WheelerLab: An interactive program for sequence stratigraphic analysis of seismic sections, outcrops and well sections and the generation of chronostratigraphic sections and dynamic chronostratigraphic sections

OpenAIRE

Adewale Amosu; Yuefeng Sun

2017-01-01

WheelerLab is an interactive program that facilitates the interpretation of stratigraphic data (seismic sections, outcrop data and well sections) within a sequence stratigraphic framework and the subsequent transformation of the data into the chronostratigraphic domain. The transformation enables the identification of significant geological features, particularly erosional and non-depositional features that are not obvious in the original seismic domain. Although there are some software produ...

Salt tectonics and sequence-stratigraphic history of minibasins near the Sigsbee Escarpment, Gulf of Mexico

Science.gov (United States)

Montoya, Patricia

The focus of this research is to understand the stratigraphic and structural evolution of lower-slope minibasins in the Gulf of Mexico by examining the influence of salt tectonics on sediment transport systems and deep-water facies architecture. Results showed that gravitational subsidence and shortening can cause variations in the relief of salt massifs on opposing sides of a minibasin. These bathymetric variations, combined with changes in sedimentation rates through time, affected not only the distribution of deep-water facies inside the minibasins, but also influenced the evolution of sediment transport systems between minibasins. In order to understand the evolution of salt massifs, this dissertation presents a new approach to evaluate qualitatively the rate of relative massif uplift based on depoaxis shifts and channel geometries identified in minibasins surrounded by mobile salt. From these results it was established that compression was long-lived, and that extension only dominated during late intervals. Stratigraphic analyses showed that there is a strong cyclicity in deep-water facies stacking patterns within lower-slope minibasins, related primarily to cyclical changes in sedimentation rates. A typical sequence starts with a period of slow sedimentation associated with drape facies above each sequence boundary. Then, towards the middle and final stages of the sequence, sedimentation rates increase and turbidity flows fill the minibasin. Previous studies describe processes of fill-and-spill for two adjacent minibasins in the upper and middle slope. However, these models fail to adequately explain fill-and-spill processes in lower slope minibasins surrounded by mobile salt. In particular, they do not consider the effect of variations in bathymetric relief of the intervening massif, nor do they examine multidirectional connections between proximal and distal minibasins. A new dynamic-salt fill-and-spill model is proposed in this dissertation in order to

Development of a shelf margin delta due to uplift of Munkagrunnur Ridge at the margin of Faroe-Shetland Basin: a seismic sequence stratigraphic study

DEFF Research Database (Denmark)

Òlavsdóttir, Jana; Boldreel, Lars Ole; Andersen, Moretn S

2010-01-01

During the last decade several 3D digital reflection seismic datasets have been acquired in the Faroese sector of the Faroe-Shetland Basin which allow detailed seismic interpretation and mapping of parts of the area. This study presents mapping and seismic sequence stratigraphic interpretation of...

Facies-succession and architecture of the third-order sequences and their stratigraphic framework of the Devonian in Yunnan-Guizhou-Guangxi area, South China

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Mei Mingxiang

2013-01-01

Full Text Available The Caledonian orogeny at the end of the Silurian resulted in great changes in the palaeogeography in the Yunnan-Guizhou-Guangxi area of South China; the continental area of the Early Paleozoic evolved into the extensive Dian-Qian-Gui Sea in the Late Paleozoic. Early in the Devonian, as a result of a major transgression, seawater encroached gradually from the south to the north and clastic facies were deposited. Carbonate deposition was then established in the Yunnan-Guizhou-Guangxi area, with a palaeogeography marked by attached platforms, isolated platforms and narrow basins. As a result of the Ziyun movement towards the end of the Devonian, the Upper Devonian strata are regressive and thin out from the open-sea to the land areas. A study of the nature and distribution of sedimentary facies in space and time recognises 13 third-order sequences in the Devonian strata in Yunnan-Guizhou-Guangxi area, and these form two second-order sequences. The strata of the Lower Devonian comprise 5 third-order sequences (SQ1 to SQ5, which are dominated by transgressive clastics. 4 third-order sequences (SQ6 to SQ9 in the Middle Devonian are characterized by alternations of transgressive clastics and highstand carbonates. In the Upper Devonian, carbonates constitute 4 third-order sequences (SQ10 to SQ13, which are generally marked by the transgressive limestones and highstand dolomites. On the basis of earlier biostratigraphic studies, sea-level changes represented by the third-order sequences with their different facies successions are explored, and the sequence stratigraphic framework is established. Therefore, the Devonian strata in the study area provide an example for further understanding of depositional trends within the sequence-stratigraphic framework.

Lithofacies and sequence stratigraphic description of the upper part of the Avon Park Formation and the Arcadia Formation in U.S. Geological Survey G–2984 test corehole, Broward County, Florida

Science.gov (United States)

Cunningham, Kevin J.; Robinson, Edward

2017-07-18

Rock core and sediment from U.S. Geological Survey test corehole G–2984 completed in 2011 in Broward County, Florida, provide an opportunity to improve the understanding of the lithostratigraphic, sequence stratigraphic, and hydrogeologic framework of the intermediate confining unit and Floridan aquifer system in southeastern Florida. A multidisciplinary approach including characterization of sequence stratigraphy, lithofacies, ichnology, foraminiferal paleontology, depositional environments, porosity, and permeability was used to describe the geologic samples from this test corehole. This information has produced a detailed characterization of the lithofacies and sequence stratigraphy of the upper part of the middle Eocene Avon Park Formation and Oligocene to middle Miocene Arcadia Formation. This enhancement of the knowledge of the sequence stratigraphic framework is especially important, because subaerial karst unconformities at the upper boundary of depositional cycles at various hierarchical scales are commonly associated with secondary porosity and enhanced permeability in the Floridan aquifer system.

Stratigraphic, Structural and Petrophysical Evaluation of borehole images obtained in oil based mud environment from Clastics of Niger Delta

International Nuclear Information System (INIS)

Ogunyemi, T.

2003-01-01

With the advent of oil-base and synthetic muds, drilling risks are substantially reduced and efficiency dramatically increased, but the benefits of borehole imaging devices were lost as it presents a 'brick-wall' and difficult environment that precludes the use of conventional water- base mud microresistivity imaging devices. The introduction of Oil Base Imager tools offers a solution to the situation and even brings additional values. Borehole images integrated with high resolution Magnetic Resonnance data and other open hole logs has been evaluated for stratigraphic, structural and petrophysical applications as well as computing high-resolution sand count. Examples will be discussed in this paper. The sequence studied is clastics with intercalated sand/shale sequences typical of Niger Delta. The use of oil based mud images and open-hole log data helped to further classify the sequence into depositional environments. Generally speaking high-resolution image data presents opportunity for accurate results especially in intercalated sand/shale sequence compare to standard open hole logs. Individual pad resistivity response offer a very high resolution measurement that was used to drive the net pay sand count analysis. This approach has been proven to be helpful in completion decision, providing accurate reservoir parameters for well/field economics and development

Stratigraphic position, origin and characteristics of manganese mineralization horizons in the Late Cretaceous volcano-sedimentary sequence, south-southwest of Sabzevar

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Sajjad Maghfouri

2014-10-01

Full Text Available Introduction The Mn mineralization occurs in the northeastern segment of the Sabzevar zone (SZ, north of the Central Iranian Microcontinent (CIM. This Zone (SZ is located between the CIM fragmentation in the south and the Kopeh dagh sedimentary sequence in the north. The ore deposits of the northeastern segment of the Sabzevar zone can be divided into three groups, each with different metal association and spatial distribution and each related to a major geodynamic event. The first mineralization with associated Ordovician host rock is characterized by Taknar polymetallic (Fe-rich massive sulfide deposit. The Cretaceous mineralization consists of Cr deposits associated with serpentinized peridotites, Cyprus type VMS, Mn deposit in pillow lava, volcano-sedimentary hosted Besshi type VMS and Mn deposit. Paleogene mineralization in eastern segment of the Sabzevar zone began with porphyry deposits, Cu Red Bed mineralization occurs in the Paleogene sandy red marl. Materials and methods A field study and sampling was performed during the autumn of 2012. To assess the geochemical characteristics of 48 systematic samples (least fractured and altered of ore-bearing layers and host rocks were collected from the deposit for polished thin section examination. In order to correctly characterize their chemical compositions, 15 least-altered and fractured samples were chosen for major elements analysis. Results The Late Cretaceous volcano-sedimentary sequence in south-southwest of Sabzevar hosts numerous manganese mineralization. The sequence based on the stratigraphic position, age and composition of the rocks, can be divided into two lower and upper parts. The lower part or K2tv unit mainly formed from marine sediments interbedded with volcanic rocks. The sedimentary rocks of this part include silicified tuff, chert, shale and sandstone, and the volcanic rocks involve pyroclastic rocks of various composition, rhyolite, dacite and andesitic lava. The upper

Stratigraphical sequence and geochronology of the volcanic rock series in caifang basin, south jiangxi

International Nuclear Information System (INIS)

Xu Xunsheng; Wu Jianhua

2010-01-01

The late Mesozoic volcanic rocks in Jiangxi constitute two volcanic belts: the northern is Xiajiang-Guangfeng volcanic belt, the volcanic rocks series belong to one volcano cycle and named Wuyi group which is subdivided into three formations (Shuangfengling formation, Ehuling formation and Shixi formation); the southern is Sannan-Xunwu volcanic belt, the volcanic rocks series in Caifang basin which locates on Sannan-Xunwu volcanic belt also belong to only one volcano cycle. It can be subdivided into two lithology and lithofacies units (upper and lower): the lower unit consists of sedimentary rocks and associated with a subordinate amount of volcanic rocks, it belongs to erupt-deposit facies which is the product of early volcanic stage; the upper unit is mostly composed of volcanic rocks, it belongs to erupt facies that is the volcanic eruption product. SHRIMP zircon U-Pb age of rhyolite? which locates at the top of the upper unit is 130.79 ± 0.73) Ma. According to the new International Stratigraphic Chart, the boundary of Jurassic and Cretaceous is (145.4 ± 4.0) Ma, so the age shows that the geologic period of Caifang volcanic rocks series is early Early Cretaceous epoch. On the basis of lithological correlation, lithofacies and stratigraphic horizon analysis, the volcanic rock series in Caifang basin fall under Wuyi group, and the lower unit could be incorporated into Shuangfengling formation, the upper unit could be incorporated into Ehuling formation. The subdivision of sequence and the determination of geochronology of the volcanic rock series in Caifang basin provide some references for the study of the late Mesozoic volcanic rocks series of the Sannan-Xunwu volcanic belt. (authors)

Some debatable problems of stratigraphic classification

Science.gov (United States)

Gladenkov, Yury

2014-05-01

Russian geologists perform large-scale geological mapping in Russia and abroad. Therefore we urge unification of legends of geological maps compiled in different countries. It seems important to continuously organize discussions on problems of stratigraphic classification. 1. The stratigraphic schools (conventionally called "European" and "American") define "stratigraphy" in different ways. The former prefers "single" stratigraphy that uses data proved by many methods. The latter divides stratigraphy into several independent stratigraphers (litho-, bio-, magneto- and others). Russian geologists classify stratigraphic units into general (chronostratigraphic) and special (in accordance with a method applied). 2. There exist different interpretations of chronostratigraphy. Some stratigraphers suppose that a chronostratigraphic unit corresponds to rock strata formed during a certain time interval (it is somewhat formalistic because a length of interval is frequently unspecified). Russian specialists emphasize the historical-geological background of chronostratigraphic units. Every stratigraphic unit (global and regional) reflects a stage of geological evolution of biosphere and stratisphere. 3. In the view of Russian stratigraphers, the main stratigraphic units may have different extent: a) global (stage), b) regional (regional stage,local zone), and c) local (suite). There is no such hierarchy in the ISG. 4. Russian specialists think that local "lithostratigraphic" units (formations) which may have diachronous boundaries are not chronostratigraphic ones in strict sense (actually they are lithological bodies). In this case "lithostratigraphy" can be considered as "prostratigraphy" and employed in initial studies of sequences. Therefore, a suite is a main local unit of the Russian Code and differs from a formation, although it is somewhat similar. It does not mean that lithostratigraphy is unnecessary. Usage of marker horizons, members and other bodies is of great help

Stratigraphic sequence and sedimentary characteristics of Lower Silurian Longmaxi Formation in Sichuan Basin and its peripheral areas

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Yuman Wang

2015-03-01

Full Text Available A high-precision sedimentary environment study of the Lower Silurian Longmaxi Formation is an important subject for shale gas exploration and development in Sichuan Basin and its surrounding areas. On the basis of outcrops and drilling data, its isochronous stratigraphic framework was built according to a particular graptolite zone and an important marker bed, and lithofacies, paleontology, calcareous content, well logging, geochemistry and other geologic information were combined to describe the sedimentary microfacies of Longmaxi Formation and its stratigraphic sequence, sedimentary evolution process and high quality shale distribution features as follows: ① with regional diachronism of the top and the bottom, the Longmaxi Formation is divided into two third-order sequences (SQ1 and SQ2, of which SQ1 is mainly an abyssal sedimentary assemblage deposited in the marine transgression period, and SQ2 is a bathyal to shallow sea sedimentary assemblage deposited in the marine regression period; ② there are eight microfacies such as deep calcareous shelf and deep argillaceous shelf in this formation and the organic-rich shale was mainly deposited in the deep water area of SQ1; and ③ from SQ1 to SQ2, the depocenter moved from the depression area in southern-eastern to northern Sichuan Basin, but the central Sichuan uplift remained an underwater one. It is concluded from this study that: ① shale gas production layers were mainly deposited in SQ1, the southern-eastern depression area was the depocenter in SQ1 and a shale gas enrichment area; and ② black shale in northern Sichuan was deposited in late SQ2, with limited distribution and relatively insufficient exploration potential, but the potential of shale gas exploration in western Hubei area is between southern-eastern and northern Sichuan Basin.

Chronostatigraphy of limistone sequency of north Brazilian coast based on data from stronium isotope

International Nuclear Information System (INIS)

Takaki, T.; Rodrigues, R.

1987-01-01

The strontium isotope composition of marine limestones can be a valuable tool for stratigraphic correlation, in addition to other techniques usually employed for this purpose. The technique can render particularly important in sequences where the fossil assemblage do not present good stratigraphic resolution. As examples, data from Mesozoic and Cenozoic limestone sequences of north Brazilian coast are here presented. Data on strontium isotope composition are compared to those obtained by De Paolo and Ingram in another geographic locations. (author) [pt

Stratigraphic analysis and geodynamic evolution of the 'Transitional Sequence' in the southern Sergipe-Alagoas Basin; Analise estratigrafica e evolucao geodinamica da 'Sequencia Transicional' na porcao sul da Bacia de Sergipe-Alagoas

Energy Technology Data Exchange (ETDEWEB)

Cruz, Liliane Rabelo [Petrobras, Natal/Fortaleza, RN/CE (Brazil). Unidade de Operacoes de Exploracao e Producao. Avaliacao de Blocos e Interpretacao Geologica e Geofisica], E-mail: lilianerabelo@petrobras.com.br; Cordoba, Valeria Centurion; Sa, Emanuel Ferraz Jardim de [Universidade Federal do Rio Grande do Norte (UFRN), Natal, RN (Brazil). Centro de Ciencias Exatas e da Terra. Programa de Pos-Graduacao em Geodinamica e Geofisica], Emails: valeria.geo@ufrnet.br, emanuel@ccet.ufrn.br

2009-11-15

This paper presents a stratigraphic analysis and considerations about the tectonic activity and subsidence processes that controlled the deposition of the 'Transitional Sequence' in the Sergipe Sub-basin (SBSE), southern Sergipe-Alagoas Basin, during the Neoaptian (upper Alagoas), the transition between the rift and drift stages in this basin. The stratigraphic analysis of selected wells led to the recognition of five third order depositional sequences, that were deposited in decreasing conditions of water circulation, from continental siliciclastic systems to lagoonar-evaporitic systems and, finally, to restricted marine systems, indicating an increase of the base level. In terms of a second order cycle, the 'Transitional Sequence' represents the deposition in a stage of base-level rise and the beginning deposition of a transgressive system tract, whose transition to the overlying marine transgressive sequence is marked by flooding. In terms of a third order cycle, this transition is marked by a local unconformity, which laterally changes to a correlative conformity. Such unconformity is interpreted as a breakup unconformity, of pre-Albian age in the SBSE, contrasting with the more expressive (especially for its angular character) of the Pre-Upper Alagoas Unconformity (DPAL), at the base of the 'Transitional Sequence', frequently regarded in the literature as the breakup unconformity. Even though, the Pre-Albian Unconformity is here favoured as the major change in depositional context and tectonic environment (rift to drift) in the SBSE. The deposition of the 'Transitional Sequence' occurred close to the end of the Rifting Stage, with an epicontinental sea advancing along a segment of continental crust still in extension, controlled by a combination of thermal and mechanical subsidence, the latter already in pronounced decline. (author)

Stratigraphic controls on saltwater intrusion in the Dominguez Gap area of coastal Los Angeles

Science.gov (United States)

Edwards, B.D.; Ehman, K.D.; Ponti, D.J.; Reichard, E.G.; Tinsley, J.C.; Rosenbauer, R.J.; Land, M.

2009-01-01

The Los Angeles Basin is a densely populated coastal area that significantly depends on groundwater. A part of this groundwater supply is at risk from saltwater intrusion-the impetus for this study. High-resolution seismic-reflection data collected from the Los Angeles-Long Beach Harbor Complex have been combined with borehole geophysical and descriptive geological data from four nearby ??400-m-deep continuously cored wells and with borehole geophysical data from adjacent water and oil wells to characterize the Pliocene to Holocene stratigraphy of the Dominguez Gap coastal aquifer system. The new data are shown as a north-south, two- dimensional, sequence-stratigraphic model that is compared to existing lithostratigraphic models of the Los Angeles Basin in an attempt to better understand pathways of saltwater intrusion into coastal aquifers. Intrusion of saltwater into the coastal aquifer system generally is attributed to over-pumping that caused the hydraulic gradient to reverse during the mid-1920s. Local water managers have used the existing lithostratigraphic model to site closely spaced injection wells of freshwater (barrier projects) attempting to hydraulically control the saltwater intrusion. Improved understanding of the stratigraphic relationships can guide modifications to barrier design that will allow more efficient operation. Allostratigraphic nomenclature is used to define a new sequence-stratigraphic model for the area because the existing lithostratigraphic correlations that have been used to define aquifer systems are shown not to be time-correlative. The youngest sequence, the Holocene Dominguez sequence, contains the Gaspur aquifer at its base. The Gaspur aquifer is intruded with saltwater and consists of essentially flat-lying gravelly sands deposited by the ancestral Los Angeles River as broad channels that occupied a paleovalley incised into the coastal plain during the last glacio-eustatic highstand. The underlying sequences are deformed into

SDAR 1.0 a New Quantitative Toolkit for Analyze Stratigraphic Data

Science.gov (United States)

Ortiz, John; Moreno, Carlos; Cardenas, Andres; Jaramillo, Carlos

2015-04-01

Since the foundation of stratigraphy geoscientists have recognized that data obtained from stratigraphic columns (SC), two dimensional schemes recording descriptions of both geological and paleontological features (e.g., thickness of rock packages, grain size, fossil and lithological components, and sedimentary structures), are key elements for establishing reliable hypotheses about the distribution in space and time of rock sequences, and ancient sedimentary environmental and paleobiological dynamics. Despite the tremendous advances on the way geoscientists store, plot, and quantitatively analyze sedimentological and paleontological data (e.g., Macrostrat [http://www.macrostrat.org/], Paleobiology Database [http://www.paleodb.org/], respectively), there is still a lack of computational methodologies designed to quantitatively examine data from a highly detailed SCs. Moreover, frequently the stratigraphic information is plotted "manually" using vector graphics editors (e.g., Corel Draw, Illustrator), however, this information although store on a digital format, cannot be used readily for any quantitative analysis. Therefore, any attempt to examine the stratigraphic data in an analytical fashion necessarily takes further steps. Given these issues, we have developed the sofware 'Stratigraphic Data Analysis in R' (SDAR), which stores in a database all sedimentological, stratigraphic, and paleontological information collected from a SC, allowing users to generate high-quality graphic plots (including one or multiple features stored in the database). SDAR also encompasses quantitative analyses helping users to quantify stratigraphic information (e.g. grain size, sorting and rounding, proportion of sand/shale). Finally, given that the SDAR analysis module, has been written in the open-source high-level computer language "R graphics/statistics language" [R Development Core Team, 2014], it is already loaded with many of the crucial features required to accomplish basic and

Revised stratigraphic nomenclature and correlation of early proterozoic rocks of the Darwin - Katherine region, Northern Territory

International Nuclear Information System (INIS)

Needham, R.S.; Stuart-Smith, P.G.

1984-01-01

New stratigraphic names and correlations are given for parts of the Early Proterozoic Pine Creek Geosyncline metasedimentary sequence and overlying felsic volcanics of the Darwin-Katherine region. They have significant implications for the stratigraphic distribution of uranium mineralisation in the Rum Jungle, Alligator Rivers and South Alligator Valley uranium fields

Characteristics, stratigraphic architecture, and time framework of multi-order mixed siliciclastic and carbonate depositional sequences, outcropping Cisco Group (Late Pennsylvanian and Early Permian), Eastern Shelf, north-central Texas, USA

Science.gov (United States)

Yang, Wan; Kominz, Michelle A.

2003-01-01

The Cisco Group on the Eastern Shelf of the Midland Basin is composed of fluvial, deltaic, shelf, shelf-margin, and slope-to-basin carbonate and siliciclastic rocks. Sedimentologic and stratigraphic analyses of 181 meter-to-decimeter-scale depositional sequences exposed in the up-dip shelf indicated that the siliciclastic and carbonate parasequences in the transgressive systems tracts (TST) are thin and upward deepening, whereas those in highstand systems tracts (HST) are thick and upward shallowing. The sequences can be subdivided into five types on the basis of principal lithofacies, and exhibit variable magnitude of facies shift corresponding to variable extents of marine transgression and regression on the shelf. The sequence stacking patterns and their regional persistence suggest a three-level sequence hierarchy controlled by eustasy, whereas local and regional changes in lithology, thickness, and sequence type, magnitude, and absence were controlled by interplay of eustasy, differential shelf subsidence, depositional topography, and pattern of siliciclastic supply. The outcropping Cisco Group is highly incomplete with an estimated 6-11% stratigraphic completeness. The average duration of deposition of the major (third-order) sequences is estimated as 67-102 ka on the up-dip shelf and increases down dip, while the average duration of the major sequence boundaries (SB) is estimated as 831-1066 ka and decreases down dip. The nondepositional and erosional hiatus on the up-dip shelf was represented by lowstand deltaic systems in the basin and slope.

Early Permian transgressive-regressive cycles: Sequence stratigraphic reappraisal of the coal-bearing Barakar Formation, Raniganj Basin, India

Science.gov (United States)

Bhattacharya, Biplab; Bhattacharjee, Joyeeta; Bandyopadhyay, Sandip; Banerjee, Sudipto; Adhikari, Kalyan

2018-03-01

The present research is an attempt to assess the Barakar Formation of the Raniganj Gondwana Basin, India, in the frame of fluvio-marine (estuarine) depositional systems using sequence stratigraphic elements. Analysis of predominant facies associations signify deposition in three sub-environments: (i) a river-dominated bay-head delta zone in the inner estuary, with transition from braided fluvial channels (FA-B1) to tide-affected meandering fluvial channels and flood plains (FA-B2) in the basal part of the succession; (ii) a mixed energy central basin zone, which consists of transitional fluvio-tidal channels (FA-B2), tidal flats, associated with tidal channels and bars (FA-B3) in the middle-upper part of the succession; and (iii) a wave-dominated outer estuary (coastal) zone (FA-B4 with FA-B3) in the upper part of the succession. Stacked progradational (P1, P2)-retrogradational (R1, R2) successions attest to one major base level fluctuation, leading to distinct transgressive-regressive (T-R) cycles with development of initial falling stage systems tract (FSST), followed by lowstand systems tract (LST) and successive transgressive systems tracts (TST-1 and TST-2). Shift in the depositional regime from regressive to transgressive estuarine system in the early Permian Barakar Formation is attributed to change in accommodation space caused by mutual interactions of (i) base level fluctuations in response to climatic amelioration and (ii) basinal tectonisms (exhumation/sagging) related to post-glacial isostatic adjustments in the riftogenic Gondwana basins.

