors, sum-and-difference method for the classification system has been built. (2)After weight of factors being determined by analytic hierarchy process and membership function of Accumulative slopes stability being built in virtue of fuzzy mathematics, AHP-FM model of Accumulative slopes stability has been completed. In the end of this paper, having been applied on stability of Accumulative slopes in Three Gorge area and compared with result by limit equilibrium, classification system has good effect.