Revised Cretaceous and Tertiary stratigraphic nomenclature in the Colville Basin, Northern Alaska

Science.gov (United States)

Mull, Charles G.; Houseknecht, David W.; Bird, Kenneth J.

2003-01-01

A revised stratigraphic nomenclature is proposed for Cretaceous and Tertiary geologic units of the central and western North Slope of Alaska. This revised nomenclature is a simplified and broadly applicable scheme suitable for a suite of digital geologic quadrangle maps being prepared jointly by the U.S. Geological Survey and the Alaska Department of Natural Resources, Division of Geological and Geophysical Surveys and Division of Oil and Gas. This revised nomenclature scheme is a simplification of a complex stratigraphic terminology that developed piecemeal during five decades of geologic investigations of the North Slope. It is based on helicopter-supported geologic field investigations incorporating information from high-resolution aerial photography, satellite imagery, paleontology, reflection seismic records, and sequence stratigraphic concepts. This revised nomenclature proposes the abandonment of the Colville Group; demotion of the Nanushuk Group to formation status; abandonment of six formations (Kukpowruk, Tuktu, Grandstand, Corwin, Chandler, and Ninuluk); revision of four formations (Sagavanirktok, Prince Creek, Schrader Bluff, and Seabee); elevation of the Tuluvak Tongue of the Prince Creek Formation to formation status; revision of two members (Franklin Bluffs Member and Sagwon Member of the Sagavanirktok Formation); abandonment of eight members or tongues (Kogosukruk, Rogers Creek, Barrow Trail, Sentinel Hill, Ayiyak, Shale Wall, Niakogon, and Killik); and definition of one new member (White Hills Member of the Sagavanirktok Formation).

Sequence stratigraphic analysis of Cenomanian greenhouse palaeosols: A case study from southern Patagonia, Argentina

Science.gov (United States)

Varela, Augusto N.; Veiga, Gonzalo D.; Poiré, Daniel G.

2012-10-01

proximal fluvial floodplains, respectively. The palaeosol succession for the Mata Amarilla Formation can be analysed within a sequence stratigraphic scheme considering changes in depositional environments in relation to accommodation/supply conditions. The results contrast with classical models, mainly in that the palaeosols of the Mata Amarilla Formation are relatively well-developed throughout the whole sequence, including transgressive periods of relatively high aggradation rate. Also, even when during regressive episodes, when a thick palaeosol succession that marks the sequence boundary is developed in the classical models, the lack of incised valleys in this succession led to the preservation of thick palaeosol successions during lowstand conditions. The vertical and lateral palaeosol distribution identified in the Mata Amarilla Formation could be eventually extrapolated to other sequences deposited during climate optimums.

High-resolution sequence stratigraphic correlation of the braided river and vertical distribution characteristics of sand body-Take upper member of saihan formation of lower cretaceous in Bayanwula deposit, for instance

International Nuclear Information System (INIS)

Dai Mingjian; Peng Yunbiao; Yang Jianxin; Shen Kefeng

2014-01-01

In recent years, the high-resolution sequence stratigraphy of which reference surface is base level cycle get rapid development. Its biggest advantage is the ability to apply to the continental sedimentary basins controlled by multiple factors, especially applied to the thin layer contrast of the paleochannel sandstone type uranium reservoir. This paper, by using drill core and logging data, has made the high resolution sequence stratigraphy studies on braided river uranium reservoir of Upper Member of Saihan Formation of Lower Cretaceous (Kls2) in Bayanwula deposit and identified the base level cycle interface. The study interval is divided into one long-term cycle and seven mid-term base level cycle, and high-resolution time stratigraphic framework of the deposit is established. Depth analysis is taken for the relationship between the braided river sand body and base level cycles. And the position, distribution, and genesis in vertical of the braided river sand body are discussed in detail. Ore body is mainly hosted in edge of braided bar sand body, which formed in the low accommodation space, and braided channel and the braided bar interchange. So uranium enriched in the mid-term base level cycle MSC2-MSC5 in the study area. (authors)

Study on the application of seismic sedimentology in a stratigraphic-lithologic reservoir in central Junggar Basin

Science.gov (United States)

Yu, Yixin; Xia, Zhongmou

2017-06-01

This paper discusses the research idea of description for stratigraphic-lithologic reservoir based on seismic sedimentology methods. The sandstone reservoir of Jurrassic XiShanyao Formation in Junggar Basin is studied according to the theory and approaches of seismic sedimentology. By making full use of borehole data, the technologies of layer correlation based on the stratigraphic sequence framework, the forward seismic modeling, the stratal slicing and lithologic inversion are applied. It describes the range of denudation line, the distribution characteristics of sedimentary facies of the strata, the vertical and horizontal distribution of sand bodies and the favourable oil-gas bearing prospective area. The results shows that study area are dominated braided delta deposition including underwater distributary channel and distributary bay microfacies, the nip-out lines of the formation are northeast to southwest from north to south, the second Middle Jurassic sand body is the most widely distributed one among three sand bodies, the prospective oil-gas bearing area located in the south part and around the YG2 well area. The study result is effective on the practice of exploration in study area.

Formation and distribution of large lithologic-stratigraphic oil & gas fields (provinces

Directory of Open Access Journals (Sweden)

Shizhen Tao

2018-02-01

Full Text Available Since the “Tenth Five-Year Plan”, lithologic and stratigraphic reservoirs have been the main contribution of both the discovery as well as reserve and production increase in China; there were about 80% of proven reserves. The typical reservoirs in six major basins in the eastern, central, and western China were adopted as reservoir forming models. The reservoir forming models in three types of slopes, three types of depressions, and three types of lithologic reservoir assemblages have been built on the basis of application of new technologies, physical modeling of reservoir forming mechanism, and investigation to the formation and distribution of the reservoirs. The evaluation methods for large lithologic reservoirs provinces were established based on the forming mechanism and main controlling factors mentioned above. In addition, the study reveals the main controlling factors and the laws of enrichment of two types of stratigraphic reservoirs (pinch-out and weathered karst reservoirs based on the evaluation methods for large stratigraphic reservoir provinces that have been established. By comprehensively understanding the laws of enrichment of lithologic-stratigraphic reservoirs in four types of basins, specific evaluation methods and fine exploration techniques have been developed. The findings led to an exploration direction in the “Thirteenth Five-Year Plan” period. The study supported the exploration and selection of oil and gas plays, as well as promoted the exploration of lithologic and stratigraphic reservoirs. Keywords: Lithologic trap, Stratigraphic trap, Lithostratigraphic reservoir, Large oil and gas field, Large oil and gas province, Formation and distribution, Exploration potential

Fine reservoir structure modeling based upon 3D visualized stratigraphic correlation between horizontal wells: methodology and its application

Science.gov (United States)

Chenghua, Ou; Chaochun, Li; Siyuan, Huang; Sheng, James J.; Yuan, Xu

2017-12-01

As the platform-based horizontal well production mode has been widely applied in petroleum industry, building a reliable fine reservoir structure model by using horizontal well stratigraphic correlation has become very important. Horizontal wells usually extend between the upper and bottom boundaries of the target formation, with limited penetration points. Using these limited penetration points to conduct well deviation correction means the formation depth information obtained is not accurate, which makes it hard to build a fine structure model. In order to solve this problem, a method of fine reservoir structure modeling, based on 3D visualized stratigraphic correlation among horizontal wells, is proposed. This method can increase the accuracy when estimating the depth of the penetration points, and can also effectively predict the top and bottom interfaces in the horizontal penetrating section. Moreover, this method will greatly increase not only the number of points of depth data available, but also the accuracy of these data, which achieves the goal of building a reliable fine reservoir structure model by using the stratigraphic correlation among horizontal wells. Using this method, four 3D fine structure layer models have been successfully built of a specimen shale gas field with platform-based horizontal well production mode. The shale gas field is located to the east of Sichuan Basin, China; the successful application of the method has proven its feasibility and reliability.

Sequence stratigraphic analysis and the origins of Tertiary brown coal lithotypes, Latrobe Valley, Gippsland Basin, Australia

Energy Technology Data Exchange (ETDEWEB)

Holdgate, G R; Kershaw, A P; Sluiter, I R.K. [Monash University, Clayton, Vic. (Australia). Dept. of Earth Sciences

1995-11-01

Sequence analysis methods have been applied to the onshore Gippsland Basin and to the Latrobe Valley Group coal measures. In the east of the Latrobe Valley evidence for marine transgressions into the coal measures are recorded in most of the interseam sediment splits by the presence of contained foraminifer and dinoflagellates. To the west these splits pinch out into continuous coal. However, they can be followed westwards as enhanced organic sulphur levels along sharply defined boundaries between light coal lithotypes below and dark coal lithotypes above. The dark lithotype immediately overlying each of these boundaries contains the highest sulphur value and warmer climate pollen assemblages. Colorimeter and lithotype logging supports an upwards lightening cyclicity to coal colour at 12-20 m intervals through the approx. 100 m thick seams, with cycle boundaries defined at sharp planar to undulating surfaces. The lightening upward lithotype cycles together with their unique boundary conditions are interpreted as parasequences and parasequence boundaries respectively. Each major coal seam can comprise up to five parasequences and is interpreted to represent deposition during an outbuilding high stand systems tract at one of several maximum periods of Tertiary coastal onlap. Stratigraphic correlation of the sequence boundaries identified in the coal measures to the internationally dated marine Seaspray Group, provides a basis for chronostratigraphic correlation of the coal successions to the coastal onlap charts of Haq et al (1989). It appears that each major seam is confined to high standards of third order eustatic cycles. It follows that the lithotype cycles that comprise each seam are related to fourth order eustatic cycles. 49 refs., 11 figs., 1 tab.

The stratigraphic distribution of large marine vertebrates and shell beds in the Pliocene of Tuscany

Science.gov (United States)

Dominici, Stefano; Benvenuti, Marco; Danise, Silvia

2015-04-01

The record of 337 shark fossils, 142 cetaceans and 10 sea cows from the Pliocene of Tuscany, mostly from historical museum collections, is revised. The majority of these fossils are concentrated at a few geographic sites from separated hinterland basins, on the South-Western side of the Northern Apennines. To better understand the meaning of these concentrations, the sequence stratigraphic distribution of more recent findings of large marine vertebrates is reconstructed against a high-resolution framework based on sedimentary facies analysis. These remains are usually covered by, or included in mudstones deposited far from the coast (N=12), skeletons being usually articulated, slightly displaced, and often bioeroded. A minor part of better preserved articulated skeletons is associated with sandstones from deltaic paleonenvironments (N=2). Marine mammal and shark remains may be associated with laterally-continuous shell accumulations, a type of concentration occurring at maximum flooding surfaces, separating relatively coarse-grained facies from open marine mudstones. Shell beds were bulk-sampled at 66 locations from six basins, covering a wide range of sedimentary facies, and spanning a chronologic interval of about 2.5 million years. A dataset of 62,655 mollusc specimens belonging to 496 species formed the basis of a statistical study to reconstruct the structure of the benthic communities, and to estimate paleodepths from intertidal to upper bathyal settings. Mollusc associations closely mirror the distribution of sedimentary facies, allowing for a fine tuning of the sequence stratigraphic architecture. Merging paleogeographic, stratigraphic and paleoecologic data, we conclude that the more abundant and diverse accumulations of large vertebrates took place in settings under the influence of coastal upwelling. A modern analogue occurs today in the Ligurian Sea, on the Tuscan offshore, where abundant nutrients carried by deep-marine currents of Western origin

Geomorphologic, stratigraphic and sedimentologic evidences of ...

Indian Academy of Sciences (India)

The EPF particularly has acted significantly and influenced in evolving the geomorphological landscape and the stratigraphic architecture of the area. The block bounded by the two faults has earlier been considered as a single entity, constituting a half-graben. The present investigation (by morpho-stratigraphic and ...

Stratigraphic condensation of marine transgressive records: Origin of major shell deposits in the Miocene of Maryland

Energy Technology Data Exchange (ETDEWEB)

Kidwell, S.M. (Univ. of Chicago, IL (USA))

1989-01-01

Cyclic stratigraphic sequences in shallow marine records are commonly charaterized by a condensed transgressive lag at the base of thicker, shallowing-upward facies. The standard actualistic model for these thin fossiliferous lags, by which most of the shelf is starved owing to coastal trapping of sediment and fossils are suspected of being reworked because of the association with an erosional ravinement, is contradicted by detailed stratigraphic and taphonomic analysis of Miocene examples in the Maryland coastal plain. The complex internal stratigraphies of the shell deposits and the mixture of soft- and shell-bottom faunas indicate condensation under a regime of dynamic bypassing rather than complete sediment starvation; bypassed fine sediments accumulated in deeper water environments below storm wavebase. Deeper, even more basinward parts of the shelf were starved of all sediment size fractions and accumulated shell-poor, bone-rich condensed deposits that lie mid-cycle (bracketing the time of maximum water depth). The base-of-cycle shell deposits and mid-cycle bone bed differ not only in composition and in environment and dynamics of condensation, but also in chronostratigraphic value: the onlapping shell deposits must be diachronous to some degree, whereas the mid-cycle bone bed approximates an isochronous marker for correlation. Thus, in some settings at least, transgressive shelves present a spatial mosaic of condensational and depositional regimes. Regardless of origin, all condensed intervals can time-average assemblages and telescope biostratigraphic datums. They otherwise differ widely, however, in paleontologic attributes and are characterized by highly variable and complex stratigraphic anatomies.

Automated recognition of stratigraphic marker shales from geophysical logs in iron ore deposits

Science.gov (United States)

Silversides, Katherine; Melkumyan, Arman; Wyman, Derek; Hatherly, Peter

2015-04-01

The mining of stratiform ore deposits requires a means of determining the location of stratigraphic boundaries. A variety of geophysical logs may provide the required data but, in the case of banded iron formation hosted iron ore deposits in the Hamersley Ranges of Western Australia, only one geophysical log type (natural gamma) is collected for this purpose. The information from these logs is currently processed by slow manual interpretation. In this paper we present an alternative method of automatically identifying recurring stratigraphic markers in natural gamma logs from multiple drill holes. Our approach is demonstrated using natural gamma geophysical logs that contain features corresponding to the presence of stratigraphically important marker shales. The host stratigraphic sequence is highly consistent throughout the Hamersley and the marker shales can therefore be used to identify the stratigraphic location of the banded iron formation (BIF) or BIF hosted ore. The marker shales are identified using Gaussian Processes (GP) trained by either manual or active learning methods and the results are compared to the existing geological interpretation. The manual method involves the user selecting the signatures for improving the library, whereas the active learning method uses the measure of uncertainty provided by the GP to select specific examples for the user to consider for addition. The results demonstrate that both GP methods can identify a feature, but the active learning approach has several benefits over the manual method. These benefits include greater accuracy in the identified signatures, faster library building, and an objective approach for selecting signatures that includes the full range of signatures across a deposit in the library. When using the active learning method, it was found that the current manual interpretation could be replaced in 78.4% of the holes with an accuracy of 95.7%.

A three-dimensional stratigraphic model for aggrading submarine channels based on laboratory experiments, numerical modeling, and sediment cores

Science.gov (United States)

Limaye, A. B.; Komatsu, Y.; Suzuki, K.; Paola, C.

2017-12-01

Turbidity currents deliver clastic sediment from continental margins to the deep ocean, and are the main driver of landscape and stratigraphic evolution in many low-relief, submarine environments. The sedimentary architecture of turbidites—including the spatial organization of coarse and fine sediments—is closely related to the aggradation, scour, and lateral shifting of channels. Seismic stratigraphy indicates that submarine, meandering channels often aggrade rapidly relative to lateral shifting, and develop channel sand bodies with high vertical connectivity. In comparison, the stratigraphic architecture developed by submarine, braided is relatively uncertain. We present a new stratigraphic model for submarine braided channels that integrates predictions from laboratory experiments and flow modeling with constraints from sediment cores. In the laboratory experiments, a saline density current developed subaqueous channels in plastic sediment. The channels aggraded to form a deposit with a vertical scale of approximately five channel depths. We collected topography data during aggradation to (1) establish relative stratigraphic age, and (2) estimate the sorting patterns of a hypothetical grain size distribution. We applied a numerical flow model to each topographic surface and used modeled flow depth as a proxy for relative grain size. We then conditioned the resulting stratigraphic model to observed grain size distributions using sediment core data from the Nankai Trough, offshore Japan. Using this stratigraphic model, we establish new, quantitative predictions for the two- and three-dimensional connectivity of coarse sediment as a function of fine-sediment fraction. Using this case study as an example, we will highlight outstanding challenges in relating the evolution of low-relief landscapes to the stratigraphic record.

A preliminary guidebook for identifying stratigraphic contacts at the Nevada Test Site

International Nuclear Information System (INIS)

Pawloski, G.A.; McKague, H.L.; Wagoner, J.L.; McKinnis, W.B.

1992-01-01

Lithologic variation, regional depositional trends, and the lack of written guidelines have resulted in inconsistencies in the recognition of stratigraphic contacts in drill holes at the Nevada Test Site (NTS). Stratigraphic identification, based on mineralogy of discrete samples, can be augmented by geophysical logs and downhole movies to more accurately and consistently locate contacts between units. Criteria are established for locating the base of the Pahute Mesa ash-flow tuff, the top of the Ammonia Tanks ash-flow tuff, the top of the Ammonia Tanks bedded tuff, and the top and the base of the Rainier Mesa Tuff

Tectonic-stratigraphic evolution of Cumuruxatiba Basin - Brazil; Evolucao tectono-estratigrafica da Bacia de Cumuruxatiba

Energy Technology Data Exchange (ETDEWEB)

Lobato, Gustavo; Fernandes, Flavio L.; Silva, Eric Zagotto; Ferreira Neto, Walter Dias [Universidade Federal do Rio de Janeiro (UFRJ), RJ (Brazil). Coordenacao dos Programas de Pos-graduacao de Engenharia (COPPE). Lab. de Modelagem Multidisciplinar de Bacias Sedimentares; Ribeiro, Juliana [Agencia Nacional do Petroleo, Gas Natural e Biocombustiveis (ANP), Brasilia, DF (Brazil)

2008-07-01

In recent years, the exploratory interest on Cumuruxatiba Basin has been inconstant, with modest discoveries of oil. Aiming to deepen the geological knowledge of the basin and in order to attract the interest of oil companies, the ANP (National Agency of Petroleum, Natural Gas and Biofuels) signed contract with COPPE/UFRJ for carrying out an analysis basin project. The project was developed by the Basin Analysis Multidisciplinary Modeling Laboratory (Lab2M/UFRJ) in the period 2006/2007, and was with the main objective outline the main structural and seismo-stratigraphic features of the basin, and in an integrated and multidisciplinary way, build a model of its sedimentation and tectono-stratigraphic evolution. This paper presents the results of the regional seismic mapping, aided by well and potential methods data. The stratigraphic succession the basin has been divided into genetic units (UN-B, UN-C e UN-D) corresponding to second order depositional sequences, they are: UN-B, corresponding by a rift and sag-rift siliciclastic deposits, plus the Aptian evaporitic deposits; UN-C, characterized by carbonatic deposits, and shelf related sediments; and UN-D, corresponding by a final transgressive (siliciclastic) - regressive (mix) cycle, between Cenomanian and actual days. (author)

Microfacies characteristics, sedimentary environments and sequence stratigraphy of Upper Cretaceous deposits in northwest of Nehbandan (Basiran section

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Mohammad nabi Gorgij

2015-10-01

Full Text Available Introduction   The Basiran stratigraphic section is located about 160 km northwest of Nehbandan.The section was measured in detail at 59 06 30 N and 31 52 50 E. Nehbandan area with respect to fourfold geological subdivision of Iran is part of Central Iran that is located in the eastern flank of Lut Block which first time are studied by Stocklin et al.in 1972. Gorgij (2001 stratigraphically and paleontologically investigate Upper Cretaceous deposits in Mighan and Basiran sections. Upper Cretaceous deposits in in this area consists of 275m conglomerate,alternation of conglomerate-sandstone, sandy limestone -marl and limy marl, marl with intercalation of limestone-sandy limestone thin beds and medium-bedded to massive limestone. Microfacies analysis led to the recognition of 9 microfacies that are related to 5 belts; Coast, tidal flat, lagoon, shoal, shallow open marine and deep open marine environments. Main part of the section are deposited in the open marine environment that consist of marl,marly limestone and limestone. The doals of this study are : (1 describing and determining main carbonate and siliciclastic microfacies of late Cretaceous deposits (2 interpreting and providing depositional model for reconstruction of its paleoenvironmental setting based on microfacies characteristics (3 dividing the section based on lithostratigraphic principles and (4 recognizing a sequence stratigraphic model of this successions based on the vertical variation of facies,stratal key beds and stratal packing pattern.       Material and Method   The Basiran section as a complete stratigraphic section was measured and described. Up to 68 samples (indicated by KB1 to KB68 were collected and 170 thin sections are prepared. Based on field observations, sedimentological characteristics, parasequence stacking patterns, sequence boundary types and other key stratigraphical surfaces are identified and were obtained. Scheme of Dunham (1962 and Embry and Klovan

Microfacies characteristics, sedimentary environments and sequence stratigraphy of Upper Cretaceous deposits in northwest of Nehbandan (Basiran section

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Azadeh Bordbar

2015-09-01

Full Text Available   Introduction   The Basiran stratigraphic section is located about 160 km northwest of Nehbandan.The section was measured in detail at 59 06 30 N and 31 52 50 E. Nehbandan area with respect to fourfold geological subdivision of Iran is part of Central Iran that is located in the eastern flank of Lut Block which first time are studied by Stocklin et al.in 1972. Gorgij (2001 stratigraphically and paleontologically investigate Upper Cretaceous deposits in Mighan and Basiran sections. Upper Cretaceous deposits in in this area consists of 275m conglomerate,alternation of conglomerate-sandstone, sandy limestone -marl and limy marl, marl with intercalation of limestone-sandy limestone thin beds and medium-bedded to massive limestone. Microfacies analysis led to the recognition of 9 microfacies that are related to 5 belts Coast, tidal flat, lagoon, shoal, shallow open marine and deep open marine environments. Main part of the section are deposited in the open marine environment that consist of marl,marly limestone and limestone. The doals of this study are : (1 describing and determining main carbonate and siliciclastic microfacies of late Cretaceous deposits (2 interpreting and providing depositional model for reconstruction of its paleoenvironmental setting based on microfacies characteristics (3 dividing the section based on lithostratigraphic principles and (4 recognizing a sequence stratigraphic model of this successions based on the vertical variation of facies,stratal key beds and stratal packing pattern.       Material and Method   The Basiran section as a complete stratigraphic section was measured and described. Up to 68 samples (indicated by KB1 to KB68 were collected and 170 thin sections are prepared. Based on field observations, sedimentological characteristics, parasequence stacking patterns, sequence boundary types and other key stratigraphical surfaces are identified and were obtained. Scheme of Dunham (1962 and Embry

Tectonic-stratigraphic evolution of Espirito Santo Basin - Brazil; Evolucao tectono-estratigrafica da Bacia do Espirito Santo

Energy Technology Data Exchange (ETDEWEB)

Silva, Eric Zagotto; Fernandes, Flavio L.; Lobato, Gustavo; Ferreira Neto, Walter Dias [Universidade Federal do Rio de Janeiro (UFRJ), RJ (Brazil). Coordenacao dos Programas de Pos-graduacao de Engenharia (COPPE). Lab. de Modelagem de Bacias (LAB2M); Petersohn, Eliane [Agencia Nacional do Petroleo, Gas Natural e Biocombustiveis (ANP), Brasilia, DF (Brazil)

2008-07-01

This paper documents the analysis of seismic data of the Espirito Santo basin obtained during the project realized through partnership between COPPE/UFRJ/Lab2M with the Agencia Nacional do Petroleo, Gas Natural e Biocombustiveis (ANP) during 2006 and 2007. The major objective of the seismic data interpretation in the project was to define the main structural and stratigraphic features in order to build a sedimentation model and a tectonic-stratigraphic evolution model of the Espirito Santo basin. Thus, the sedimentary package has been divided into eight genetic units (UN), grouped into five third order stratigraphic sequences, namely: UN-B, represented by siliciclastics rocks of the rift stage and evaporitic sag-rift stage, deposited during the Aptian; UN-C, which represents the carbonatic rocks deposited in a marine environment, and siliciclastics rocks located in the proximal portions during the Albian; and UN-D, represented by sediments, composed mainly by pelites, deposited in between the Cenomanian and Recent, and includes the Eocene volcanic event, which one changed the sedimentation pattern of the basin. (author)

Seismic stratigraphic architecture of the Disko Bay trough-mouth fan system, West Greenland

Science.gov (United States)

Hofmann, Julia C.; Knutz, Paul C.

2015-04-01

Spatial and temporal changes of the Greenland Ice Sheet on the continental shelf bordering Baffin Bay remain poorly constrained. Then as now, fast-flowing ice streams and outlet glaciers have played a key role for the mass balance and stability of polar ice sheets. Despite their significance for Greenland Ice Sheet dynamics and evolution, our understanding of their long-term behaviour is limited. The central West Greenland margin is characterized by a broad continental shelf where a series of troughs extend from fjords to the shelf margin, acting as focal points for trough-mouth fan (TMF) accummulations. The sea-ward bulging morphology and abrupt shelf-break of these major depositional systems is generated by prograding depocentres that formed during glacial maxima when ice streams reached the shelf edge, delivering large amounts of subglacial sediment onto the continental slope (Ó Cofaigh et al., 2013). The aim of this study is to unravel the seismic stratigraphic architecture and depositional processes of the Disko Bay TMF, aerially the largest single sedimentary system in West Greenland, using 2D and 3D seismic reflection data, seabed bathymetry and stratigraphic information from exploration well Hellefisk-1. The south-west Disko Bay is intersected by a deep, narrow trough, Egedesminde Dyb, which extends towards the southwest and links to the shallower and broader cross-shelf Disko Trough (maximum water depths of > 1000 m and a trough length of c. 370 km). Another trough-like depression (trough length of c. 120 km) in the northern part of the TMF, indicating a previous position of the ice stream, can be distinguished on the seabed topographic map and the seismic images. The Disko Bay TMF itself extends from the shelf edge down to the abyssal plain (abyssal floor depths of 2000 m) of the southern Baffin Bay. Based on seismic stratigraphic configurations relating to reflection terminations, erosive patterns and seismic facies (Mitchum et al., 1977), the TMF

Iowa Stratigraphic Data Points

Data.gov (United States)

Iowa State University GIS Support and Research Facility — The Iowa stratigraphic column consists of rock materials of varying geologic age that have been categorized into a shapefile for summarizing the 3 dimensional aspect...

Sedimentology, sequence-stratigraphy, and geochemical variations in the Mesoproterozoic Nonesuch Formation, northern Wisconsin, USA

Science.gov (United States)

Kingsbury Stewart, Esther; Mauk, Jeffrey L.

2017-01-01

We use core descriptions and portable X-ray fluorescence analyses to identify lithofacies and stratigraphic surfaces for the Mesoproterozoic Nonesuch Formation within the Ashland syncline, Wisconsin. We group lithofacies into facies associations and construct a sequence stratigraphic framework based on lithofacies stacking and stratigraphic surfaces. The fluvial-alluvial facies association (upper Copper Harbor Conglomerate) is overlain across a transgressive surface by the fluctuating-profundal facies association (lower Nonesuch Formation). The fluctuating-profundal facies association comprises a retrogradational sequence set overlain across a maximum flooding surface by an aggradational-progradational sequence set comprising fluctuating-profundal, fluvial-lacustrine, and fluvial-alluvial facies associations (middle Nonesuch through lower Freda Formations). Lithogeochemistry supports sedimentologic and stratigraphic interpretations. Fe/S molar ratios reflect the oxidation state of the lithofacies; values are most depleted above the maximum flooding surface where lithofacies are chemically reduced and are greatest in the chemically oxidized lithofacies. Si/Al and Zr/Al molar ratios reflect the relative abundance of detrital heavy minerals vs. clay minerals; greater values correlate with larger grain size. Vertical facies association stacking records depositional environments that evolved from fluvial and alluvial, to balanced-fill lake, to overfilled lake, and returning to fluvial and alluvial. Elsewhere in the basin, where accommodation was greatest, some volume of fluvial-lacustrine facies is likely present below the transgressive stratigraphic surface. This succession of continental and lake-basin types indicates a predominant tectonic driver of basin evolution. Lithofacies distribution and geochemistry indicate deposition within an asymmetric half-graben bounded on the east by a west-dipping growth fault. While facies assemblages are lacustrine and continental

The stratigraphic imprint of a mid-Telychian (Llandovery, Early Silurian glaciation on far-field shallow-water carbonates, Anticosti Island, Eastern Canada

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François Clayer

2014-12-01

Full Text Available The near-field stratigraphic record of the Early Silurian glaciations is well documented in the literature. Data from far-field areas are, however, sparse. One of the best far-field stratigraphic records of these Llandovery glaciations is exposed on Anticosti Island in eastern Canada. Eight shallow-water paleotropical facies are present close to the mid-Telychian Jupiter–Chicotte formational boundary along the south-central coast of Anticosti Island. These can be grouped into three facies associations that include, from bottom to top: a carbonate facies association (FA-1, a mixed siliciclastic and carbonate facies association (FA-2 and an encrinitic facies association (FA-3. These mid- to outer-ramp strata represent deposition mostly from episodic, high-energy storm events as evidenced by their sharp bases, hummocky cross-stratification, large wave ripples, gutter casts and wave-enhanced sediment gravity flow deposits. Superimposed on a long-term regressive trend, one main transgressive–regressive (TR sequence and four meter-scale TR cycles are evident, indicating a multi-order stratigraphic framework developed under the influence of glacio-eustasy. The Jupiter–Chicotte formational boundary, a regional discontinuity surface caused by a forced regression, corresponds to the onset of a far-field mid-Telychian glaciation.

A method of reconstructing complex stratigraphic surfaces with multitype fault constraints

Science.gov (United States)

Deng, Shi-Wu; Jia, Yu; Yao, Xing-Miao; Liu, Zhi-Ning

2017-06-01

The construction of complex stratigraphic surfaces is widely employed in many fields, such as petroleum exploration, geological modeling, and geological structure analysis. It also serves as an important foundation for data visualization and visual analysis in these fields. The existing surface construction methods have several deficiencies and face various difficulties, such as the presence of multitype faults and roughness of resulting surfaces. In this paper, a surface modeling method that uses geometric partial differential equations (PDEs) is introduced for the construction of stratigraphic surfaces. It effectively solves the problem of surface roughness caused by the irregularity of stratigraphic data distribution. To cope with the presence of multitype complex faults, a two-way projection algorithm between threedimensional space and a two-dimensional plane is proposed. Using this algorithm, a unified method based on geometric PDEs is developed for dealing with multitype faults. Moreover, the corresponding geometric PDE is derived, and an algorithm based on an evolutionary solution is developed. The algorithm proposed for constructing spatial surfaces with real data verifies its computational efficiency and its ability to handle irregular data distribution. In particular, it can reconstruct faulty surfaces, especially those with overthrust faults.

Triassic Sequence Geological Development of the Arctic with focus on Svalbard and the Barents Shelf

Energy Technology Data Exchange (ETDEWEB)

Moerk, Atle

1998-12-31

Triassic rocks are of great interest for exploration in Arctic areas as they have proved to include both good hydrocarbon source rocks and potential hydrogen reservoir rocks. In this thesis, the stratigraphy and sedimentology of the Arctic Triassic successions are studied within a sequence stratigraphical framework. Inter-regional comparisons throughout the Arctic are based on comparisons of transgressive-regressive sequences. Improved dating of the studied sequences, and the recognition and correlation of sequence boundaries of second and third order, facilitate interpretation of facies distribution and the geological development both within and between the studied areas. Main emphasis is given to the Triassic succession of Svalbard and the Barents Shelf, which through this study is integrated within a circum-Arctic sequence stratigraphical framework. Good correspondence of the Triassic sequence boundaries between the different Arctic areas indicate that they are mainly controlled by eustacy, while decreasing correspondence of the sequence boundaries in the Jurassic and Cretaceous periods indicate that local and large scale tectonism becomes progressively more dominant in the circum-Arctic Realm through the Mesozoic Era. These hypotheses are further discussed. 701 refs., 110 figs., 12 tabs.

Stratigraphic model deposit Ofi Inf SDZ-2X A1, Jun in block in Orinoco Oil belt

International Nuclear Information System (INIS)

Martinez, E.; Sandoval, D.

2010-01-01

This work is about the Stratigraphic model deposit O fi I nf SDZ-2X A1, Junin block in Orinoco Oil belt.This model was based on a chrono stratigraphic interpretation and was defined the correlation between the main and secondary surfaces. The wells of the study area pass through the Cambrian, Cretaceous and Miocene sediments. The last is more interesting for the study because of the stratigraphic and sand body surface presence

Tectonic evolution of the Paranoá basin: New evidence from gravimetric and stratigraphic data

Science.gov (United States)

Martins-Ferreira, Marco Antonio Caçador; Campos, José Eloi Guimarães; Von Huelsen, Monica Giannoccaro

2018-06-01

Field gravimetric and stratigraphic surveys were conducted with the aim to constraint the mechanisms responsible for the initiation of the Stenian-Tonian Paranoá basin, central Brazil, a subject not yet studied in detail. The Paranoá Group crops out in the external zone of the Brasília Belt, a Neoproterozoic orogen in the western margin of the São Francisco Craton. Detailed geological mapping confirmed the existence of a regional scale fault that controlled sedimentation of the Paranoá Group during the deposition of its basal formations, revealing important details about basin initiation and early evolution. Gravimetric modeling indicates the existence of paleorift structures beneath the Paranoá sequence in the study area. Results from both stratigraphic and gravimetric surveys show strong evidence of mechanical subsidence by faulting during basin initiation. Unsorted, angular, clasts cut by quartz veins and brecciated boulders present in the basal conglomerate, support this hypothesis. Basin initiation faults coincide with deeper paleorift faults and are thus interpreted as reactivations of the older Statherian Araí Rift. The reactivations favored an initial regime of mechanical subsidence, dominated by the development of epirogenic arches subsiding at different rates. Apart from faulting activity, the post-basal sequence presents no evidence of rift environment in the strict sense. Besides, the great lateral continuity and relatively constant thickness of facies, indicate that an initial mechanic subsidence rapidly gave way to flexural subsidence during subsequent stages of basin evolution. The Paranoá Group do not present reliable characteristics that would allow its strict classification as a passive margin. Its main stratigraphic characteristics, tectonic location and basement architecture, indicate that the Paranoá Group was deposited in a cratonic margin basin, and may have been either connected to a passive margin basin at times of sea level rise

Use of stratigraphic models as soft information to constrain stochastic modeling of rock properties: Development of the GSLIB-Lynx integration module

International Nuclear Information System (INIS)

Cromer, M.V.; Rautman, C.A.

1995-10-01

Rock properties in volcanic units at Yucca Mountain are controlled largely by relatively deterministic geologic processes related to the emplacement, cooling, and alteration history of the tuffaceous lithologic sequence. Differences in the lithologic character of the rocks have been used to subdivide the rock sequence into stratigraphic units, and the deterministic nature of the processes responsible for the character of the different units can be used to infer the rock material properties likely to exist in unsampled regions. This report proposes a quantitative, theoretically justified method of integrating interpretive geometric models, showing the three-dimensional distribution of different stratigraphic units, with numerical stochastic simulation techniques drawn from geostatistics. This integration of soft, constraining geologic information with hard, quantitative measurements of various material properties can produce geologically reasonable, spatially correlated models of rock properties that are free from stochastic artifacts for use in subsequent physical-process modeling, such as the numerical representation of ground-water flow and radionuclide transport. Prototype modeling conducted using the GSLIB-Lynx Integration Module computer program, known as GLINTMOD, has successfully demonstrated the proposed integration technique. The method involves the selection of stratigraphic-unit-specific material-property expected values that are then used to constrain the probability function from which a material property of interest at an unsampled location is simulated

Geological Identification of Seismic Source at Opak Fault Based on Stratigraphic Sections of the Southern Mountains

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Hita Pandita

2016-08-01

Full Text Available Earthquake is one of the unpredicted natural disasters on our earth. Despite of the absence of high-accuracy method to precisely predict the occurrence of earthquake, numerous studies have been carried out by seismologists to find it. One of the efforts to address the vulnerability of a region to earthquakes is by recognizing the type of rock as the source of the earthquake. Opak Fault is an active fault which was thought to be the source of earthquakes in Yogyakarta and adjacent areas. This study aimed to determine the seismic source types of rocks in Yogyakarta and adjacent areas. The methods were by measuring stratigraphic sections and the layer thickness in the western part of Southern Mountains. Field study was done in 6 (six research sites. Results of stratigraphic measurement indicated the sedimentary rocks in the Southern Mountains was 3.823 km in thick, while the bedrock was more than 1.042 km in thick. Based on the result, the rock types as the seismic source were thought to originate from the continental crust rocks formed of granite and metamorphic complex.

Sedimentology and sequence stratigraphy of the Lopingian (Late Permian) coal measures in southwestern China

Energy Technology Data Exchange (ETDEWEB)

Wang, Hao [School of Geosciences and Surveying Engineering, China University of Mining and Technology, Beijing (China); School of Earth and Environment, University of Leeds (United Kingdom); Shao, Longyi; Hao, Liming; Zhang, Pengfei [School of Geosciences and Surveying Engineering, China University of Mining and Technology, Beijing (China); Glasspool, Ian J. [Department of Geology, Field Museum of Natural History, Chicago, Illinois (United States); Wheeley, James R.; Hilton, Jason [School of Geography, Earth and Environmental Sciences, University of Birmingham (United Kingdom); Wignall, Paul B. [School of Earth and Environment, University of Leeds (United Kingdom); Yi, Tongsheng [Guizhou Bureau of Coal Geological Exploration, Guiyang, Guizhou (China); Zhang, Mingquan [Coal Geology and Prospecting Institute of Yunnan Province, Kunming, Yunnan (China)

2011-01-01

The Lopingian coal measures of southwestern China were deposited within a range of facies associations spanning a spectrum of settings from fluvial to marine carbonate platform. The transitional to terrestrial coal measures are dominated by siliciclastics, but they also contain fifteen laterally extensive marine bands (limestone beds and mudstone). These bands act as marker horizons that enable correlation between fully marine and terrestrial facies. Examination of this range of facies and their sedimentology has enabled the development of a high-resolution sequence stratigraphic framework. Set against the established backdrop of second-order Lopingian transgression, sixteen fourth-order sequences and three composite sequences (third-order) are recognized. Results show that, in the composite sequences, peat accumulation in the seaward parts of the study area predominantly correlates with early transgressive sequence sets (TSS), while in more landward areas it correlates with the middle TSS to late highstand sequence sets (HSS). Differences in peat-accumulation regimes within the sequence stratigraphic framework are attributed to variations in subsidence and background siliciclastic input rates in different depositional settings, with these combining to produce differences in the rate of accommodation change. The preservation of coal resources in the middle to late HSS in this area was most likely related to the rise of the regional base level throughout the Lopingian. (author)

Stratigraphic Profiles for Selected Hanford Site Seismometer Stations and Other Locations

Energy Technology Data Exchange (ETDEWEB)

Last, George V. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

2014-02-01

Stratigraphic profiles were constructed for eight selected Hanford Site seismometer stations, five Hanford Site facility reference locations, and seven regional three-component broadband seismometer stations. These profiles provide interpretations of the subsurface layers to support estimation of ground motions from past earthquakes, and the prediction of ground motions from future earthquakes. In most cases these profiles terminated at the top of the Wanapum Basalt, but at selected sites profiles were extended down to the top of the crystalline basement. The composite one-dimensional stratigraphic profiles were based primarily on previous interpretations from nearby boreholes, and in many cases the nearest deep borehole is located kilometers away.

The Cenozoic geological evolution of the Central and Northern North Sea based on seismic sequence stratigraphy

Energy Technology Data Exchange (ETDEWEB)

Jordt, Henrik

1996-03-01

This thesis represents scientific results from seismic sequence stratigraphic investigations. These investigations and results are integrated into an ongoing mineralogical study of the Cenozoic deposits. the main results from this mineralogical study are presented and discussed. The seismic investigations have provided boundary conditions for a forward modelling study of the Cenozoic depositional history. Results from the forward modelling are presented as they emphasise the influence of tectonics on sequence development. The tectonic motions described were important for the formation of the large oil and gas fields in the North Sea.

A MATLAB®-based program for 3D visualization of stratigraphic setting and subsidence evolution of sedimentary basins: example application to the Vienna Basin

Science.gov (United States)

Lee, Eun Young; Novotny, Johannes; Wagreich, Michael

2015-04-01

In recent years, 3D visualization of sedimentary basins has become increasingly popular. Stratigraphic and structural mapping is highly important to understand the internal setting of sedimentary basins. And subsequent subsidence analysis provides significant insights for basin evolution. This study focused on developing a simple and user-friendly program which allows geologists to analyze and model sedimentary basin data. The developed program is aimed at stratigraphic and subsidence modelling of sedimentary basins from wells or stratigraphic profile data. This program is mainly based on two numerical methods; surface interpolation and subsidence analysis. For surface visualization four different interpolation techniques (Linear, Natural, Cubic Spline, and Thin-Plate Spline) are provided in this program. The subsidence analysis consists of decompaction and backstripping techniques. The numerical methods are computed in MATLAB® which is a multi-paradigm numerical computing environment used extensively in academic, research, and industrial fields. This program consists of five main processing steps; 1) setup (study area and stratigraphic units), 2) loading of well data, 3) stratigraphic modelling (depth distribution and isopach plots), 4) subsidence parameter input, and 5) subsidence modelling (subsided depth and subsidence rate plots). The graphical user interface intuitively guides users through all process stages and provides tools to analyse and export the results. Interpolation and subsidence results are cached to minimize redundant computations and improve the interactivity of the program. All 2D and 3D visualizations are created by using MATLAB plotting functions, which enables users to fine-tune the visualization results using the full range of available plot options in MATLAB. All functions of this program are illustrated with a case study of Miocene sediments in the Vienna Basin. The basin is an ideal place to test this program, because sufficient data is

Sequence Stratigraphic Analysis and Facies Architecture of the Cretaceous Mancos Shale on and Near the Jicarilla Apache Indian Reservation, New Mexico-their relation to Sites of Oil Accumulation; FINAL

International Nuclear Information System (INIS)

Ridgley, Jennie

2001-01-01

The purpose of phase 1 and phase 2 of the Department of Energy funded project Analysis of oil- bearing Cretaceous Sandstone Hydrocarbon Reservoirs, exclusive of the Dakota Sandstone, on the Jicarilla Apache Indian Reservation, New Mexico was to define the facies of the oil producing units within the Mancos Shale and interpret the depositional environments of these facies within a sequence stratigraphic context. The focus of this report will center on (1) redefinition of the area and vertical extent of the ''Gallup sandstone'' or El Vado Sandstone Member of the Mancos Shale, (2) determination of the facies distribution within the ''Gallup sandstone'' and other oil-producing sandstones within the lower Mancos, placing these facies within the overall depositional history of the San Juan Basin, (3) application of the principals of sequence stratigraphy to the depositional units that comprise the Mancos Shale, and (4) evaluation of the structural features on the Reservation as they may control sites of oil accumulation

The Cretaceous-Paleogene transition and Chicxulub impact ejecta in the northwestern Gulf of Mexico: Paleoenvironments, sequence stratigraphic setting and target lithologies

Science.gov (United States)

Schulte, Peter

2003-07-01

The Cretaceous-Paleogene (K-P) transition is characterized by a period of mass extinctions, the Chicxulub impact event, sea-level changes, and considerable climate changes (e.g., cooling). The Gulf of Mexico region is a key area for addressing these issues, specifically because of the proximity to the large Chicxulub impact structure in southern Mexico, and because of its shallow shelf areas throughout the Maastrichtian to Danian period. This study presents the results of a multidisciplinary investigation of Chicxulub impact ejecta and marine sediments from the K-P transition in the western Gulf of Mexico. Sedimentological, mineralogical, and geochemical aspects of K-P sections and cores from northeastern Mexico, Texas, and Alabama have been by studied with focus on Chicxulub ejecta, long- or short-term facies change, and sequence stratigraphic setting. CHICXULUB EJECTA: The Chicxulub ejecta (or impact spherule) deposits from northeastern Mexico and Texas revealed an unexpected complex and localized ejecta composition. Fe-Mg-rich chlorite- as well as Si-Al-K-rich glass-spherules are the predominant silicic ejecta components in northeastern Mexico, whereas in Texas, spherules of Mg-rich smectite compositions were encountered. Spherules contain Fe-Ti-K-rich schlieren, Fe-Mg-rich globules, and rare µm-sized metallic and sulfidic Ni-Co-(Ir-?) rich inclusions. This composition provides evidence for a distinct range of target rocks of mafic to intermediate composition, presumably situated in the northwestern sector of the Chicxulub impact structure, in addition to the possibility of contamination by meteoritic material. The absence of spinels and the ubiquitous presence of hematite and goethite points to high oxygen fugacity during the impact process. Besides these silicic phases, the most prominent ejecta component is carbonate.! Carbonate is found in ejecta deposits as unshocked clasts, accretionary lapilli-like grains, melt globules (often with quenching textures

Determination of Heat Capacity of Yucca Mountain Stratigraphic Layers

International Nuclear Information System (INIS)

T. Hadgu; C. Lum; J.E. Bean

2006-01-01

The heat generated from the radioactive waste to be placed in the proposed geologic repository at Yucca Mountain, Nevada, will affect the thermal-hydrology of the Yucca Mountain stratigraphic layers. In order to assess the effect of the movement of repository heat into the fractured rocks accurate determination of thermodynamic and hydraulic properties is important. Heat capacity is one of the properties that are required to evaluate energy storage in the fractured rock. Rock-grain heat capacity, the subject of this study, is the heat capacity of the solid part of the rock. Yucca Mountain consists of alternating lithostratigraphic units of welded and non-welded ash-flow tuff, mainly rhyolitic in composition and displaying varying degrees of vitrification and alteration. A number of methods exist that can be used to evaluate heat capacity of the stratigraphic layers that consist of different compositions. In this study, the mineral summation method has been used to quantify the heat capacity of the stratigraphic layers based on Kopp's rule. The mineral summation method is an addition of the weighted heat capacity of each mineral found in a specific layer. For this study the weighting was done based on the mass percentage of each mineral in the layer. The method utilized a mineralogic map of the rocks at the Yucca Mountain repository site. The Calico Hills formation and adjacent bedded tuff layers display a bimodal mineral distribution of vitric and zeolitic zones with differing mineralogies. Based on this bimodal distribution in zeolite abundance, the boundary between the vitric and zeolitic zones was selected to be 15% zeolitic abundance. Thus, based on the zeolite abundance, subdivisions have been introduced to these layers into ''vitric'' and ''zeolitic'' zones. Heat capacity values have been calculated for these layers both as ''layer average'' and ''zone average''. The heat capacity determination method presented in this report did not account for spatial

CORE-BASED INTEGRATED SEDIMENTOLOGIC, STRATIGRAPHIC, AND GEOCHEMICAL ANALYSIS OF THE OIL SHALE BEARING GREEN RIVER FORMATION, UINTA BASIN, UTAH

Energy Technology Data Exchange (ETDEWEB)

Lauren P. Birgenheier; Michael D. Vanden Berg,

2011-04-11

An integrated detailed sedimentologic, stratigraphic, and geochemical study of Utah's Green River Formation has found that Lake Uinta evolved in three phases (1) a freshwater rising lake phase below the Mahogany zone, (2) an anoxic deep lake phase above the base of the Mahogany zone and (3) a hypersaline lake phase within the middle and upper R-8. This long term lake evolution was driven by tectonic basin development and the balance of sediment and water fill with the neighboring basins, as postulated by models developed from the Greater Green River Basin by Carroll and Bohacs (1999). Early Eocene abrupt global-warming events may have had significant control on deposition through the amount of sediment production and deposition rates, such that lean zones below the Mahogany zone record hyperthermal events and rich zones record periods between hyperthermals. This type of climatic control on short-term and long-term lake evolution and deposition has been previously overlooked. This geologic history contains key points relevant to oil shale development and engineering design including: (1) Stratigraphic changes in oil shale quality and composition are systematic and can be related to spatial and temporal changes in the depositional environment and basin dynamics. (2) The inorganic mineral matrix of oil shale units changes significantly from clay mineral/dolomite dominated to calcite above the base of the Mahogany zone. This variation may result in significant differences in pyrolysis products and geomechanical properties relevant to development and should be incorporated into engineering experiments. (3) This study includes a region in the Uinta Basin that would be highly prospective for application of in-situ production techniques. Stratigraphic targets for in-situ recovery techniques should extend above and below the Mahogany zone and include the upper R-6 and lower R-8.

Stratigraphic inversion of pre-stack multicomponent data; Inversion stratigraphique multicomposante avant sommation

Energy Technology Data Exchange (ETDEWEB)

Agullo, Y.

2005-09-15

This thesis present the extension of mono-component seismic pre-stack data stratigraphical inversion method to multicomponent data, with the objective of improving the determination of reservoir elastic parameters. In addiction to the PP pressure waves, the PS converted waves proved their interest for imaging under gas clouds; and their potential is highly significant for the characterization of lithologies, fluids, fractures... Nevertheless the simultaneous use ol PP and PS data remains problematic because of their different the time scales. To jointly use the information contained in PP and PS data, we propose a method in three steps first, mono-component stratigraphic inversions of PP then PS data; second, estimation of the PP to PS time conversion law; third, multicomponent stratigraphic inversion. For the second point, the estimation of the PP to PS conversion law is based on minimizing the difference between the S impedances obtained from PP and PS mono-component stratigraphic inversion. The pre-stack mono-component stratigraphic inversions was adapted to the case of multicomponent data by leaving each type of data in its own time scale in order to avoid the distortion of the seismic wavelet. The results obtained on a realistic synthetic PP-PS case show on one hand that determining PP to PS conversion law (from the mono-component inversion results) is feasible, and on the other hand that the joint inversion of PP and PS data with this conversion law improves the results compared to the mono-component inversion ones. Although this is presented within the framework of the PP and PS multi-component data, the developed methodology adapts directly to PP and SS data for example. (author)

The stratigraphic filter and bias in measurement of geologic rates

Science.gov (United States)

Schumer, Rina; Jerolmack, Douglas; McElroy, Brandon

2011-01-01

Erosion and deposition rates estimated from the stratigraphic record frequently exhibit a power-law dependence on measurement interval. This dependence can result from a power-law distribution of stratigraphic hiatuses. By representing the stratigraphic filter as a stochastic process called a reverse ascending ladder, we describe a likely origin of power-law hiatuses, and thus, rate scaling. While power-law hiatuses in certain environments can be a direct result of power-law periods of stasis (no deposition or erosion), they are more generally the result of randomness in surface fluctuations irrespective of mean subsidence or uplift. Autocorrelation in fluctuations can make hiatuses more or less heavy-tailed, but still exhibit power-law characteristics. In addition we show that by passing stratigraphic data backward through the filter, certain statistics of surface kinematics from their formative environments can be inferred.

Mio-Pliocene to Pleistocene paleotopographic evolution of Brittany (France) from a sequence stratigraphic analysis: relative influence of tectonics and climate

Science.gov (United States)

Brault, N.; Bourquin, S.; Guillocheau, F.; Dabard, M.-P.; Bonnet, S.; Courville, P.; Estéoule-Choux, J.; Stepanoff, F.

2004-01-01

The Mio-Pliocene in Western Europe is a period of major climatic and tectonic change with important topographic consequences. The aim of this paper is to reconstruct these topographic changes (based on sedimentological analysis and sequence stratigraphy) for the Armorican Massif (western France) and to discuss their significance. The Mio-Pliocene sands of the Armorican Massif (Red Sands) are mainly preserved in paleovalleys and are characterized by extensive fluvial sheetflood deposits with low-preservation and by-pass facies. This sedimentological study shows that the Red Sands correspond to three main sedimentary environments: fluvial (alluvial fan, low-sinuosity rivers and braided rivers), estuarine and some rare open marine deposits (marine bioclastic sands: "faluns" of French authors). Two orders of sequences have been correlated across Brittany with one or two minor A/ S cycles comprised within the retrogradational trend of a major cycle. The unconformity at the base of the lower cycle is more marked than the unconformity observed at the top, which corresponds to a re-incision of the paleovalley network. A comparison of the results of the sequence stratigraphy analysis with eustatic variations and tectonic events during the Mio-Pliocene allows (1) to discuss their influence on the evolution of the Armorican Massif and (2) to compare the stratigraphic record with other west-European basins. The unconformity observed at the base of the first minor cycle may be attributed to Serravallian-Tortonian tectonic activity and/or eustatic fall, and the unconformity of the second minor cycle may be attributed to Late Tortonian-Early Messinian tectonic activity. The earlier unconformity is coeval with the development of a "smooth" paleovalley network compared to the jagged present-day relief. A single episode of Mio-Pliocene deformation recorded in Brittany may be dated as Zanclean, thus explaining the lack of the maximum flooding surface except in isolated areas. From

Milankovitch cyclicity in modern continental margins: stratigraphic cycles in terrigenous shelf settings; El registro de la ciclicidad de Milankovitch en margenes continentales actuales: ciclos estratigraficos en plataformas terrigenas

Energy Technology Data Exchange (ETDEWEB)

Lobo, F. J.; Ridente, D.

2013-06-01

We present a synthesis of the sedimentary responses to Late Quaternary Milankovitch-type sea-level cycles (100 and 20 kyr periodicities) as a basis for our investigations into the patterns and concepts of composite sequences in shallow-shelf settings. We describe the record of both 100 and 20 kyr cycles as documented worldwide and discuss the pattern of composite cyclicity mainly on the basis of previously published data from the Adriatic Sea and Gulf of Cadiz margins. Cycles of 100 kyr are those most frequently documented in Quaternary margins; they occur in the form of unconformity-bounded depositional sequences dominated by fairly uniform pro gradational-regressive units and more variable, though less well developed, transgressive deposits. Sequence boundaries correspond to prominent polygenic (regressive-transgressive) erosional surfaces that bear witness to considerable transgressive reworking of the original sub-aerial unconformity. Although the progradational units making up the greater part of these sequences have usually been interpreted as a record of a falling sea-level stage, recent evidence is pointing towards a more complex stratigraphic picture, including a distinction between relative highstand and lowstand deposits. The 20-kyr stratigraphic motifs show greater variation compared to that displayed by the more common 100-kyr sequences, particularly in the basic structure of systems tracts and the nature of bounding surfaces. The two case studies described here, the Adriatic Sea and Gulf of Cadiz margins, highlight the fact that, concomitantly with an increase in frequencies of cycles and sequences, sediment supply and the dynamics of their dispersal significantly affected the stratigraphic response to the main controlling factor, which was sea-level, thus determining the variety of expression in the 20 kyr cycles. (Author)

Measuring Stratigraphic Congruence Across Trees, Higher Taxa, and Time.

Science.gov (United States)

O'Connor, Anne; Wills, Matthew A

2016-09-01

The congruence between the order of cladistic branching and the first appearance dates of fossil lineages can be quantified using a variety of indices. Good matching is a prerequisite for the accurate time calibration of trees, while the distribution of congruence indices across large samples of cladograms has underpinned claims about temporal and taxonomic patterns of completeness in the fossil record. The most widely used stratigraphic congruence indices are the stratigraphic consistency index (SCI), the modified Manhattan stratigraphic measure (MSM*), and the gap excess ratio (GER) (plus its derivatives; the topological GER and the modified GER). Many factors are believed to variously bias these indices, with several empirical and simulation studies addressing some subset of the putative interactions. This study combines both approaches to quantify the effects (on all five indices) of eight variables reasoned to constrain the distribution of possible values (the number of taxa, tree balance, tree resolution, range of first occurrence (FO) dates, center of gravity of FO dates, the variability of FO dates, percentage of extant taxa, and percentage of taxa with no fossil record). Our empirical data set comprised 647 published animal and plant cladograms spanning the entire Phanerozoic, and for these data we also modeled the effects of mean age of FOs (as a proxy for clade age), the taxonomic rank of the clade, and the higher taxonomic group to which it belonged. The center of gravity of FO dates had not been investigated hitherto, and this was found to correlate most strongly with some measures of stratigraphic congruence in our empirical study (top-heavy clades had better congruence). The modified GER was the index least susceptible to bias. We found significant differences across higher taxa for all indices; arthropods had lower congruence and tetrapods higher congruence. Stratigraphic congruence-however measured-also varied throughout the Phanerozoic, reflecting

Spectral and stratigraphic mapping of hydrated minerals associated with interior layered deposits near the southern wall of Melas Chasma, Mars

Science.gov (United States)

Liu, Yang; Goudge, Timothy A.; Catalano, Jeffrey G.; Wang, Alian

2018-03-01

Orbital remote sensing data acquired from the Compact Reconnaissance Imaging Spectrometer for Mars (CRISM) onboard Mars Reconnaissance Orbiter (MRO), in conjunction with other datasets, are used to perform detailed spectral and stratigraphic analyses over a portion of south Melas Chasma, Mars. The Discrete Ordinate Radiative Transfer (DISORT) model is used to retrieve atmospherically corrected single scattering albedos from CRISM I/F data for mineral identification. A sequence of interbedded poly- and monohydrated sulfates associated with interior layered deposits (ILDs) is identified and mapped. Analyses from laboratory experiments and spectral unmixing of CRISM hyperspectral data support the hypothesis of precipitation and dehydration of multiple inputs of complex Mg-Ca-Fe-SO4-Cl brines. In this scenario, the early precipitated Mg sulfates could dehydrate into monohydrated sulfate due to catalytic effects, and the later-precipitated Mg sulfates from the late-stage "clean" brine could terminate their dehydration at mid-degree of hydration to form a polyhydrated sulfate layer due to depletion of the catalytic species (e.g., Ca, Fe, and Cl). Distinct jarosite-bearing units are identified stratigraphically above the hydrated sulfate deposits. These are hypothesized to have formed either by oxidation of a fluid containing Fe(II) and SO4, or by leaching of soluble phases from precursor intermixed jarosite-Mg sulfate units that may have formed during the later stages of deposition of the hydrated sulfate sequence. Results from stratigraphic analysis of the ILDs show that the layers have a consistent northward dip towards the interior of the Melas Chasma basin, a mean dip angle of ∼6°, and neighboring strata that are approximately parallel. These strata are interpreted as initially sub-horizontal layers of a subaqueous, sedimentary evaporite deposits that underwent post-depositional tilting from slumping into the Melas Chasma basin. The interbedded hydrated sulfate

3D stratigraphic forward modelling of Shu'aiba Platform stratigraphy in the Bu Hasa Field, Abu Dhabi, United Arab Emirates.

Science.gov (United States)

Hu, J.; Lokier, S. W.

2012-04-01

This paper presents the results of three dimensional sequence stratigraphic forward modelling of the Aptian age Shu'aiba Formation from Abu Dhabi, United Arab Emirates (UAE). The Shu'aiba Formation lies within the uppermost part of the Lower Cretaceous Thamama Group and forms one of the most prolific hydrocarbon reservoir intervals of the Middle East with production dating back to the 1960's. The Shu'aiba Formation developed as a series of laterally-extensive shallow-water carbonate platforms in an epeiric sea that extended over the northern margin of the African-Arabian Plate. This shallow sea was bounded by the Arabian Shield to the west and the passive margin with the Neo-Tethys Ocean towards the north and east (Droste, 2010). The exposed Arabian Shield acted as a source of siliciclastic sediments to westernmost regions, however, more offshore areas were dominated by shallow-water carbonate deposition. Carbonate production was variously dominated by Lithocodium-Baccinella, orbitolinid foraminifera and rudist bivalves depending on local conditions. While there have been numerous studies of this important stratigraphic interval (for examples see van Buchem et al., 2010), there has been little attempt to simulate the sequence stratigraphic development of the formation. During the present study modelling was undertaken utilising the CARBONATE-3D stratigraphic forward modelling software (Warrlich et al., 2008; Warrlich et al., 2002)) thus allowing for the control of a diverse range of internal and external parameters on carbonate sequence development. This study focuses on platform development in the onshore Bu Hasa Field - the first giant oilfield to produce from the Shu'aiba Formation in Abu Dhabi. The carbonates of the Bu Hasa field were deposited on the southwest slope of the intra-shelf Bab Basin, siliciclastic content is minor. Initially these carbonates were algal dominated with rudist mounds becoming increasingly important over time (Alsharhan, 1987

Fossil preservation and the stratigraphic ranges of taxa

Science.gov (United States)

Foote, M.; Raup, D. M.

1996-01-01

The incompleteness of the fossil record hinders the inference of evolutionary rates and patterns. Here, we derive relationships among true taxonomic durations, preservation probability, and observed taxonomic ranges. We use these relationships to estimate original distributions of taxonomic durations, preservation probability, and completeness (proportion of taxa preserved), given only the observed ranges. No data on occurrences within the ranges of taxa are required. When preservation is random and the original distribution of durations is exponential, the inference of durations, preservability, and completeness is exact. However, reasonable approximations are possible given non-exponential duration distributions and temporal and taxonomic variation in preservability. Thus, the approaches we describe have great potential in studies of taphonomy, evolutionary rates and patterns, and genealogy. Analyses of Upper Cambrian-Lower Ordovician trilobite species, Paleozoic crinoid genera, Jurassic bivalve species, and Cenozoic mammal species yield the following results: (1) The preservation probability inferred from stratigraphic ranges alone agrees with that inferred from the analysis of stratigraphic gaps when data on the latter are available. (2) Whereas median durations based on simple tabulations of observed ranges are biased by stratigraphic resolution, our estimates of median duration, extinction rate, and completeness are not biased.(3) The shorter geologic ranges of mammalian species relative to those of bivalves cannot be attributed to a difference in preservation potential. However, we cannot rule out the contribution of taxonomic practice to this difference. (4) In the groups studied, completeness (proportion of species [trilobites, bivalves, mammals] or genera [crinoids] preserved) ranges from 60% to 90%. The higher estimates of completeness at smaller geographic scales support previous suggestions that the incompleteness of the fossil record reflects loss of

Stratigraphic and tectonic revision of Cerro Olivo Complex located of Southeastern of Uruguay

International Nuclear Information System (INIS)

Masquelin, E.

2004-01-01

This paper presents a stratigraphic and tectonic revision of Cerro Olivo Complex, located in the Southeastern part of the Uruguayan Predevonian Shield. This informal lithostratigraphic unit constitutes the country rock for the emplacement of late-orogenic granitoids, during Neoproterozoic to Cambrian times. This unit groups all the lithodemes affected by deformation and metamorphism. Recent studies indicate the presence of straight gneisses of quartzo-feldspathic composition in the coast of Maldonado Department. These rocks were interpreted as the result of intense deformation in high temperature. These tectonites base a new stratigraphic insight for the complex. They allow their lithotypes to be organized by petrotectonic features, being a function of PT conditions for every last strain process [es

Diversity and Distribution of Archaea Community along a Stratigraphic Permafrost Profile from Qinghai-Tibetan Plateau, China

Directory of Open Access Journals (Sweden)

Shiping Wei

2014-01-01

Full Text Available Accompanying the thawing permafrost expected to result from the climate change, microbial decomposition of the massive amounts of frozen organic carbon stored in permafrost is a potential emission source of greenhouse gases, possibly leading to positive feedbacks to the greenhouse effect. In this study, the community composition of archaea in stratigraphic soils from an alpine permafrost of Qinghai-Tibetan Plateau was investigated. Phylogenic analysis of 16S rRNA sequences revealed that the community was predominantly constituted by Crenarchaeota and Euryarchaeota. The active layer contained a proportion of Crenarchaeota at 51.2%, with the proportion of Euryarchaeota at 48.8%, whereas the permafrost contained 41.2% Crenarchaeota and 58.8% Euryarchaeota, based on 16S rRNA gene sequence analysis. OTU1 and OTU11, affiliated to Group 1.3b/MCG-A within Crenarchaeota and the unclassified group within Euryarchaeota, respectively, were widely distributed in all sediment layers. However, OTU5 affiliated to Group 1.3b/MCG-A was primarily distributed in the active layers. Sequence analysis of the DGGE bands from the 16S rRNAs of methanogenic archaea showed that the majority of methanogens belonged to Methanosarcinales and Methanomicrobiales affiliated to Euryarchaeota and the uncultured ZC-I cluster affiliated to Methanosarcinales distributed in all the depths along the permafrost profile, which indicated a dominant group of methanogens occurring in the cold ecosystems.

Study on high-resolution sequence stratigraphy framework of uranium-hosting rock series in Qianjiadian sag

International Nuclear Information System (INIS)

Chen Fanghong; Zhang Mingyu

2005-01-01

The ore-hosting Yaojia Formation is composed of a set of braided stream medium-fine grained sediments. Guided by the basic theory of high-resolution sequence stratigraphy, and based on the core observation, the analysis of chemical composition of rocks, and data of natural potential logging and apparent resistivity logging, the authors have set up the high-resolution sequence stratigraphy framework of the ore-hosting Yaojia Formation, and discussed the relation of the stratigraphic structure of the middle cycle, as well as the paleotopography, the micro-facies to the formation of uranium deposit. (authors)

Stratigraphic and structural configuration of the Navajo (Jurassic) through Ouray (Mississippian-Devonian) formations in the vicinity of Davis and Lavender Canyons, southeastern Utah

International Nuclear Information System (INIS)

McCleary, J.R.; Romie, J.E.

1986-04-01

This study developed a three-dimensional computer model of stratigraphic and structural relationships within a 3497-km 2 (1350-mi 2 ) study area centered on the proposed site for a high-level nuclear waste repository in southeastern Utah. The model consists of a sequence of internally reconciled isopach and structure contour maps horizontally registered and stored in stratigraphic order. This model can be used to display cross sections, perspective block diagrams, or fence diagrams at any orientation; estimate depth of formation contacts and thicknesses for any new stratigraphic or hydrologic boreholes; facilitate ground-water modeling studies; and evaluate the structural and stratigraphic evolution of the study area. This study also includes limited evaluations of aquifer continuity in the Elephant Canyon and Honaker Trail Formations, and of salt dissolution and flowage features as interpreted from geophysical logs. The study identified a long history of movement in the fault system in the north-central part of the study area and a major salt flowage feature in the northeastern part. It describes the Elephant Canyon Formation aquifer as laterally limited, the Honaker Trail Formation aquifer as fairly continuous over the area, and Beef Basin in the southern part of the area as a probable dissolution feature. It also concludes that the Shay-Bridger Jack-Salt Creek Graben system is apparently a vertically continuous feature between the basement and ground surface. No stratigraphic or structural discontinuities were detected in the vicinity of Davis Canyon that appear to be detrimental to the siting of a waste repository

Litho-stratigraphic and Hydrogeological Evaluation of Groundwater ...

African Journals Online (AJOL)

ADOWIE PERE

2015-10-30

://www.ajol.info/index.php/jasem http://www.bioline.org.br/ja. Litho-stratigraphic and Hydrogeological Evaluation of Groundwater System in Parts of. Benin Metropolis, Benin City Nigeria: The Key to Groundwater Sustainability.

Depositional environments and sequence stratigraphy of the Bahram Formation (middle–late Devonian in north of Kerman, south-central Iran

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Afshin Hashmie

2016-09-01

Full Text Available This study is focused on sedimentary environments, facies distribution, and sequence stratigraphy. The facies and sequence stratigraphic analyses of the Bahram Formation (middle–late Devonian in south-central Iran are based on two measured stratigraphic sections in the southern Tabas block. The Bahram Formation overlies red sandstones Padeha Formation in sections Hutk and Sardar and is overlain by Carboniferous carbonate deposits of Hutk Formation paraconformably, with a thickness of 354 and 386 m respectively. Mixed siliciclastic and carbonate sediments are present in this succession. The field observations and laboratory studies were used to identify 14 micro/petrofacies, which can be grouped into 5 depositional environments: shore, tidal flat, lagoon, shoal and shallow open marine. A mixed carbonate-detrital shallow shelf is suggested for the depositional environment of the Bahram Formation which deepens to the east (Sardar section and thins in southern locations (Hutk section. Three 3rd-order cyclic siliciclastic and carbonate sequences in the Bahram Formation and one sequence shared with the overlying joint with Hutk Formation are identified, on the basis of shallowing upward patterns in the micro/pertofacies.

Stratigraphic evolution of the Late Jurassic Hanifa Formation along the Tuwaiq Escarpment, Saudi Arabia: Evidence for a carbonate ramp system

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Fallatah, Mohammed I.; Kerans, Charles

2018-01-01

A sequence stratigraphic framework of the Late Jurassic (Oxfordian) Hanifa Formation at its exposure in Central Arabia is presented for the first time. This study offers the first high-resolution stratigraphic framework of the Hanifa along the Tuwaiq Escarpment by measuring 15 sections ( 770 m total thickness) over an oblique-to-dip distance of 260 km and collecting 295 samples for petrographic analysis. On the basis of these data, the Hanifa Formation can be subdivided into eight facies; 1) tabular cross-bedded quartz-peloidal-skeletal grainstone, 2) cross-bedded skeletal-peloidal grainstone, 3) bioturbated foraminiferal wackestone/mud-dominated packstone, 4) oncolitic rudstone, 5) stromatoporoid-coral biostrome/bioherm, 6) peloidal/composite-grain grain-dominated packstone/grainstone, 7) bioturbated spiculitic wackestone/mud-dominated packstone, and 8) thinly-bedded argillaceous mudstone/wackestone. The vertical and lateral distributions of these facies along the exposure define their sequence setting using the principals of sequence stratigraphy. By recognizing erosional surfaces, facies offset, and changes in facies proportions, five third-order sequences, with an average duration of 1.1 Myr, are interpreted for the Hanifa Formation. The correlation of the sequences across the study area shows that only four sequences are preserved in the north where shallow-water deposits are well-developed. Facies trends within these sequences are further illustrated in depositional models representing the highstand systems tracts (HST) and the transgressive systems tracts (TST) of the Hanifa Formation. These proposed models represent depositional settings of a carbonate ramp with normal open-marine conditions. The HST depositional model is characterized by a high-energy shoreline and depicts the presence of an offshore, structurally controlled skeletal-peloidal shoal body described here for the first time at the Hanifa exposure in the Hozwa area. This work provides a

Reevaluation of the Piermont-Frontenac allochthon in the Upper Connecticut Valley: Restoration of a coherent Boundary Mountains–Bronson Hill stratigraphic sequence

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Rankin, Douglas W.; Tucker, Robert D.; Amelin, Yuri

2013-01-01

The regional extent and mode and time of emplacement of the Piermont-Frontenac allochthon in the Boundary Mountains–Bronson Hill anticlinorium of the Upper Connecticut Valley, New Hampshire–Vermont, are controversial. Moench and coworkers beginning in the 1980s proposed that much of the autochthonous pre–Middle Ordovician section of the anticlinorium was a large allochthon of Silurian to Early Devonian rocks correlated to those near Rangeley, Maine. This ∼200-km-long allochthon was postulated to have been transported westward in the latest Silurian to Early Devonian as a soft-sediment gravity slide on a hypothesized Foster Hill fault. New mapping and U-Pb geochronology do not support this interpretation. The undisputed Rangeley sequence in the Bean Brook slice is different from the disputed sequence in the proposed larger Piermont-Frontenac allochthon, and field evidence for the Foster Hill fault is lacking. At the type locality on Foster Hill, the postulated “fault” is a stratigraphic contact within the Ordovician Ammonoosuc Volcanics. The proposed Foster Hill fault would place the Piermont-Frontenac allochthon over the inverted limb of the Cornish(?) nappe, which includes the Emsian Littleton Formation, thus limiting the alleged submarine slide to post-Emsian time. Mafic dikes of the 419 Ma Comerford Intrusive Complex intrude previously folded strata attributed to the larger Piermont-Frontenac allochthon as well as the autochthonous Albee Formation and Ammonoosuc Volcanics. The Lost Nation pluton intruded and produced hornfels in previously deformed Albee strata. Zircons from an apophysis of the pluton in the hornfels have a thermal ionization mass spectrometry 207Pb/206Pb age of 444.1 ± 2.1 Ma. Tonalite near Bath, New Hampshire, has a zircon sensitive high-resolution ion microprobe 206Pb/238U age of 492.5 ± 7.8 Ma. The tonalite intrudes the Albee Formation, formerly interpreted as the Silurian Perry Mountain Formation of the proposed allochthon

Sequence-Stratigraphic Analysis of the Regional Observation Monitoring Program (ROMP) 29A Test Corehole and Its Relation to Carbonate Porosity and Regional Transmissivity in the Floridan Aquifer System, Highlands County, Florida

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Ward, W. C.; Cunningham, K.J.; Renken, R.A.; Wacker, M.A.; Carlson, J.I.

2003-01-01

An analysis was made to describe and interpret the lithology of a part of the Upper Floridan aquifer penetrated by the Regional Observation Monitoring Program (ROMP) 29A test corehole in Highlands County, Florida. This information was integrated into a one-dimensional hydrostratigraphic model that delineates candidate flow zones and confining units in the context of sequence stratigraphy. Results from this test corehole will serve as a starting point to build a robust three-dimensional sequence-stratigraphic framework of the Floridan aquifer system. The ROMP 29A test corehole penetrated the Avon Park Formation, Ocala Limestone, Suwannee Limestone, and Hawthorn Group of middle Eocene to Pliocene age. The part of the Avon Park Formation penetrated in the ROMP 29A test corehole contains two composite depositional sequences. A transgressive systems tract and a highstand systems tract were interpreted for the upper composite sequence; however, only a highstand systems tract was interpreted for the lower composite sequence of the deeper Avon Park stratigraphic section. The composite depositional sequences are composed of at least five high-frequency depositional sequences. These sequences contain high-frequency cycle sets that are an amalgamation of vertically stacked high-frequency cycles. Three types of high-frequency cycles have been identified in the Avon Park Formation: peritidal, shallow subtidal, and deeper subtidal high-frequency cycles. The vertical distribution of carbonate-rock diffuse flow zones within the Avon Park Formation is heterogeneous. Porous vuggy intervals are less than 10 feet, and most are much thinner. The volumetric arrangement of the diffuse flow zones shows that most occur in the highstand systems tract of the lower composite sequence of the Avon Park Formation as compared to the upper composite sequence, which contains both a backstepping transgressive systems tract and a prograding highstand systems tract. Although the porous and permeable

The Oligocene-Miocene stratigraphic evolution of the Majella carbonate platform (Central Apennines, Italy)

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Brandano, Marco; Cornacchia, Irene; Raffi, Isabella; Tomassetti, Laura

2016-03-01

The stratigraphic architecture of the Bolognano Formation documents the evolution of the Majella carbonate platform in response to global and local changes that affected the Mediterranean area during the Oligocene-Miocene interval. The Bolognano Formation consists of a homoclinal ramp that developed in a warm, subtropical environment. Five different lithofacies associations have been identified: Lepidocyclina calcarenites, cherty marly limestones, bryozon calcarenites, hemipelagic marls and marly limestones, and Lithothamnion limestones. Each association corresponds to a single lithostratigraphic unit except for the Lepidocyclina calcarenites that form two distinct lithostratigraphic units (Lepidocyclina calcarenites 1 and 2). These six units reflect alternation of shallow-water carbonate production and drowning. Specifically, two of the three stages of shallow-water carbonate production regard the development of wide dune fields within the middle ramp, one stage dominated by red algae and a sea-grass carbonate factory, whereas the two drowning phases are represented by marly cherty limestones and calcareous marls. A new biostratigraphic framework for Bolognano Formation is presented, based on high-resolution analysis of calcareous nannofossil assemblages, which proved to be very useful for biostratigraphic constraints also in shallow-water settings. Using this approach, we have linked the first drowning phase, late Chattian-Aquitanian p.p. in age, to western Mediterranean volcanism and the Mi-1 event, and the second drowning phase, late Burdigalian-Serravallian in age, to the closure of the Indo-Pacific passage and the occurrence of the global Monterey event. These results permit a new deciphering, in terms of sequence stratigraphy, of the Bolognano Formation that is interpreted as a 2nd-order super-sequence that can be subdivided into 3 transgressive-regressive sequences.

Application of organic facies in sedimentological-stratigraphical model of the Oligo-Miocene and Miocene of the Campos Basin; Aplicacao da faciologia organica no modelo sedimentologico-estratigrafico do Oligo-Mioceno e Mioceno da Bacia de Campos

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Mendonca Filho, Joao Graciano; Mendonca, Joalice de Oliveira; Oliveira, Antonio Donizeti de; Torres, Jaqueline [Universidade Federal do Rio de Janeiro (UFRJ). Centro de Ciencias Exatas e da Natureza. Inst. de Geociencias (Brazil)], e-mails: graciano@geologia.ufrj.br, donizeti@lafo.geologia.ufrj.br, joalice@lafo.geologia.ufrj.br, jaqueline@lafo.geologia.ufrj.br; Menezes, Taissa Rego [Centro de Pesquisas da Petrobras (CENPES), RJ (Brazil). P e D em Geociencias. Gerencia de Geoquimica], e-mail: taissamenezes@petrobras.com.br; Santos, Viviane Sampaio Santiago dos; Arienti, Luci Maria [Centro de Pesquisas da Petrobras (CENPES), RJ (Brazil). P e D em Geociencias. Gerencia de Sedimentologia e Estratigrafia], e-mails: vsss@petrobras.com.br, arienti@petrobras.com.br

2010-05-15

This study integrates palynofacies analyses and the sedimentological and stratigraphic model of the Oligo-Miocene/Miocene siliciclastic deposits from the stratigraphic interval of the shallow continental platform up to the slope/basin of the Oligo-Miocene/ Miocene of the Campos Basin proposed. The main objective of the palynofacies study was to characterize the particulate sedimentary organic matter to obtain information about the proximal-distal relationship and the sedimentary organic matter preservation and depositional environmental conditions. The 158 core samples collected in 29 wells of the 9 oil production fields (Albacora, Barracuda, Marlim Sul, Marlim, Voador, Marlim Leste, Moreia and Albacora Leste), were studied. This technique provides information about the proximal-distal relationship and the paleoenvironmental conditions of deposition and preservation of sedimentary organic matter, to facilitate the evaluation and comparisons between the associations of particulate organic components. Thus, the palynofacies technique can be used as another tool in the characterization of depositional systems, based on the spatial and temporal distribution of sedimentary intervals. In general the palynofacies assemblages showed the predominance of the Phytoclast Group (terrestrial derived organic matter) at various degradation stages due to the selective preservation process diagnosed in the studied samples. Some samples, revealed high dinocysts percentages indicative of transgressive depositional conditions. From the obtained data, it was possible to characterize the stratigraphic sequences according to the distribution of particulate organic content (e.g. influence of fluvio-deltaic systems, oxygen system, regressive-transgressive tendencies of each sequence). Additional analyses of Total Organic Carbon (% wt) showed the control of the particulate components from the Phytoclast Group on the TOC (% wt) content, suggesting that the relative sea-level variation curves

Applying and improving a sedimentary facies model for exploration of stratigraphic traps in the Austrian Molasse basin

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Hinsch, R.; Kofler, N. [Rohoel-Aufsuchungs AG (RAG), Vienna (Austria); Hubbard, S. [Calgary Univ., Calgary (Canada). Dept. of Geology and Geophysics

2007-09-13

In the Molasse foreland basin of Upper Austria gas is produced from deep-water sandstones and conglomerates of the Puchkirchen and basal Hall formations (Oligocene-Lower Miocene). The basin is mature, with >750 wells drilled by RAG to date. An extensive 3-D seismic reflection dataset that covers much of the paleo-basin foredeep has been acquired in the study area over the last 15 years. Seismic stratigraphic analysis has revealed that deepwater sedimentation in the basin was dominated by a channel belt up to 5 km wide that transported sediment derived from the Central and Eastern Alps eastward along the basin axis (Linzer, 2001; de Ruig, 2003). Based on these findings, a detailed sedimentary facies model has been developed, outlining several distinct depositional elements that reveal numerous possible stratigraphic trap types (de Ruig and Hubbard, 2006). This depositional model is currently being applied and tested in exploration and refined by ongoing research. Channel abandonment and migration are important processes that resulted in stratigraphic configurations consisting of coarse-grained sandstones and conglomerates overlain by channel and overbank mudstones. This represents ideal reservoir architecture, including porous reservoir facies sealed by impermeable deposits. Additional stratigraphic trapping conditions can result from special spatial arrangements of depositional elements, for example a sandstone-filled tributary channel that is sealed by an overlying mudstone-filled abandonment channel. Recognizing and further improving such stratigraphic trapping configurations are important for future exploration in Upper Austria, where most of the structural traps have been drilled. (orig.)

Stratigraphic, Granulometric and Geochemical Studies of a Major Plinian Eruption on Dominica, Lesser Antilles

Science.gov (United States)

Smith, A. L.; Daly, G.; Killingsworth, N.; Deuerling, K.; Schneider, S.; Fryxell, J. E.

2008-12-01

The island of Dominica, located in the center of the Lesser Antilles island arc has witnessed, probably within the last 100,000 years, three large volume Plinian eruptions. One of these, associated with the Morne Diablotins center, forms the Grande Savane pyroclastic flow fan, that extends off shore as a distinctive submarine feature for a distance of at least 14 km. Stratigraphical studies of road cuts and well-exposed sea cliffs indicate the fan is composed of an older unit composed of reworked deposits at the base followed by at least four sequences, based on the presence of paleosols, of block and ash flow deposits. The upper unit of block and ash flows is overlain, with no evidence of an intervening paleosol, by a sequence of ignimbrites and pumiceous surges (representing the Plinian eruption). There is no evidence of an initial Plinian fall deposit, so the lowest bed in the succession is an ignimbrite with a highly irregular base that cuts into the underlying block and ash flow deposits, the upper parts of which are colored red due to thermal effects. This lowest ignimbrite is welded (minimum porosity of 15%) throughout its thickness (maximum thickness of greater than 21 m), although a few outcrops near the margins show a thin (20-30 cm) non-welded but lithified zone beneath the welded zone. The remainder of the sequence is composed of lithified ignimbrite that can be subdivided into three units separated by pumiceous surge layers. The ignimbrite succession is overlain, with no obvious break, by a thin fall deposit containing accretionary lapilli and gas cavities, followed by three pumiceous surge deposits (lower and upper show planar stratification and the middle surge shows massive bedding); towards the north the upper two surge deposits are separated by thin pumiceous lapilli fall and ash fall deposits. This surge sequence extends laterally outside of the main area of ignimbrite deposition. The pumice clasts from the ignimbrites are andesitic in

Correlation between high resolution sequence stratigraphy and mechanical stratigraphy for enhanced fracture characteristic prediction

Science.gov (United States)

Al Kharusi, Laiyyan M.

Sequence stratigraphy relates changes in vertical and lateral facies distribution to relative changes in sea level. These relative changes in carbonates effect early diagenesis, types of pores, cementation and dissolution patterns. As a result, in carbonates, relative changes in sea level significantly impact the lithology, porosity, diagenesis, bed and bounding surfaces which are all factors that control fracture patterns. This study explores these relationships by integrating stratigraphy with fracture analysis and petrophysical properties. A special focus is given to the relationship between mechanical boundaries and sequence stratigraphic boundaries in three different settings: (1) Mississippian strata in Sheep Mountain Anticline, Wyoming, (2) Mississippian limestones in St. Louis, Missouri, and (3) Pennsylvanian limestones intermixed with elastics in the Paradox Basin, Utah. The analysis of these sections demonstrate that a fracture hierarchy exists in relation to the sequence stratigraphic hierarchy. The majority of fractures (80%) terminate at genetic unit boundaries or the internal flooding surface that separates the transgressive from regressive hemicycle. Fractures (20%) that do not terminate at genetic unit boundaries or their internal flooding surface terminate at lower order sequence stratigraphic boundaries or their internal flooding surfaces. Secondly, the fracture spacing relates well to bed thickness in mechanical units no greater than 0.5m in thickness but with increasing bed thickness a scatter from the linear trend is observed. In the Paradox Basin the influence of strain on fracture density is illustrated by two sections measured in different strain regimes. The folded strata at Raplee Anticline has higher fracture densities than the flat-lying beds at the Honaker Trail. Cemented low porosity rocks in the Paradox Basin do not show a correlation between fracture pattern and porosity. However velocity and rock stiffness moduli's display a slight

Early evolution of the southern margin of the Neuquén Basin, Argentina: Tectono-stratigraphic implications for rift evolution and exploration of hydrocarbon plays

Science.gov (United States)

D'Elia, Leandro; Bilmes, Andrés; Franzese, Juan R.; Veiga, Gonzalo D.; Hernández, Mariano; Muravchik, Martín

2015-12-01

Long-lived rift basins are characterized by a complex structural and tectonic evolution. They present significant lateral and vertical stratigraphic variations that determine diverse basin-patterns at different timing, scale and location. These issues cause difficulties to establish facies models, correlations and stratal stacking patterns of the fault-related stratigraphy, specially when exploration of hydrocarbon plays proceeds on the subsurface of a basin. The present case study corresponds to the rift-successions of the Neuquén Basin. This basin formed in response to continental extension that took place at the western margin of Gondwana during the Late Triassic-Early Jurassic. A tectono-stratigraphic analysis of the initial successions of the southern part of the Neuquén Basin was carried out. Three syn-rift sequences were determined. These syn-rift sequences were located in different extensional depocentres during the rifting phases. The specific periods of rifting show distinctly different structural and stratigraphic styles: from non-volcanic to volcanic successions and/or from continental to marine sedimentation. The results were compared with surface and subsurface interpretations performed for other depocentres of the basin, devising an integrated rifting scheme for the whole basin. The more accepted tectono-stratigraphic scheme that assumes the deposits of the first marine transgression (Cuyo Cycle) as indicative of the onset of a post-rift phase is reconsidered. In the southern part of the basin, the marine deposits (lower Cuyo Cycle) were integrated into the syn-rift phase, implying the existence of different tectonic signatures for Cuyo Cycle along the basin. The rift climax becomes younger from north to south along the basin. The post-rift initiation followed the diachronic ending of the main syn-rift phase throughout the Neuquén Basin. Thus, initiation of the post-rift stage started in the north and proceeded towards the south, constituting a

Stratigraphic implications of uranium deposits

International Nuclear Information System (INIS)

Langford, F.F.

1980-01-01

One of the most consistent characteristics of economic uranium deposits is their restricted stratigraphic distribution. Uraninite deposited with direct igneous affiliation contains thorium, whereas chemical precipitates in sedimentary rocks are characterized by thorium-free primary uranium minerals with vanadium and selenium. In marine sediments, these minerals form low-grade disseminations; but in terrestrial sediments, chiefly fluvial sandstones, the concentration of uranium varies widely, with the high-grade portions constituting ore. Pitchblende vein deposits not only exhibit the same chemical characteristics as the Colorado-type sandstone deposits, but they have a stratigraphically consistent position at unconformities covered by fluvial sandstones. If deposits in such diverse situations have critical features in common, they are likely to have had many features of their origin in common. Thus, vein deposits in Saskatchewan and Australia may have analogues in areas that contain Colorado-type sandstone deposits. In New Mexico, the presence of continental sandstones with peneconformable uranium deposits should also indicate good prospecting ground for unconformity-type vein deposits. All unconformities within the periods of continental deposition ranging from Permian to Cretaceous should have uranium potential. Some situations, such as the onlap of the Abo Formation onto Precambrian basement in the Zuni Mountains, may be directly comparable to Saskatchewan deposition. However, uranium occurrences in the upper part of the Entrada Sandstone suggest that unconformities underlain by sedimentary rocks may also be exploration targets

Comparative genomics beyond sequence-based alignments

DEFF Research Database (Denmark)

Þórarinsson, Elfar; Yao, Zizhen; Wiklund, Eric D.

2008-01-01

Recent computational scans for non-coding RNAs (ncRNAs) in multiple organisms have relied on existing multiple sequence alignments. However, as sequence similarity drops, a key signal of RNA structure--frequent compensating base changes--is increasingly likely to cause sequence-based alignment me...

Sequence and facies architecture of the upper Blackhawk Formation and the Lower Castlegate Sandstone (Upper Cretaceous), Book Cliffs, Utah, USA

Science.gov (United States)

Yoshida, S.

2000-11-01

High-frequency stratigraphic sequences that comprise the Desert Member of the Blackhawk Formation, the Lower Castlegate Sandstone, and the Buck Tongue in the Green River area of Utah display changes in sequence architecture from marine deposits to marginal marine deposits to an entirely nonmarine section. Facies and sequence architecture differ above and below the regionally extensive Castlegate sequence boundary, which separates two low-frequency (106-year cyclicity) sequences. Below this surface, high-frequency sequences are identified and interpreted as comprising the highstand systems tract of the low-frequency Blackhawk sequence. Each high-frequency sequence has a local incised valley system on top of the wave-dominated delta, and coastal plain to shallow marine deposits are preserved. Above the Castlegate sequence boundary, in contrast, a regionally extensive sheet sandstone of fluvial to estuarine origin with laterally continuous internal erosional surfaces occurs. These deposits above the Castlegate sequence boundary are interpreted as the late lowstand to early transgressive systems tracts of the low-frequency Castlegate sequence. The base-level changes that generated both the low- and high-frequency sequences are attributed to crustal response to fluctuations in compressive intraplate stress on two different time scales. The low-frequency stratigraphic sequences are attributed to changes in the long-term regional subsidence rate and regional tilting of foreland basin fill. High-frequency sequences probably reflect the response of anisotropic basement to tectonism. Sequence architecture changes rapidly across the faulted margin of the underlying Paleozoic Paradox Basin. The high-frequency sequences are deeply eroded and stack above the Paradox Basin, but display less relief and become conformable updip. These features indicate that the area above the Paradox Basin was more prone to vertical structural movements during formation of the Blackhawk

Stratigraphic Stacking of Deepmarine Channel Levee Turbidites: Scales of Cyclicity and their Origin. Examples from the Laingsburg Fm. (Karoo, South Africa) and the Rosario Fm. (Baja, Mexico)

Science.gov (United States)

Kane, I. A.; Hodgson, D.

2009-12-01

Thinning upwards of the turbidite beds that form deepmarine channel levees is a common motif reported from modern and recent levees on the seafloor, from subsurface examples, and from outcropping ancient examples. Because levees are thought to be built by deposition from turbidity currents superelevated over their channel form, the volume and style of overbank deposition are controlled primarily by the relationship between levee height (i.e., thalweg to crest) and flow thickness, determining the amount of overspill. Thus stratigraphic variability of turbidite thickness is explained by some change in either or both of those factors, which may arise autocyclicly or allocyclicly. Variation in the ratio of intra-channel and extra-channel deposition can be an autocyclic stratigraphic response, e.g., in bypass dominated systems, thalweg aggradation may be retarded with respect to levee aggradation, hence as levee relief increases, flows become more confined and, given a relatively narrow range of flow sizes, the volume of overbank flow and deposit thickness decrease with stratigraphic height. However, the same stratigraphic response of the levee may occur due to allocyclic flow magnitude variation, i.e., through decreasing flow magnitude. In both the autocyclic and allocyclic case the stratigraphic response of the levee may be one of thinning upwards, even if the overall system response may be one of progradation (autocyclic bypassing case) or retrogradation (allocyclic decreasing flow magnitude case), with entirely different connotations for sequence stratigraphic interpretation. Here we report examples of different scales of bed thickness cyclicity (both thickening and thinning upward cycles superimposed by smaller scale cycles) within levees of the Rosario Formation, Baja California, Mexico, and from the Laingsburg Formation, Karoo, South Africa, and, together with published examples, discuss criteria for the recognition, and drivers of, autocyclic and allocyclic bed

The stratigraphic record of Khawr Al Maqta, Abu Dhabi, United Arab Emirates

Science.gov (United States)

Lokier, S. W.; Herrmann, S.

2012-04-01

Well-constrained modern depositional analogues are vital to the development of accurate geological reservoir models. The development of realistic hydrocarbon reservoir models requires the application of high-precision, well-constrained outcrop and sub-surface data sets with accurately-documented facies geometries and depositional sequence architectures. The Abu Dhabi coastline provides the best modern analogue for the study of ramp-style carbonate depositional facies akin to those observed in the sub-surface reservoirs of the United Arab Emirates (UAE). However, all previous studies have relied on temporally limited surface datasets. This study employed thirty five shallow subsurface cores spanning the width of the Khawr Al Maqta - the narrow shallow tidal channel that separates Abu Dhabi Island from the mainland. The cores were taken over a transect measuring 1.2 km in length by 50 m wide thus providing a high-resolution record of sub-surface facies geometries in a stratigraphically complex setting. Geometries in these Pleistocene to Holocene facies are complex with interdigitating, laterally heterogeneous carbonate, siliciclastic and evaporite units represented throughout the area of the study. Carbonate facies range from molluscan rudstones to marls and are all indicative of deposition in a shallow, relatively low energy marine setting akin to that seen in the environs of Abu Dhabi Island today. Texturally mature quartz sands occur as thin lenses and as thin cross bedded or laminated horizons up to twenty five centimetres thick. Glauconitic mudstones are common and locally exhibit evidence of rootlets and desiccation cracks. Evaporites are present in the form of gypsum occurring as isolated crystals and nodules or as massive chicken-wire units in excess of three metres thick. All of these textures are consistent with evaporite development in the shallow subsurface. Early, shallow-burial diagenesis has been important. Bioclasts are pervasively leached throughout

Stratigraphical discontinuities, tropical landscape evolution and soil distribution relationships in a case study in SE-Brazil

Directory of Open Access Journals (Sweden)

M. Cooper

2002-09-01

Full Text Available On a regional summit surface in the county of Piracicaba (SP within the Peripheric Depression of São Paulo, formed of discontinued flattened tops, there is an abrupt transition between a Typic Hapludox and a Kandiudalfic Eutrudox, together with two stoneline layers. Using stratigraphical, mineralogical, and cartographic studies, this transition and the soil distribution of this surface were studied, correlating them with the different parent materials and the morphoclimatic model of landscape evolution in Southeastern Brazil. The Typic Hapludox was formed on a sandy Cenozoic deposit (Q that overlies a pellitic deposit of the Iratí formation (Pi, representing a regional erosive discordance. Westwards to the Piracicaba River, this sequence is interrupted by a diabase sill overlain by a red clayey material which gave origin to the Kandiudalfic Eutrudox. Two post-Permian depositional events were identified by the two stonelines and stratigraphical discontinuities. The first event generated the deposition of a sandy sediment in the form of levelled alveoluses on regional barriers, most of these formed by dikes and diabase sills, probably during a drier phase. The second depositional event, leading to the deposition of the red clay was probably the dissection of the previously formed pediplane during a humid climate, followed by another pedimentation process during a later, drier period.

Stratigraphic cross section of measured sections and drill holes of the Neslan Formation and adjacent formations, Book Cliffs Area, Colorado and Utah

Science.gov (United States)

Kirshbaum, Mark A.; Spear, Brianne D.

2012-01-01

This study updates a stratigraphic cross section published as plate 2 in Kirschbaum and Hettinger (2004) Digital Data Series 69-G (http://pubs.usgs.gov/dds/dds-069/dds-069-g/). The datum is a marine/tidal ravinement surface within the Cozzette Sandstone Member of the Iles Formation and the Thompson Canyon Sandstone and Sulphur Canyon Sandstone Beds of the Neslen Formation. One of the cores shown was included on the original cross section, and new core descriptions have been added to the upper part of the cored interval. A new core description (S178) is included in this report. Cores are stored in the U.S. Geological Survey Core Research Facility at the Denver Federal Center, Colorado. The following information has also been added to help define the stratigraphic framework: 1) At least five claystones interpreted as altered volcanic ashes have been identified and may give future workers a correlation tool within the largely continental section. 2) Thickness and general geometry of the Sego Sandstone, Buck Tongue of the Mancos Shale, and Castlegate Sandstone have been added to provide additional stratigraphic context. 3) The geometry in the Sego Sandstone, Buck Tongue of the Mancos Shale, and Castlegate Sandstone has been added to provide additional stratigraphic context. 4) Ammonite collections are from Gill and Hail. The zone of Didymoceras nebrascense projected into the East Salt Wash area is based on correlation of the flooding surface at the base of the Cozzette Member to this point as shown in Kirschbaum and Hettinger. 5) A leaf locality of the Denver Museum of Nature and Science is shown in its approximate stratigraphic position near Thompson Canyon. 6) A dinosaur locality of the Natural History Museum of Utah is shown in the Horse Canyon area measured section at the stratigraphic position where it was extracted.

Social and environmental impact of volcaniclastic flows related to 472 AD eruption at Vesuvius from stratigraphic and geoarcheological data

Science.gov (United States)

Di Vito, Mauro A.; de Vita, Sandro; Rucco, Ilaria; Bini, Monica; Zanchetta, Giovanni; Aurino, Paola; Cesarano, Mario; Ebanista, Carlo; Rosi, Mauro; Ricciardi, Giovanni

2017-04-01

There is a growing number of evidences in the surrounding plain of Somma-Vesuvius volcano which indicate that along with primary volcanic processes (i.e. fallout, pyroclastic density currents) the syn-eruptive and post-eruptive volcaniclastic remobilization has severely impacted the ancient civilizations, which flourished in the area. This represents an important starting point for understanding the future hazard related to a potential (and not remote) renewal of volcanic activity of the Campaniana volcanoes. We present geoarcheological and stratigraphic data obtained from the analysis of more than 160 sections in the Campanian plain showing the widespread impact of volcaniclastic debris flows and floods originated from the rapid remobilization of the products of the AD 472 eruption of Somma-Vesuvius, both on the environment and on the human landscape. This eruption was one of the two sub-Plinian historical events of Somma Vesuvius. This event largely impacted the northern and eastern territory surrounding the volcano with deposition of a complex sequence of pyroclastic-fallout and -current deposits. These sequences were variably affected by syn- and post-eruptive mobilization both along the Somma-Vesuvius slopes and the Apennine valleys with the emplacement of thick mud- and debris-flows which strongly modified the preexisting paleogeography of the Plain with irretrievable damages to the agricultural and urban landscape. The multidisciplinary approach to the study of the sequences permitted to reconstruct the palaeoenvironment before the eruption and the timing of the emplacement of both pyroclastic and volcanoclastic deposits. The preexisting landscape was characterized by intense human occupation, although showing strong evidences of degradation and abandonment due to the progressive decline of the Roman Empire. The impact of volcaniclastic flows continued for decades after the eruption as highlighted in the studied sequences by stratigraphic and archaeologic

Lithostratigraphy and volcanology of the Serra Geral Group, Paraná-Etendeka Igneous Province in Southern Brazil: Towards a formal stratigraphical framework

Science.gov (United States)

Rossetti, Lucas; Lima, Evandro F.; Waichel, Breno L.; Hole, Malcolm J.; Simões, Matheus S.; Scherer, Claiton M. S.

2018-04-01

The volcanic rocks of the Lower Cretaceous Paraná-Etendeka Igneous Province, in Brazil, are grouped in the Serra Geral Group. The province can be chemically divided into low-TiO2, and high-TiO2. In southern Brazil, the low-TiO2 lava pile reaches a thickness of 1 km and is formed of heterogeneous lava packages here divided into four lava formations. Torres Formation (TF) is characterized by chemically more primitive basaltic (> 5 wt% MgO) compound pahoehoe flow fields; these lavas stratigraphically overly aeolian sandstones of Botucatu Formation and represent the onset of the volcanic activity. Vale do Sol Formation (VSF) groups vertically stacked sheet-like rubbly pahoehoe basaltic andesites (SiO2 > 51 wt%; MgO < 5 wt%). These lavas covered the former basalts in the Torres Syncline axis and pinch out towards southwest and represent the most voluminous mafic lava flows. Dacites and rhyolites of Palmas Formation (PF) overlay VSF flows in the central and eastern outcrop area and rest directly upon TF lavas in the west. The acidic units were emplaced as lava domes and widespread tabular lava flows. Esmeralda Formation (EF) is the upper stratigraphic unit and it is formed by a basaltic pahoehoe flow field emplaced during the waning phase of volcanic activity of the low-TiO2 lava sequence. Sedimentary interbeds are preserved throughout the whole lava pile and were deposited during quiescence periods of volcanic activity, and represent important stratigraphic markers (e.g. TF-VSF contact). The newly proposed stratigraphy provides promptly recognized stratigraphic units in a regional framework of fundamental importance for future correlations and provide vital information in the understanding of how the Paraná-Etendeka Igneous Province evolved through time.

Sedimentology and High Resolution Sequence Stratigraphy of the Middle Jurassic Dhruma Formation Carbonates Outcrops in the Central Saudi Arabia

Science.gov (United States)

Yousif, Ibrahim; Abdullatif, Osman; Makkawi, Mohammed; Abdulghani, Waleed

2017-04-01

This study investigates the microfacies and sequence stratigraphic frame work of the Middle Jurassic Dhruma Formation in outcrops in central Saudi Arabia. The study contributes to the efforts to understand and enhance local and regional stratigraphic relationship and correlation of the Jurassic carbonate sequences and their significance to reservoir description and prediction in the subsurcae. The study describes and characterizes the sedimentology, microfacies and the stratigraphy of Dhruma Formation from outcrop sections having a total thickness of 70 m. Detailed microfacies and high-resolution stratigraphical analysis were carried out to determine microfacies, cyclicity, sequences and staking pattern. The study revealed ten lithofacies namely: oolitic grainstone,bioclastic oolitic grainstone, oolitic grapestone, bioclastic grainstone,foraminiferal packstone, echinoderm packstone, peloidal packstone to grainstone,skeletal wackestone to packstone, mudstone, and marlstone.These lithofacies were grouped into five lithofacies associations that deposited on a carbonate ramp setting. The depositional environment ranging from low energy lagoonal setting to high-energy shoals and banks to low energy outer ramp setting. Five high-resolution composite sequences have been defined and each sequence is composed at the bottom of intercalated mudstone/wackestone that passing up into grainstone lithofacies.The composite sequences range in thickness from 7 to 15 m, while the parasequences range from 0.5 to 1.5 m. The composite sequences extend laterally for a distance of more than 350 m. The overall composite section shows a shallowing upward succession of the 4th to the 5th order high-resolution sequences.The dominant lithofacies are the grainy ones, which constitute 30%, 50% and 80% of the studied sections. Furthermore, the parasequences thickness and their bio-components are increasing towards the top. The muddy lithofacies intensively affected the vertical continuity of the

High-resolution sequence stratigraphy of lower Paleozoic sheet sandstones in central North America: The role of special conditions of cratonic interiors in development of stratal architecture

Science.gov (United States)

Runkel, Anthony C.; Miller, J.F.; McKay, R.M.; Palmer, A.R.; Taylor, John F.

2007-01-01

Well-known difficulties in applying sequence stratigraphic concepts to deposits that accumulated across slowly subsiding cratonic interior regions have limited our ability to interpret the history of continental-scale tectonism, oceanographic dynamics of epeiric seas, and eustasy. We used a multi-disciplinary approach to construct a high-resolution stratigraphic framework for lower Paleozoic strata in the cratonic interior of North America. Within this framework, these strata proved readily amenable to modern sequence stratigraphic techniques that were formulated based on successions along passive margins and in foreland basins, settings markedly different from the cratonic interior. Parasequences, parasequence stacking patterns, systems tracts, maximum flooding intervals, and sequence-bounding unconformities can be confidently recognized in the cratonic interior using mostly standard criteria for identification. The similarity of cratonic interior and foreland basin successions in size, geometry, constituent facies, and local stacking patterns of nearshore parasequences is especially striking. This similarity indicates that the fundamental processes that establish shoreface morphology and determine the stratal expression of retreat and progradation were likewise generally the same, despite marked differences in tectonism, physiography, and bathymetry between the two settings. Our results do not support the widespread perception that Paleozoic cratonic interior successions are so anomalous in stratal geometries, and constitute such a poor record of time, that they are poorly suited for modern sequence stratigraphic analyses. The particular arrangement of stratal elements in the cratonic interior succession we studied is no more anomalous or enigmatic than the variability in architecture that sets all sedimentary successions apart from one another. Thus, Paleozoic strata of the cratonic interior are most appropriately considered as a package that belongs in a

Mixed Sequence Reader: A Program for Analyzing DNA Sequences with Heterozygous Base Calling

Science.gov (United States)

Chang, Chun-Tien; Tsai, Chi-Neu; Tang, Chuan Yi; Chen, Chun-Houh; Lian, Jang-Hau; Hu, Chi-Yu; Tsai, Chia-Lung; Chao, Angel; Lai, Chyong-Huey; Wang, Tzu-Hao; Lee, Yun-Shien

2012-01-01

The direct sequencing of PCR products generates heterozygous base-calling fluorescence chromatograms that are useful for identifying single-nucleotide polymorphisms (SNPs), insertion-deletions (indels), short tandem repeats (STRs), and paralogous genes. Indels and STRs can be easily detected using the currently available Indelligent or ShiftDetector programs, which do not search reference sequences. However, the detection of other genomic variants remains a challenge due to the lack of appropriate tools for heterozygous base-calling fluorescence chromatogram data analysis. In this study, we developed a free web-based program, Mixed Sequence Reader (MSR), which can directly analyze heterozygous base-calling fluorescence chromatogram data in .abi file format using comparisons with reference sequences. The heterozygous sequences are identified as two distinct sequences and aligned with reference sequences. Our results showed that MSR may be used to (i) physically locate indel and STR sequences and determine STR copy number by searching NCBI reference sequences; (ii) predict combinations of microsatellite patterns using the Federal Bureau of Investigation Combined DNA Index System (CODIS); (iii) determine human papilloma virus (HPV) genotypes by searching current viral databases in cases of double infections; (iv) estimate the copy number of paralogous genes, such as β-defensin 4 (DEFB4) and its paralog HSPDP3. PMID:22778697

Geoscience/engineering characterization of the interwell environment in carbonate reservoirs based on outcrop analogs, Permian Basin, West Texas and New Mexico-stratigraphic hierarchy and cycle stacking facies distribution, and interwell-scale heterogeneity: Grayburg Formation, New Mexico. Final report

Energy Technology Data Exchange (ETDEWEB)

Barnaby, R.J.; Ward, W.B.; Jennings, J.W. Jr.

1997-06-01

The Grayburg Formation (middle Guadalupian) is a major producing interval in the Permian Basin and has yielded more than 2.5 billion barrels of oil in West Texas. Grayburg reservoirs have produced, on average, less than 30 percent of their original oil in place and are undergoing secondary and tertiary recovery. Efficient design of such enhanced recovery programs dictates improved geological models to better understand and predict reservoir heterogeneity imposed by depositional and diagenetic controls. The Grayburg records mixed carbonate-siliciclastic sedimentation on shallow-water platforms that rimmed the Delaware and Midland Basins. Grayburg outcrops in the Guadalupe and Brokeoff Mountains region on the northwest margin of the Delaware Basin present an opportunity to construct a detailed, three-dimensional image of the stratigraphic and facies architecture. This model can be applied towards improved description and characterization of heterogeneity in analogous Grayburg reservoirs. Four orders of stratigraphic hierarchy are recognized in the Grayburg Formation. The Grayburg represents a long-term composite sequence composed of four high-frequency sequences (HFS 1-4). Each HFS contains several composite cycles comprising two or more cycles that define intermediate-scale transgressive-regressive successions. Cycles are the smallest scale upward-shoaling vertical facies successions that can be recognized and correlated across various facies tracts. Cycles thus form the basis for establishing the detailed chronostratigraphic correlations needed to delineate facies heterogeneity.

Biostratigraphy and sequence stratigraphy of the Sarvak Formation at Fahliyan Anticline (South of Yasuj)

International Nuclear Information System (INIS)

Ahmadi, A.; Vaziri-Moghaddam, A.; Sayrafian, A.; Taheri, A.

2016-01-01

In this study, bio stratigraphy, depositional environment and sequence stratigraphy of the Sarvak Formation at Fahliyan Anticline was studied. 8 species of benthic foraminifera (4 genera) and 8 species of planktonic foraminifera (11 genera) in the study area were recognized. 6 biozones have been recognized by distribution of the foraminifera, which in stratigraphic order are: Favusella washitensis Zone, Orbitolina-Alveolinids Assemblage Zone, Rudist debris Zone, Oligostegina flood Zone, Whiteinella archaeocretacea Zone and Helvetoglobotruncana helvetica Zone. On the basis of these, the age of Albian–Turonian was considered for the Sarvak Formation. Based on petrography and analysis of microfacies features 9 different microfacies types have been recognized, which can be grouped into 3 depositional environments: lagoon, shoal and open marine. The Sarvak Formation represents sedimentation on a carbonate ramp. Sequence stratigraphy analysis led to identification of 4 third-order sequences.

Subsurface geology of the Lusi region: preliminary results from a comprehensive seismic-stratigraphic study.

Science.gov (United States)

Moscariello, Andrea; Do Couto, Damien; Lupi, Matteo; Mazzini, Adriano

2016-04-01

We investigate the subsurface data of a large sector in the Sidoarjo district (East Java, Indonesia) where the sudden catastrophic Lusi eruption started the 26th May 2006. Our goal is to understand the stratigraphic and structural features which can be genetically related to the surface manifestations of deep hydrothermal fluids and thus allow us to predict possible future similar phenomena in the region. In the framework of the Lusi Lab project (ERC grant n° 308126) we examined a series of densely spaced 2D reflection commercial seismic lines This allowed the reconstruction of the lateral variability of key stratigraphic horizons as well as the main tectonic features. In particular, we shed light on the deep structure of the Watukosek fault system and the associated fracture corridors crossing the entire stratigraphic successions. To the South-West, when approaching the volcanic complex, we could identify a clear contrast in seismic facies between chaotic volcanoclastic wedges and clastic-prone sedimentary successions as well as between the deeper stratigraphic units consisting of carbonates and lateral shales units. The latter show possible ductile deformation associated to fault-controlled diapirism which control in turns deformation of overlying stratigraphic units and deep geo-fluids circulation. Large collapse structures recognized in the study area (e.g. well PRG-1) are interpreted as the results of shale movement at depth. Similarly to Lusi, vertical deformation zones ("pipes"), likely associated with deeply rooted strike-slip systems seem to be often located at the interface between harder carbonate rocks forming isolated build ups and the laterally nearby clastic (shale-prone)-units. The mechanisms of deformation of structural features (strike vs dip slip systems) which may affect either the basement rock or the overlying deeper stratigraphic rocks is also being investigated to understand the relationship between deep and shallower (i.e. meteoric) fluid

Genetic and stratigraphic significance of the Upper Devonian Frasnian Z Marker, west-central Alberta

Energy Technology Data Exchange (ETDEWEB)

Wendte, J. [Geological Survey of Canada, Calgary, AB (Canada); Stoakes, F. [Stoakes Consulting Group Ltd., Calgary, AB (Canada); Bosman, M. [Canadian Hunter Exploration Ltd., Calgary, AB (Canada); Bernstein, L. [Talisman Energy Inc., Calgary, AB (Canada)

1995-12-01

The stratigraphic model from the west-central Alberta basin was provided. It defined the Z Marker as a distinctive and widespread wireline log marker within the thick Frasnian Ireton shale basin succession. The marker represents an interval of condensed sedimentation and corresponds to an abrupt change from a calcareous signature below to an argillaceous character above. Toward the shelf, in the West Pembina area, the Z Marker correlates to a level within a conformable succession of nodular lime wackestones and corresponds to the base of a depositional cycle near the middle of the Lobstick member of the Nisku Formation. Further shelfward, the Z Marker continues as a well-defined log marker until the Nisku shelf margin. The stratigraphic significance of the Z Marker in delineating various oil bearing formations in Alberta were explained in great detail. The correct recognition and correlation of this marker was claimed to permit an understanding of basin evolution beyond that discernable from the existing lithostratigraphic nomenclature alone. 17 refs., 13 figs.

Stratigraphic relations and hydrologic properties of the Paintbrush Tuff (PTn) hydrologic unit, Yucca Mountain, Nevada

International Nuclear Information System (INIS)

Moyer, T.C.; Geslin, J.K.; Flint, L.E.

1996-01-01

Yucca Mountain is being investigated as a potential site for a high- level nuclear waste repository. The intent of this study was to clarify stratigraphic relations within the Paintbrush Tuff (PTn) unit at Yucca Mountain in order to better understand vertical and lateral variations in hydrologic properties as they relate to the lithologic character of these rocks. This report defines informal stratigraphic units within the PTn interval, demonstrates their lateral continuity in the Yucca Mountain region, describes later and vertical variations within them, and characterizes their hydrologic properties and importance to numerical flow and transport models. We present tables summarizing the depth to stratigraphic contacts in cored borehole studies, and unit descriptions and correlations in 10 measured sections

Stratigraphic relations and hydrologic properties of the Paintbrush Tuff (PTn) hydrologic unit, Yucca Mountain, Nevada

Energy Technology Data Exchange (ETDEWEB)

Moyer, T.C.; Geslin, J.K. [Science Applications International Corp., Golden, CO (United States); Flint, L.E. [U.S. Geological Survey, Yucca Mountain Project, Mercury, NV (United States)

1996-08-01

Yucca Mountain is being investigated as a potential site for a high- level nuclear waste repository. The intent of this study was to clarify stratigraphic relations within the Paintbrush Tuff (PTn) unit at Yucca Mountain in order to better understand vertical and lateral variations in hydrologic properties as they relate to the lithologic character of these rocks. This report defines informal stratigraphic units within the PTn interval, demonstrates their lateral continuity in the Yucca Mountain region, describes later and vertical variations within them, and characterizes their hydrologic properties and importance to numerical flow and transport models. We present tables summarizing the depth to stratigraphic contacts in cored borehole studies, and unit descriptions and correlations in 10 measured sections.

Temporal correlation of fluvial and alluvial sequences in the Makran Range, SE-Iran

Science.gov (United States)

Kober, F.; Zeilinger, G.; Ivy-Ochs, S.; Dolati, A.; Smit, J.; Burg, J.-P.; Bahroudi, A.; Kubik, P. W.; Baur, H.; Wieler, R.; Haghipour, N.

2009-04-01

The Makran region of southeastern Iran is an active accretionary wedge with a partially subaerial component. New investigations have revealed a rather complex geodynamic evolution of the Makran active accretionary wedge that is not yet fully understood in its entity. Ongoing convergence between the Arabian and Eurasian plates and tectonic activity since the late Mesozoic has extended all trough the Quaternary. We focus here on fluvial and alluvial sequences in tectonically separated basins that have been deposited probably in the Pliocene/Quaternary, based on stratigraphic classification in official geological maps, in order to understand the climatic and tectonic forces occurring during the ongoing accretionary wegde formation. Specifically, we investigate the influence of Quaternary climate variations (Pleistocene cold period, monsoonal variations) on erosional and depositional processes in the (semi)arid Makran as well as local and regional tectonic forces in the Coastal and Central Makran Range region. Necessary for such an analysis is a temporal calibration of alluvial and fluvial terrace sequences that will allow an inter-basin correlation. We utilize the exposure age dating method using terrestrial cosmogenic nuclides (TCN) due to the lack of otherwise datatable material in the arid Makran region. Limited radiocarbon data are only available for marine terraces (wave-cut platforms). Our preliminary 21Ne and 10Be TCN-ages of amalgamated clast samples from (un)deformed terrace and alluvial sequences range from ~250 ky to present day (modern wash). These ages agree in relative terms with sequences previously assigned by other investigations through correlation of Quaternary sequences from Central and Western Iran regions. However, our minimum ages suggest that all age sequences are of middle to late Pleistocene age, compared to Pliocene age estimates previously assigned for the oldest units. Although often suggested, a genetical relation and connection of those

SNAD: sequence name annotation-based designer

Directory of Open Access Journals (Sweden)

Gorbalenya Alexander E

2009-08-01

Full Text Available Abstract Background A growing diversity of biological data is tagged with unique identifiers (UIDs associated with polynucleotides and proteins to ensure efficient computer-mediated data storage, maintenance, and processing. These identifiers, which are not informative for most people, are often substituted by biologically meaningful names in various presentations to facilitate utilization and dissemination of sequence-based knowledge. This substitution is commonly done manually that may be a tedious exercise prone to mistakes and omissions. Results Here we introduce SNAD (Sequence Name Annotation-based Designer that mediates automatic conversion of sequence UIDs (associated with multiple alignment or phylogenetic tree, or supplied as plain text list into biologically meaningful names and acronyms. This conversion is directed by precompiled or user-defined templates that exploit wealth of annotation available in cognate entries of external databases. Using examples, we demonstrate how this tool can be used to generate names for practical purposes, particularly in virology. Conclusion A tool for controllable annotation-based conversion of sequence UIDs into biologically meaningful names and acronyms has been developed and placed into service, fostering links between quality of sequence annotation, and efficiency of communication and knowledge dissemination among researchers.

Stratigraphy of the Grande Savane Ignimbrite Sequence, Dominica, Lesser Antilles

Science.gov (United States)

Schneider, S.; Smith, A. L.; Deuerling, K.; Killingsworth, N.; Daly, G.

2007-12-01

The island of Dominica, located in the central part of the Lesser Antilles island arc has eight potentially active volcanoes. One of these, Morne Diablotins, is a composite stratovolcano with several superimposed stratigraphic sequences ranging in age from Pliocene (4-2 Ma) to "Younger" Pleistocene (22,000 and >40,000 years B.P. The ignimbrite sequences form four flow fans that reached both the east and west coasts of the island. One of these flow fans, the Grande Savane, on the west coast of the island, also extends off-shore for a distance of at least 14 km as a distinctive submarine fan. Stratigraphical studies of the on- shore deposits that make up this fan indicate an older sequence of block and ash flow deposits, within which occurs a distinctive vulcanian fall deposit. These are overlain, with no evidence of an intervening paleosol, by a sequence of ignimbrites containing welded horizons (ranging in thickness from around 4 m to 16m). The lack of fall deposits beneath the ignimbrites suggest they may have been formed by instantaneous continuous collapse of the eruption column. This whole succession is overlain by a series of planar and dune bedded pumiceous surge deposits with interbedded pumiceous lapilli fall and ash fall deposits, that extend laterally outside of the main area of ignimbrite deposition. Beds within this upper sequence often contain accretionary lapilli and gas cavities suggesting magma-water interaction. The youngest deposits from Morne Diablotins appear to be valley- fill deposits of both ignimbrite and block and ash flow. A comparison of the of the Grande Savane pyroclastic sequence with the Pointe Ronde (west coast) and Londonderry (east coast) pyroclastic flow fans will provide information on the eruptive history of this major Plinian episode.

Depositional sequence stratigraphy and architecture of the cretaceous ferron sandstone: Implications for coal and coalbed methane resources - A field excursion

Science.gov (United States)

Garrison, J.R.; Van Den, Bergh; Barker, C.E.; Tabet, D.E.

1997-01-01

of depositional parasequence sets in both near-marine and non-marine parts of fluvial-deltaic depositional sequences. Ongoing field studies, based on this concept of coal zone stratigraphy, and detailed stratigraphic mapping, have documented the existence of at least 12 parasequence sets within the Last Chance delta clastic wedge. These parasequence sets appear to form four high frequency, 4th-order depositional sequences. The dramatic erosional unconformities, associated with these 4th-order sequence boundaries, indicate that there was up to 20-30 m of erosion, signifying locally substantial base-level drops. These base-level drops were accompanied by a basin ward shift in paleo-shorelines by as much as 5-7 km. These 4th-order Upper Ferron Sequences are superimposed on the 3rd-order sea-level rise event and the 3rd-order, sediment supply/accommodation space driven, stratigraphie architecture of the Upper Ferron Sandstone. The fluvial deltaic architecture shows little response to these 4th-order sea-level events. Coal zones generally thicken landward relative to the mean position of the landward pinch-out of the underlying parasequence set, but after some distance landward, they decrease in thickness. Coal zones also generally thin seaward relative to the mean position of the landward pinch-out of the underlying parasequence set. The coal is thickest in the region between this landward pinch-out and the position of maximum zone thickness. Data indicate that the proportion of coal in the coal zone decreases progressively landward from the landward pinch-out. The effects of differential compaction and differences in original pre-peat swamp topography have the effect of adding perturbations to the general trends. These coal zone systematics have major impact on approaches to exploration and production, and the resource accessment of both coal and coalbed methane.

The Application of Seismic Attributes and Wheeler Transformations for the Geomorphological Interpretation of Stratigraphic Surfaces: A Case Study of the F3 Block, Dutch Offshore Sector, North Sea

OpenAIRE

Mohammad Afifi Ishak; Md. Aminul Islam; Mohamed Ragab Shalaby; Nurul Hasan

2018-01-01

This study was carried out in the Pliocene interval of the southern North Sea F3 Block in the Netherlands. This research paper demonstrates how an integrated interpretation of geological information using seismic attributes, sequence stratigraphic interpretation and Wheeler transformation methods allow for the accurate interpretation of the depositional environment of a basin, as well as locating seismic geomorphological features. The methodology adopted here is to generate a 3D dip-steered H...

OWL representation of the geologic timescale implementing stratigraphic best practice

Science.gov (United States)

Cox, S. J.

2011-12-01

The geologic timescale is a cornerstone of the earth sciences. Versions are available from many sources, with the following being of particular interest: (i) The official International Stratigraphic Chart (ISC) is maintained by the International Commission for Stratigraphy (ICS), following principles developed over the last 40 years. ICS provides the data underlying the chart as part of a specialized software package, and the chart itself as a PDF using the standard colours; (ii) ITC Enschede has developed a representation of the timescale as a thesaurus in SKOS, used in a Web Map Service delivery system; (iii) JPL's SWEET ontology includes a geologic timescale. This takes full advantage of the capabilities of OWL. However, each of these has limitations - The ISC falls down because of incompatibility with web technologies; - While SKOS supports multilingual labelling, SKOS does not adequately support timescale semantics, in particular since it does not include ordering relationships; - The SWEET version (as of version 2) is not fully aligned to the model used by ICS, in particular not recognizing the role of the Global Boundary Stratotype Sections and Point (GSSP). Furthermore, it is distributed as static documents, rather than through a dynamic API using SPARQL. The representation presented in this paper overcomes all of these limitations as follows: - the timescale model is formulated as an OWL ontology - the ontology is directly derived from the UML representation of the ICS best practice proposed by Cox & Richard [2005], and subsequently included as the Geologic Timescale package in GeoSciML (http://www.geosciml.org); this includes links to GSSPs as per the ICS process - key properties in the ontology are also asserted to be subProperties of SKOS properties (topConcept and broader/narrower relations) in order to support SKOS-based queries; SKOS labelling is used to support multi-lingual naming and synonyms - the International Stratigraphic Chart is implemented

New insights into structural and stratigraphic aspects of central Northern Switzerland from the Nagra 2D reflection seismic campaign 2011/12

International Nuclear Information System (INIS)

Meier, B.

2015-01-01

In this article, some findings resulting from the interpretation of reprocessed and newly acquired 2D seismic data in the central Northern Switzerland are presented. The seismic examples illustrate the relationship between basement and cover-tectonics and offer a closer look at seismic-stratigraphic characteristics which can be observed in the Middle Jurassic sequence. The new 2D seismic data have closed an important data gaps between the Nagra siting regions 'Jura Ost' and Nördlich Lägern' proposed for radioactive waste disposal and allow clarification of the general structural framework and internal composition of the Permo-Carboniferous Through. Furthermore, the kinematic relationships between the basement and cover structures can be studied and the newly acquired seismic data have allowed detailed depositional structures and seismic facies changes within the Mid-Upper Dogger sequence to be recognized, particularly east and west of the lower Aare valley. (author)

Land Snail Extinctions at Kalaeloa, O`ahu

Directory of Open Access Journals (Sweden)

T.S. Dye

2001-06-01

Full Text Available In this article we show that the interpretation of Polynesian influence drawn from the stratigraphic record of sub-fossil land snails at Kalaeloa (O'ahu, Hawai'i is based on a unique stratigraphic sequence at a single sinkhole. The interpretation was then applied to other land snail sequences, despite their lack of evidence for Polynesian influence. We present a reanalysis of the stratigraphic record to conclude that Polynesians had little, if any, effect on land snail populations in sinkholes. We show that directional change in land snail populations was underway before Polynesians colonised the islands. Decreases in the diversity of snail populations, possibly indicative of environmental stress, do occur near the end of the stratigraphic sequence. Based on available dating evidence, however, these changes probably took place in the post-Contact period when the regional environment was radically altered by sugar cane cultivation.

Ages of subsurface stratigraphic intervals in the Quaternary of Enewetak Atoll, Marshall Islands

Science.gov (United States)

Szabo, B. J.; Tracey, J.I.; Goter, E.R.

1985-01-01

Drill cores of Enewetak Atoll, Marshall Islands, reveal six stratigraphic intervals, numbered in downward sequence, which represent vertical coral growth during Quaternary interglaciations. Radiocarbon dates indicate that the Holocene sea transgressed the emergent reef platform by about 8000 yr B.P. The reef grew rapidly upward (about 5 to 10 mm/yr) until about 6500 yr B.P. Afterward vertical growth slowed to about 0.5 mm/yr, then lateral development became dominant during the last several thousand years. The second interval is dated at 131,000 ?? 3000 yr B.P. by uranium series. This unit correlates with oxygen-isotope substage 5e and with terrace VIIa of Huon Peninsula, New Guinea, and of Main Reef-2 terrace at Atauro Island. The third interval is not dated because corals were recrystallized and it is tentatively correlated with either oxygen-isotope stages 7 or 9. The age of the fourth interval is estimated at 454,000 ?? 100,000 yr B.P. from measured 234U 238U activity ratios. This unit is correlated with either oxygen-isotope stage 9, 11, or 13. ?? 1985.

Monogenetic origin of Ubehebe Crater maar volcano, Death Valley, California: Paleomagnetic and stratigraphic evidence

Science.gov (United States)

Champion, Duane E.; Cyr, Andy; Fierstein, Judy; Hildreth, Wes

2018-04-01

Paleomagnetic data for samples collected from outcrops of basaltic spatter at the Ubehebe Crater cluster, Death Valley National Park, California, record a single direction of remanent magnetization indicating that these materials were emplaced during a short duration, monogenetic eruption sequence 2100 years ago. This conclusion is supported by geochemical data encompassing a narrow range of oxide variation, by detailed stratigraphic studies of conformable phreatomagmatic tephra deposits showing no evidence of erosion between layers, by draping of sharp rimmed craters by later tephra falls, and by oxidation of later tephra layers by the remaining heat of earlier spatter. This model is also supported through a reinterpretation and recalculation of the published 10Be age results (Sasnett et al., 2012) from an innovative and bold exposure-age study on very young materials. Their conclusion of multiple and protracted eruptions at Ubehebe Crater cluster is here modified through the understanding that some of their quartz-bearing clasts inherited 10Be from previous exposure on the fan surface (too old), and that other clasts were only exposed at the surface by wind and/or water erosion centuries after their eruption (too young). Ubehebe Crater cluster is a well preserved example of young monogenetic maar type volcanism protected within a National Park, and it represents neither a protracted eruption sequence as previously thought, nor a continuing volcanic hazard near its location.

Model-based quality assessment and base-calling for second-generation sequencing data.

Science.gov (United States)

Bravo, Héctor Corrada; Irizarry, Rafael A

2010-09-01

Second-generation sequencing (sec-gen) technology can sequence millions of short fragments of DNA in parallel, making it capable of assembling complex genomes for a small fraction of the price and time of previous technologies. In fact, a recently formed international consortium, the 1000 Genomes Project, plans to fully sequence the genomes of approximately 1200 people. The prospect of comparative analysis at the sequence level of a large number of samples across multiple populations may be achieved within the next five years. These data present unprecedented challenges in statistical analysis. For instance, analysis operates on millions of short nucleotide sequences, or reads-strings of A,C,G, or T's, between 30 and 100 characters long-which are the result of complex processing of noisy continuous fluorescence intensity measurements known as base-calling. The complexity of the base-calling discretization process results in reads of widely varying quality within and across sequence samples. This variation in processing quality results in infrequent but systematic errors that we have found to mislead downstream analysis of the discretized sequence read data. For instance, a central goal of the 1000 Genomes Project is to quantify across-sample variation at the single nucleotide level. At this resolution, small error rates in sequencing prove significant, especially for rare variants. Sec-gen sequencing is a relatively new technology for which potential biases and sources of obscuring variation are not yet fully understood. Therefore, modeling and quantifying the uncertainty inherent in the generation of sequence reads is of utmost importance. In this article, we present a simple model to capture uncertainty arising in the base-calling procedure of the Illumina/Solexa GA platform. Model parameters have a straightforward interpretation in terms of the chemistry of base-calling allowing for informative and easily interpretable metrics that capture the variability in

STRATIGRAPHIC EVOLUTION, PALEOENVIRONMENTS AND HYDROCARBON POTENTIALS OF THE BENUE/DAHOMEY BASINS, NIGERIAN AND POTIGUAR/CEARA BASINS, NE BRAZIL

International Nuclear Information System (INIS)

Akande, S.O; Adekeye, O.A.; Oj, O.J; Erdtmann, B.D.; Koutsokous, E.I.

2004-01-01

The stratigraphy, facies relationship and paleoenvironment of selected West African and the Brazillian rift basins permit the recognition of at least two major petroleum systems apart from the prolific Niger Delta petroleum system. The Lower Cretaceous fluivio-lacustrine petroleum system and Upper Cretaceous to Lower Tertiary, marine dominated petroleum system. Our combined studies of the stratigraphic, structural framework, paleoenvironment and time-space relationships of the petroleum systems in the Benue/Dahomey and the Potiguar/Ceara basins indicated that rifting and subsequent drifting during the opening of the South Atlantic controlled subsidence, sediment deposition and facies associations in individual basins. Whereas in the Potiguar/Ceara basins, the best developed source rocks are within the Neomacin-Aptian fluvio- lacustrine sequence of the Pendencia and Alagamar Formations which generated reserved hydrocarbon in the Acu Formation, empirical evidence for this petroleum system in the contiguous Benue/Dahomey basins are only based on the geochemical characteristics of the lower parts of the Bima Formation and the Abeokuta Group. In contrast, the Upper Cretaceous-Lower Tertiary marine petroleum system, which is constrained by poor development of reservoirs in the Potiguar/Ceara basin is productive in the Benue/Dahomey basins where source rocks, reservoir and sealing facies occur at this interval. Considering the recent hydrocarbon discoveries of the East Niger basin, the Doba (southern Chad), the Muglad basin (southern Sudan) sourced from the fluvio-lacustrine rift sequences, we suggest that this petroleum system needs more detailed exploration and has some potentials in the Benue/Dahomey frontier basins

Facies architecture and high resolution sequence stratigraphy of an aeolian, fluvial and shallow marine system in the Pennsylvanian Piauí Formation, Parnaíba Basin, Brazil

Science.gov (United States)

Vieira, Lucas Valadares; Scherer, Claiton Marlon dos Santos

2017-07-01

The Pennsylvanian Piauí Formation records the deposition of aeolian, fluvial and shallow marine systems accumulated in the cratonic sag Parnaíba basin. Characterization of the facies associations and sequence stratigraphic framework was done by detailed description and logging of outcrops. Six facies associations were recognized: aeolian dunes and interdunes, aeolian sandsheets, fluvial channels, tidally-influenced fluvial channels, shoreface and shoreface-shelf transition. Through correlation of stratigraphic surfaces, the facies associations were organized in system tracts, which formed eight high frequency depositional sequences, bounded by subaerial unconformities. These sequences are composed of a lowstand system tract (LST), that is aeolian-dominated or fluvial-dominated, a transgressive system tract (TST) that is formed by tidally-influenced fluvial channels and/or shoreface and shoreface-shelf transition deposits with retrogradational stacking, and a highstand system tract (HST), which is formed by shoreface-shelf transition and shoreface deposits with progradational stacking. Two low frequency cycles were determined by observing the stacking of the high frequency cycles. The Lower Sequence is characterized by aeolian deposits of the LST and an aggradational base followed by a progressive transgression, defining a general TST. The Upper Sequence is characterized by fluvial deposits and interfluve pedogenesis concurring with the aeolian deposits of the LST and records a subtle regression followed by transgression. The main control on sedimentation in the Piauí Formation was glacioeustasy, which was responsible for the changes in relative sea level. Even though, climate changes were associated with glacioeustatic phases and influenced the aeolian and fluvial deposition.

Stratigraphic, regional unconformity analysis and potential petroleum plays of East Siberian Sea Basin

Science.gov (United States)

Karpov, Yury; Stoupakova, Antonina; Suslova, Anna; Agasheva, Mariia

2017-04-01

The East Siberian Sea basin (ESSB) one of the most unexplored part of the Russian Arctic shelf, extending for over 1000 km from New Siberian Islands archipelago to Wrangel Island. This region is considered as a region with probable high petroleum potential. Within the ESSB several phases of orogeny are recognized [1]: Elsmerian orogeny in Early Devonian, Early Brooks orogeny in Early Cretaceous, Late Brooks orogeny in Late Cretaceous. Two generations of the basins could be outlined. Both of these generations are controlled by the basement domains [1]: Paleozoic (post-Devonian) to Mesozoic basins preserved north of the Late Mesozoic frontal thrusts; Aptian-Albian to Quaternary basins, postdating the Verkhoyansk-Brookian orogeny, and evolving mainly over the New-Siberian-Chukchi Fold Belt. Basin is filled with siliclastic sediments and in the deepest depocentres sediments thickness exceeds 8-10 km in average. Seismic data was interpreted using methods of seismic stratigraphy. Finally, main seismic horizons were indicated and each horizon follows regional stratigraphic unconformities: mBU - in base of Cenozoic, BU - in base of Upper Cretaceous, LCU - in base of Cretaceous, JU - in middle of Jurassic, F - in top of Basement. In ESSB, we can identify Permian, Triassic, Jurassic, Cretaceous, Paleogene and Neogene seismic stratigraphy complexes. Perspective structures, investigated in ESSB were founded out by comparing seismogeological cross-sections with explored analogs in other onshore and offshore basins [2, 3, 4]. The majority of structures could be connected with stratigraphic and fault traps. The most perspective prospects are probably connected with grabens and depressions, where thickness of sediments exceed 10 km. Reservoirs in ESSB are proposed by regional geological explorations on New Siberian Islands Archipelago and Wrangel Island. Potential seals are predominantly assigned to Jurassic and Cretaceous periods. Thick clinoform units of various geometry and

Revised geochronology, correlation, and dinosaur stratigraphic ranges of the Santonian-Maastrichtian (Late Cretaceous) formations of the Western Interior of North America.

Science.gov (United States)

Fowler, Denver Warwick

2017-01-01

Interbasinal stratigraphic correlation provides the foundation for all consequent continental-scale geological and paleontological analyses. Correlation requires synthesis of lithostratigraphic, biostratigraphic and geochronologic data, and must be periodically updated to accord with advances in dating techniques, changing standards for radiometric dates, new stratigraphic concepts, hypotheses, fossil specimens, and field data. Outdated or incorrect correlation exposes geological and paleontological analyses to potential error. The current work presents a high-resolution stratigraphic chart for terrestrial Late Cretaceous units of North America, combining published chronostratigraphic, lithostratigraphic, and biostratigraphic data. 40Ar / 39Ar radiometric dates are newly recalibrated to both current standard and decay constant pairings. Revisions to the stratigraphic placement of most units are slight, but important changes are made to the proposed correlations of the Aguja and Javelina formations, Texas, and recalibration corrections in particular affect the relative age positions of the Belly River Group, Alberta; Judith River Formation, Montana; Kaiparowits Formation, Utah; and Fruitland and Kirtland formations, New Mexico. The stratigraphic ranges of selected clades of dinosaur species are plotted on the chronostratigraphic framework, with some clades comprising short-duration species that do not overlap stratigraphically with preceding or succeeding forms. This is the expected pattern that is produced by an anagenetic mode of evolution, suggesting that true branching (speciation) events were rare and may have geographic significance. The recent hypothesis of intracontinental latitudinal provinciality of dinosaurs is shown to be affected by previous stratigraphic miscorrelation. Rapid stepwise acquisition of display characters in many dinosaur clades, in particular chasmosaurine ceratopsids, suggests that they may be useful for high resolution biostratigraphy.

Sedimentary facies analysis of the Mesozoic clastic rocks in Southern Peru (Tacna, 18°S): Towards a paleoenvironmental Redefinition and stratigraphic Reorganization

Science.gov (United States)

Alván, Aldo; Jacay, Javier; Caracciolo, Luca; Sánchez, Elvis; Trinidad, Inés

2018-07-01

The Mesozoic rocks of southern Peru comprise a Middle Jurassic to Early Cretaceous sedimentary sequence deposited during a time interval of approximately 34 Myr. In Tacna, these rocks are detrital and constitute the Yura Group (Callovian to Tithonian) and the Hualhuani Formation (Berriasian). Basing on robust interpretation of facies and petrographic analysis, we reconstruct the depositional settings of such units and provide a refined stratigraphic framework. Accordingly, nine types of sedimentary facies and six architectural elements are defined. They preserve the record of a progradational fluvial system, in which two styless regulated the dispersion of sediments: (i) a high-to moderate-sinuosity meandering setting (Yura Group), and a later (ii) incipient braided setting (Hualhuani Formation). The Yura Group (Callovian-Tithonian) represents the onset of floodplain deposits and lateral accretion of point-bar deposits sited on a semi-flat topography. Nonetheless, the progradational sequence was affected by at least two rapid marine ingressions occurred during Middle Callovian and Tithonian times. Such marine ingressions reveal the proximity of a shallow marine setting and incipient carbonate deposition. In response to increase in topographic gradient, the Hualhuani Formation (Berriasian) deposited as extensive multistory sandy channels. The mineralogy of the Mesozoic sediments suggests sediment supplies and intense recycling from a craton interior (i.e. Amazon Craton and/or plutonic sources) located eastward of the study area.

The role of sediment supply in large-scale stratigraphic architecture of ancient Gilbert-type deltas (Pliocene Siena-Radicofani Basin, Italy)

Science.gov (United States)

Martini, Ivan; Ambrosetti, Elisa; Sandrelli, Fabio

2017-04-01

Aggradation, progradation and retrogradation are the main patterns that define the large-scale architecture of Gilbert-type deltas. These patterns are governed by the ratio between the variation in accommodation space and sediment supply experienced during delta growth. Sediment supply variations are difficult to estimate in ancient settings; hence, it is rarely possible to assess its significance in the large-scale stratigraphic architecture of Gilbert-type deltas. This paper presents a stratigraphic analysis of a Pliocene deltaic complex composed of two coeval and narrowly spaced deltaic branches. The two branches recorded the same tectonic- and climate-induced accommodation space variations. As a result, this deltaic complex represents a natural laboratory for testing the effects of sediment supply variations on the stratigraphic architecture of Gilbert-type deltas. The field data suggest that a sediment supply which is able to counteract the accommodation generated over time promotes the aggradational/progradational attitude of Gilbert-type deltas, as well as the development of thick foreset deposits. By contrast, if the sediment supply is not sufficient for counterbalancing the generated accommodation, an aggradational/retrogradational stratigraphic architecture is promoted. In this case, the deltaic system is forced to withdraw during the different phases of generation of accommodation, with the subsequent flooding of previously deposited sub-horizontal topset deposits (i.e., the delta plain). The subsequent deltaic progradation occurs above these deposits and, consequently, the available space for foresets growth is limited to the water depth between the base-level and the older delta plain. This leads to the vertical stacking of relatively thin deltaic deposits with an overall aggradatational/retrogradational attitude.

Geochronological correlation of the late Precambrian sequences on and around the stable zones of Equatorial Africa

International Nuclear Information System (INIS)

Cahen, L.

1982-01-01

Very few radiometric age determinations have a bearing on the late Precambrian sequences of the stable zones of Equatorial Africa. A geochronological correlation of these sequences must therefore rest upon a compilation of ages from these stable zones and the corresponding mobile zones. About 15 ages of varying precision more or less well tied up with the stratigraphical sequences, together with results of the study of stromatolite assemblages allow a provisional correlation to be made. One conclusion of this correlation is that most mixtites surrounding the Congo basin are in a 950 +- 50 Ma age bracket and are presumably to be correlated. (Auth.)

Glacial morphology and depositional sequences of the Antarctic Continental Shelf

Science.gov (United States)

ten Brink, Uri S.; Schneider, Christopher

1995-01-01

Proposes a simple model for the unusual depositional sequences and morphology of the Antarctic continental shelf. It considers the regional stratal geometry and the reversed morphology to be principally the results of time-integrated effects of glacial erosion and sedimentation related to the location of the ice grounding line. The model offers several guidelines for stratigraphic interpretation of the Antarctic shelf and a Northern Hemisphere shelf, both of which were subject to many glacial advances and retreats. -Authors

Venusian extended ejecta deposits as time-stratigraphic markers

Science.gov (United States)

Izenberg, Noam R.

1992-01-01

Use of impact crater ejects at time-stratigraphic markers was established during lunar geologic mapping efforts. The basic premise is that the deposition of impact ejecta, either by itself or mixed with impact-excavated material, is superimposed on a surface. The deposit becomes an observable, mappable unit produced in a single instant in geologic time. Up to two-thirds of Venus craters exhibit extended ejecta deposits. A reconnaissance survey of 336 craters (about 40 percent of the total population) was conducted. About half the craters examined were located in and around the Beta-Atla-Themis region, and half were spread over the western hemisphere of the planet. The survey was conducted using primarily C1-MIDR images. The preliminary survey shows: (1) of the 336 craters, 223 were found to have extended ejecta deposits. This proportion is higher than that found in other Venus crater databases by up to a factor of 2. (2) 53 percent of all extended ejecta craters were unambiguously superimposed on all volcanic and tectonic units. Crater Annia Faustina's associated parabolic ejecta deposit is clearly superimposed on volcanic flows coming from Gula Mons to the west. Parabola material from Faustina has covered the lava flows, smoothing the surface and reducing its specific backscatter cross section. The stratigraphy implies that the parabola material is the youngest observable unit in the region. (3) 12 percent of extended ejecta deposits are superimposed by volcanic materials. Crater Hwangcini has extended ejecta that has been covered by volcanic flows from a dome field to the northwest, implying that the volcanic units were emplaced subsequent to the ejecta deposit and are the youngest units in the locality. (4) It is difficult to determine the stratigraphic relationships of the remaining extended ejecta deposits in SAR at C1-MIDR resolution. Examination of higher resolution images and application of the other Magellan datasets in systematic manner should resolve

An Analysis of Delay-based and Integrator-based Sequence Detectors for Grid-Connected Converters

DEFF Research Database (Denmark)

Khazraj, Hesam; Silva, Filipe Miguel Faria da; Bak, Claus Leth

2017-01-01

-signal cancellation operators are the main members of the delay-based sequence detectors. The aim of this paper is to provide a theoretical and experimental comparative study between integrator and delay based sequence detectors. The theoretical analysis is conducted based on the small-signal modelling......Detecting and separating positive and negative sequence components of the grid voltage or current is of vital importance in the control of grid-connected power converters, HVDC systems, etc. To this end, several techniques have been proposed in recent years. These techniques can be broadly...... classified into two main classes: The integrator-based techniques and Delay-based techniques. The complex-coefficient filter-based technique, dual second-order generalized integrator-based method, multiple reference frame approach are the main members of the integrator-based sequence detector and the delay...

Sequence stratigraphy on an early wet Mars

Science.gov (United States)

Barker, Donald C.; Bhattacharya, Janok P.

2018-02-01

The evolution of Mars as a water-bearing body is of considerable interest for the understanding of its early history and evolution. The principles of terrestrial sequence stratigraphy provide a useful conceptual framework to hypothesize about the stratigraphic history of the planets northern plains. We present a model based on the hypothesized presence of an early ocean and the accumulation of lowland sediments eroded from highland terrain during the time of the valley networks and later outflow channels. Ancient, global environmental changes, induced by a progressively cooling climate would have led to a protracted loss of surface and near surface water from low-latitudes and eventual cold-trapping at higher latitudes - resulting in a unique and prolonged, perpetual forced regression within basins and lowland depositional environments. The Messinian Salinity Crisis (MSC) serves as a potential terrestrial analogue of the depositional and environmental consequences relating to the progressive removal of large standing bodies of water. We suggest that the evolution of similar conditions on Mars would have led to the emplacement of diagnostic sequences of deposits and regional scale unconformities, consistent with intermittent resurfacing of the northern plains and the progressive loss of an early ocean by the end of the Hesperian era.

Metre-scale cyclicity in Middle Eocene platform carbonates in northern Egypt: Implications for facies development and sequence stratigraphy

Science.gov (United States)

Tawfik, Mohamed; El-Sorogy, Abdelbaset; Moussa, Mahmoud

2016-07-01

The shallow-water carbonates of the Middle Eocene in northern Egypt represent a Tethyan reef-rimmed carbonate platform with bedded inner-platform facies. Based on extensive micro- and biofacies documentation, five lithofacies associations were defined and their respective depositional environments were interpreted. Investigated sections were subdivided into three third-order sequences, named S1, S2 and S3. Sequence S1 is interpreted to correspond to the Lutetian, S2 corresponds to the Late Lutetian and Early Bartonian, and S3 represents the Late Bartonian. Each of the three sequences was further subdivided into fourth-order cycle sets and fifth-order cycles. The complete hierarchy of cycles can be correlated along 190 km across the study area, and highlighting a general "layer-cake" stratigraphic architecture. The documentation of the studied outcrops may contribute to the better regional understanding of the Middle Eocene formations in northern Egypt and to Tethyan pericratonic carbonate models in general.

Centroid based clustering of high throughput sequencing reads based on n-mer counts.

Science.gov (United States)

Solovyov, Alexander; Lipkin, W Ian

2013-09-08

Many problems in computational biology require alignment-free sequence comparisons. One of the common tasks involving sequence comparison is sequence clustering. Here we apply methods of alignment-free comparison (in particular, comparison using sequence composition) to the challenge of sequence clustering. We study several centroid based algorithms for clustering sequences based on word counts. Study of their performance shows that using k-means algorithm with or without the data whitening is efficient from the computational point of view. A higher clustering accuracy can be achieved using the soft expectation maximization method, whereby each sequence is attributed to each cluster with a specific probability. We implement an open source tool for alignment-free clustering. It is publicly available from github: https://github.com/luscinius/afcluster. We show the utility of alignment-free sequence clustering for high throughput sequencing analysis despite its limitations. In particular, it allows one to perform assembly with reduced resources and a minimal loss of quality. The major factor affecting performance of alignment-free read clustering is the length of the read.

Trait-based diversification shifts reflect differential extinction among fossil taxa.

Science.gov (United States)

Wagner, Peter J; Estabrook, George F

2014-11-18

Evolution provides many cases of apparent shifts in diversification associated with particular anatomical traits. Three general models connect these patterns to anatomical evolution: (i) elevated net extinction of taxa bearing particular traits, (ii) elevated net speciation of taxa bearing particular traits, and (iii) elevated evolvability expanding the range of anatomies available to some species. Trait-based diversification shifts predict elevated hierarchical stratigraphic compatibility (i.e., primitive→derived→highly derived sequences) among pairs of anatomical characters. The three specific models further predict (i) early loss of diversity for taxa retaining primitive conditions (elevated net extinction), (ii) increased diversification among later members of a clade (elevated net speciation), and (iii) increased disparity among later members in a clade (elevated evolvability). Analyses of 319 anatomical and stratigraphic datasets for fossil species and genera show that hierarchical stratigraphic compatibility exceeds the expectations of trait-independent diversification in the vast majority of cases, which was expected if trait-dependent diversification shifts are common. Excess hierarchical stratigraphic compatibility correlates with early loss of diversity for groups retaining primitive conditions rather than delayed bursts of diversity or disparity across entire clades. Cambrian clades (predominantly trilobites) alone fit null expectations well. However, it is not clear whether evolution was unusual among Cambrian taxa or only early trilobites. At least among post-Cambrian taxa, these results implicate models, such as competition and extinction selectivity/resistance, as major drivers of trait-based diversification shifts at the species and genus levels while contradicting the predictions of elevated net speciation and elevated evolvability models.

Facies analysis and sequence stratigraphy of neoproterozoic Platform deposits in Adrar of Mauritania, Taoudeni basin, West Africa

Science.gov (United States)

Benan, C. A. A.; Deynoux, M.

The Neoproterozoic and Palaeozoic Taoudeni basin forms the flat-lying and unmetamorphosed sedimentary cover of the West African Craton. In the western part of this basin, the Char Group and the lower part of the Atar Group make up a 400-m-thick Neoproterozoic siliciclastic succession which rests on the Palaeoproterozoic metamorphic and granitic basement. Five erosional bounding surfaces of regional extent have been identified in this succession. These surfaces separate five stratigraphic units with lithofacies associations ranging from fluvial to coastal and fluvial-, tide-, or wave-dominated shallow marine deposits. Owing to their regional extent and their position within the succession, the erosive bounding surfaces correspond to relative sea-level falls, and accordingly the five stratigraphic units they bound represent allocyclic transgressive-regressive depositional sequences (S1-S5). Changes in the nature of the deposits forming the transgressive-regressive cycles reflect landward or seaward shifts of the stacked sequences. These successive relative sea-level changes are related to the reactivation of basement faults and tilting during rifting of the Pan-Afro-Brasiliano supercontinent 1000 m.y. ago. The stromatolite bearing carbonate-shale sequences which form the rest of the Atar Group mark the onset of a quiet period of homogeneous subsidence contemporaneous with the Pan-African I oceanization 800-700 m.y. ago.

Structural and stratigraphic constraints on tsunamigenic rupture along the frontal Sunda megathrust from MegaTera bathymetric and seismic reflection data

Science.gov (United States)

Bradley, K. E.; Qin, Y.; Villanueva-Robles, F.; Hananto, N.; Leclerc, F.; Singh, S. C.; Tapponnier, P.; Sieh, K.; Wei, S.; Carton, H. D.; Permana, H.; Avianto, P.; Nugroho, A. B.

2017-12-01

The joint EOS/IPG/LIPI 2015 MegaTera expedition collected high-resolution seismic reflection profiles and bathymetric data across the Sunda trench, updip of the Mw7.7, 2010 Mentawai tsunami-earthquake rupture patch. These data reveal rapid lateral variations in both the stratigraphic level of the frontal Sunda megathrust and the vergence of frontal ramp faults. The stratigraphic depth of the megathrust at the deformation front correlates with ramp-thrust vergence and with changes in the basal friction angle inferred by critical-taper wedge theory. Where ramp thrusts verge uniformly seaward and have an average dip of 30°, the megathrust decollement resides atop a high-amplitude reflector that marks the inferred top of pelagic sediments. Where ramp thrusts are bi-vergent (similar throw on both landward- and seaward-vergent faults) and have an average dip of 42°, the decollement is higher, within the incoming clastic sequence, above a seismically transparent unit inferred to represent distal fan muds. Where ramp thrusts are uniformly landward vergent, the decollement sits directly on top of the oceanic crust that forms the bathymetrically prominent, subducting Investigator Ridge. The two, separate regions of large tsunamigenic ground-surface uplift during the 2010 tsunami earthquake that have been inferred from joint inversions of seismic, GPS, and tsunami data (e.g. Yue et al., 2014; Satake et al., 2013) correspond to the areas of frontal bi-vergence in the MegaTera data. We propose that enhanced surface uplift and tsunamigenesis during this event occurred when rupture propagated onto areas where the decollement sits directly above the basal muds of the incoming clastic sequence. Thus we hypothesize that frontal bi-vergence may mark areas of enhanced tsunami hazard posed by small magnitude, shallow megathrust ruptures that propagate to the trench. [Yue, H. et al., 2014, Rupture process of the…, JGR 119 doi:10.1002/2014JB011082; Satake, K. et al., 2013, Tsunami

Sedimentology and sequence stratigraphy of the Nkporo Group (Campanian–Maastrichtian, Anambra Basin, Nigeria

Directory of Open Access Journals (Sweden)

Shirley O. Odunze

2013-04-01

Full Text Available Integration of sedimentologic and sequence stratigraphic interpretations of the Nkporo Group has provided the basis for a basin-wide framework for prediction of potential source, seal and reservoir rocks in the Anambra Basin, Nigeria. Lithofacies and biostratigraphic data show that the Nkporo Group in the Anambra Basin contains three main facies associations (fluvio-deltaic facies, estuarine central basin/shallow shelf facies and estuarine channel fill facies that determine the reservoir containers, flow units and seals. The units are arranged to form two stratigraphic sequences represented by the Nkporo Shale–Owelli Sandstone and Owelli Sandstone–Enugu Shale successions, respectively. The transgressive systems tract in each sequence comprises coarse-grained fluvio-deltaic sandstone and an overlying open marine black carbonaceous mud rock. The highstand systems tracts comprise delta front deposits with average porosity, permeability and net-to-gross values estimated in the ranges of 30%, 3000 md and 0.9, respectively. The fluvio-deltaic and delta front facies which are encased in organically rich estuarine central basin/shallow shelf mud rocks are likely the potential reservoirs. Trapping capacity is enhanced by the presence of several N–S trending normal faults, and other microstructures related to the post-Santonian tensional regime in the Benue. The new information presented in this paper on potential seal, source and reservoir lithofacies within the Nkporo Group should serve as a useful contribution to the geological modelling of reservoirs within the Late Cretaceous–Paleocene succession in the Anambra Basin.

The Early to Middle Triassic continental–marine transition of NW Bulgaria: sedimentology, palynology and sequence stratigraphy

Directory of Open Access Journals (Sweden)

Ajdanlijsky George

2018-04-01

Full Text Available Sedimentary facies and cycles of the Triassic continental–marine transition of NW Bulgaria are documented in detail from reference sections along the Iskar river gorge between the villages of Tserovo and Opletnya. The depositional environments evolved from anastomosing and meandering river systems in the Petrohan Terrigenous Group to mixed fluvial and tidal settings in the Svidol Formation, and to peritidal and shallow-marine conditions in the Opletnya Member of the Mogila Formation. For the first time, the palynostratigraphic data presented here allow for dating the transitional interval and for the precise identification of a major sequence boundary between the Petrohan Terrigenous Group and the Svidol Formation (Iskar Carbonate Group. This boundary most probably corresponds to the major sequence boundary Ol4 occurring in the upper Olenekian of the Tethyan realm and thus enables interregional correlation. The identification of regionally traceable sequence boundaries based on biostratigraphic age control is a first step towards a more accurate stratigraphic correlation and palaeogeographic interpretation of the Early to early Middle Triassic in NW Bulgaria.

The Early to Middle Triassic continental-marine transition of NW Bulgaria: sedimentology, palynology and sequence stratigraphy

Science.gov (United States)

Ajdanlijsky, George; Götz, Annette E.; Strasser, André

2018-04-01

Sedimentary facies and cycles of the Triassic continental-marine transition of NW Bulgaria are documented in detail from reference sections along the Iskar river gorge between the villages of Tserovo and Opletnya. The depositional environments evolved from anastomosing and meandering river systems in the Petrohan Terrigenous Group to mixed fluvial and tidal settings in the Svidol Formation, and to peritidal and shallow-marine conditions in the Opletnya Member of the Mogila Formation. For the first time, the palynostratigraphic data presented here allow for dating the transitional interval and for the precise identification of a major sequence boundary between the Petrohan Terrigenous Group and the Svidol Formation (Iskar Carbonate Group). This boundary most probably corresponds to the major sequence boundary Ol4 occurring in the upper Olenekian of the Tethyan realm and thus enables interregional correlation. The identification of regionally traceable sequence boundaries based on biostratigraphic age control is a first step towards a more accurate stratigraphic correlation and palaeogeographic interpretation of the Early to early Middle Triassic in NW Bulgaria.

Recognition of Milankovitch cycles in the stratigraphic record:application of the CWT and the FFT to well-log data

Institute of Scientific and Technical Information of China (English)

YU Ji-feng; SUI Feng-gui; LI Zeng-xue; LIU Hua; WANG Yu-lin

2008-01-01

The authors applied a the combination of Continuous Wavelet Transform (CWT) and Fast Fourier Transform (FFF)methods to gamma ray well-log data from the Q3, G1 and D2 wells. This high-resolution stratigraphic study was based on Milankovitch's orbital cycle theory. It was found that the CWT scale factors, 'a,' of 12, 24 and 60 match the ratios of the periodicities of precession, obliquity and eccentricity very well. Nine intervals of the Permo-carboniferous strata were recognized to have Milankovitch cycles in them. For example, section A of well Q3 has 29 precession cycles, 15 obliquity cycles and 7 short eccentricity cycles. The wavelengths are 2.7, 4.4 and 7.8 m for precession, obliquity and eccentricity, respectively. Important geological parameters such as the stratigraphic completeness and the accumulation rate were also estimated. These results provide basic information for further cyclostratigraphic correlation studies in the area. They are of great significance for the study of ancient and future climate change.

Stratigraphic dictionary of the mesozoic and cenozoic deposits of the western Siberian lowland. Stratigraficheskii slovar' mezozoiskikh i kainozoiskikh otlozhenii zapadno-Sibirskoi nizmennosti

Energy Technology Data Exchange (ETDEWEB)

Rostovtseva, N N

1978-01-01

The dictionary contains 655 descriptions of stratigraphic subdivisions (series, suites, subsuites, layers, packets, horizons, strata) of Triassic, Jurassic, Cretaceous, Tertiary, Neogene, and Quaternary deposits of the western Siberian lowland. Also presented are maps indicating the demarcation limits of all of the adopted stratigraphic subdivisions (Appendices 1 to 14), and correlative stratigraphic diagrams (Appendices 15 to 21). The dictionary may be of use as a reference manual for geologists of all fields of specialization, particularly for those working in western Siberia. 202 references, 21 figures.

Prediction of Protein Structural Classes for Low-Similarity Sequences Based on Consensus Sequence and Segmented PSSM

Directory of Open Access Journals (Sweden)

Yunyun Liang

2015-01-01

Full Text Available Prediction of protein structural classes for low-similarity sequences is useful for understanding fold patterns, regulation, functions, and interactions of proteins. It is well known that feature extraction is significant to prediction of protein structural class and it mainly uses protein primary sequence, predicted secondary structure sequence, and position-specific scoring matrix (PSSM. Currently, prediction solely based on the PSSM has played a key role in improving the prediction accuracy. In this paper, we propose a novel method called CSP-SegPseP-SegACP by fusing consensus sequence (CS, segmented PsePSSM, and segmented autocovariance transformation (ACT based on PSSM. Three widely used low-similarity datasets (1189, 25PDB, and 640 are adopted in this paper. Then a 700-dimensional (700D feature vector is constructed and the dimension is decreased to 224D by using principal component analysis (PCA. To verify the performance of our method, rigorous jackknife cross-validation tests are performed on 1189, 25PDB, and 640 datasets. Comparison of our results with the existing PSSM-based methods demonstrates that our method achieves the favorable and competitive performance. This will offer an important complementary to other PSSM-based methods for prediction of protein structural classes for low-similarity sequences.

THE TYRRHENIAN SECTION OF SAN GIOVANNI DI SINIS (SARDINIA:STRATIGRAPHIC RECORD OF AN IRREGULAR SINGLE HIGH STAND

Directory of Open Access Journals (Sweden)

LUCIANO LECCA

2007-11-01

Full Text Available A new analysis of the most representative Upper Pleistocene (Tyrrhenian, MIS 5e section of San Giovanni di Sinis (Oristano, Sardinia has provided a more detailed genetic stratigraphy of a low wave energy beach and temperate lagoon up to emerged peri-lagoonal facies deposits. These peri-lagoonal facies contain remains of fossil vertebrates, which, though few and fragmentary, bear witness to an at least temporary freshwater palaeoenvironment and the presence of deers and terrapins. Besides, the stratigraphy of this outcrop shows shoreface-backshore sandstones overlaying an erosion surface cut on the vertebrate-bearing layers. Facies analysis and sequence stratigraphy of the succession have provided support to a new eustatic interpretation significance. In fact, there appears to be evidence of one irregular single eustatic highstand, rather than two eustatic peaks as previously believed. The facies evolution and the local stratigraphic disconformities are interpreted as being associated with a lateral shift of the depositional environment within the same system formed during the MIS 5e sea level variations. As sea water level continued to rise so an erosional unconformity, caused by wave ravinement, formed between the low wave energy beach-lagoon sequence and the successive wave dominated beach facies sequence. This interpretation is supported by comparison with other sections of the Tyrrhenian in western Sardinia. The maximum sea level attained during the Tyrrhenian stage is a clear indication of a warm-temperate climate which can be correlated to the well known orbital interglacial configuration when the eustatic signal of Greenland's ice sheet melting occurred. SHORT NOTES

Sawfishes and Other Elasmobranch Assemblages from the Mio-Pliocene of the South Caribbean (Urumaco Sequence, Northwestern Venezuela)

Science.gov (United States)

2015-01-01

The Urumaco stratigraphic sequence, western Venezuela, preserves a variety of paleoenvironments that include terrestrial, riverine, lacustrine and marine facies. A wide range of fossil vertebrates associated with these facies supports the hypothesis of an estuary in that geographic area connected with a hydrographic system that flowed from western Amazonia up to the Proto-Caribbean Sea during the Miocene. Here the elasmobranch assemblages of the middle Miocene to middle Pliocene section of the Urumaco sequence (Socorro, Urumaco and Codore formations) are described. Based on new findings, we document at least 21 taxa of the Lamniformes, Carcharhiniformes, Myliobatiformes and Rajiformes, and describe a new carcharhiniform species (†Carcharhinus caquetius sp. nov.). Moreover, the Urumaco Formation has a high number of well-preserved fossil Pristis rostra, for which we provide a detailed taxonomic revision, and referral in the context of the global Miocene record of Pristis as well as extant species. Using the habitat preference of the living representatives, we hypothesize that the fossil chondrichthyan assemblages from the Urumaco sequence are evidence for marine shallow waters and estuarine habitats. PMID:26488163

Sawfishes and Other Elasmobranch Assemblages from the Mio-Pliocene of the South Caribbean (Urumaco Sequence, Northwestern Venezuela.

Directory of Open Access Journals (Sweden)

Jorge D Carrillo-Briceño

Full Text Available The Urumaco stratigraphic sequence, western Venezuela, preserves a variety of paleoenvironments that include terrestrial, riverine, lacustrine and marine facies. A wide range of fossil vertebrates associated with these facies supports the hypothesis of an estuary in that geographic area connected with a hydrographic system that flowed from western Amazonia up to the Proto-Caribbean Sea during the Miocene. Here the elasmobranch assemblages of the middle Miocene to middle Pliocene section of the Urumaco sequence (Socorro, Urumaco and Codore formations are described. Based on new findings, we document at least 21 taxa of the Lamniformes, Carcharhiniformes, Myliobatiformes and Rajiformes, and describe a new carcharhiniform species (†Carcharhinus caquetius sp. nov.. Moreover, the Urumaco Formation has a high number of well-preserved fossil Pristis rostra, for which we provide a detailed taxonomic revision, and referral in the context of the global Miocene record of Pristis as well as extant species. Using the habitat preference of the living representatives, we hypothesize that the fossil chondrichthyan assemblages from the Urumaco sequence are evidence for marine shallow waters and estuarine habitats.

Sawfishes and Other Elasmobranch Assemblages from the Mio-Pliocene of the South Caribbean (Urumaco Sequence, Northwestern Venezuela).

Science.gov (United States)

Carrillo-Briceño, Jorge D; Maxwell, Erin; Aguilera, Orangel A; Sánchez, Rodolfo; Sánchez-Villagra, Marcelo R

2015-01-01

The Urumaco stratigraphic sequence, western Venezuela, preserves a variety of paleoenvironments that include terrestrial, riverine, lacustrine and marine facies. A wide range of fossil vertebrates associated with these facies supports the hypothesis of an estuary in that geographic area connected with a hydrographic system that flowed from western Amazonia up to the Proto-Caribbean Sea during the Miocene. Here the elasmobranch assemblages of the middle Miocene to middle Pliocene section of the Urumaco sequence (Socorro, Urumaco and Codore formations) are described. Based on new findings, we document at least 21 taxa of the Lamniformes, Carcharhiniformes, Myliobatiformes and Rajiformes, and describe a new carcharhiniform species (†Carcharhinus caquetius sp. nov.). Moreover, the Urumaco Formation has a high number of well-preserved fossil Pristis rostra, for which we provide a detailed taxonomic revision, and referral in the context of the global Miocene record of Pristis as well as extant species. Using the habitat preference of the living representatives, we hypothesize that the fossil chondrichthyan assemblages from the Urumaco sequence are evidence for marine shallow waters and estuarine habitats.

Sequence Stratigraphic Framework Analysis of Putaohua Oil Reservoir in Chaochang Area of Songliao Basin

Science.gov (United States)

Chang, Yan; Liu, Dameng; Yao, Yanbin

2018-01-01

The regional structure of the Changchang area in the Songliao Basin is located on the Chaoyangou terrace and Changchunling anticline belt in the central depression of the northern part of the Songliao Basin, across the two secondary tectonic units of the Chaoyanggou terrace and Changchunling anticline. However, with the continuous development of oil and gas, the unused reserves of Fuyu oil reservoir decreased year by year, and the oil field faced a serious shortage of reserve reserves. At the same time, during the evaluation process, a better oil-bearing display was found during the drilling and test oil in the Putao depression to the Chaoyanggou terraces, the Yudong-Taipingchuan area, and in the process of drilling and testing oil in the Putaohua reservoir. Zhao41, Zhao18-1, Shu38 and other exploration wells to obtain oil oil, indicating that the area has a further evaluation of the potential. Based on the principle of stratification, the Putao area was divided into three parts by using the core, logging and logging. It is concluded that the middle and western strata of the study area are well developed, including three sequences, one cycle from bottom to top (three small layers), two cycles (one small layer), three cycles (two small layers) Rhythm is positive-anti-positive. From the Midwest to the southeastern part of the strata, the strata are overtaken, the lower strata are missing, and the top rhythms become rhythmic.

Salt Repository Project site study plan for stratigraphic boreholes: Revision 1, December 18, 1987

International Nuclear Information System (INIS)

1987-01-01

This site study describes the Stratigraphic Boreholes field work to be conducted during the early stages of Site Characterization at the Deaf Smith County, Texas site. The field program has been designed to provide data useful in addressing information/data needs resulting from Federal/State/local regulations, and repository program requirements. Four Stratigraphic Holes will be drilled near the perimeter of the site to document the subsurface geologic conditions in that area and to provide data necessary for design and construction of the Exploratory Shaft Facilities. Continuous samples will be recovered from the ground surface to the total depth of each sell. Geophysical well logs will provide additional coverage of the stratigraphic section. In-situ down hole testing will include short term hydrologic tests and hydraulic fracture tests to provide information on deep groundwater characteristics and regional stress patterns, respectively. Field methods/tests are chosen that provide the best or only means of obtaining the required data. The Salt Repository Project (SRP) Networks specify the schedule which the program will operate. The Technical Services Contractor is responsible for conducting the field program of drilling and testing. Samples and data will be handled and reported in accordance with established SRP procedures. A quality assurance program will be utilized to assure that activities affecting quality are performed correctly and that the appropriate documentation is maintained. 30 refs., 13 figs., 4 tabs

Explorability and predictability of the paleozoic sedimentary sequence beneath the Bruce nuclear site

International Nuclear Information System (INIS)

Parmenter, A.; Jensen, M.; Crowe, R.; Raven, K.

2011-01-01

Ontario Power Generation (OPG) is proposing to develop a Deep Geologic Repository (DGR) for the long-term management of its Low and Intermediate Level Waste (L&ILW) at the Bruce nuclear site located in the Municipality of Kincardine, Ontario. A 4-year program of geoscientific studies to assess the suitability of the 850 m thick Palaeozoic age sedimentary sequence beneath the site to host the DGR was completed in 2010. The studies provide evidence of a geologic setting in which the DGR concept would be safely implemented at a nominal depth of 680 m within the argillaceous limestone of the Cobourg Formation. This paper describes the geologic framework of the Bruce nuclear site with a focus on illustrating the high degree of stratigraphic continuity and traceability at site-specific and regional scales within the Ordovician sediments proposed to host and enclose the DGR. As part of the site-specific studies, a program of deep drilling/coring (6 boreholes) and in-situ testing through the sedimentary sequence was completed from 4 drill sites situated beyond the DGR footprint, approximately 1 km apart. Core logging reveals that the stratigraphic sequence comprises 34 distinct bedrock formations/members/units consistent with the known regional stratigraphic framework. These layered sedimentary formations dip 0.6 o (~10 m/km) to the southwest with highly uniform thicknesses both at the site- and regional-scale, particularly, the Ordovician sediments, which vary on the order of metres. The occurrence of steeply-dipping faults within the sedimentary sequence is not revealed through surface outcrop fracture mapping, micro-seismic (M ≥ 1) monitoring, inclined borehole coring or intersection of hydrothermal type dolomitized reservoir systems. Potential fault structures, interpreted from a 2-D seismic survey, were targeted by angled boreholes which found no evidence for their existence. Formation specific continuity is also evidence by the lateral traceability of physical rock

Mapping Base Modifications in DNA by Transverse-Current Sequencing

Science.gov (United States)

Alvarez, Jose R.; Skachkov, Dmitry; Massey, Steven E.; Kalitsov, Alan; Velev, Julian P.

2018-02-01

Sequencing DNA modifications and lesions, such as methylation of cytosine and oxidation of guanine, is even more important and challenging than sequencing the genome itself. The traditional methods for detecting DNA modifications are either insensitive to these modifications or require additional processing steps to identify a particular type of modification. Transverse-current sequencing in nanopores can potentially identify the canonical bases and base modifications in the same run. In this work, we demonstrate that the most common DNA epigenetic modifications and lesions can be detected with any predefined accuracy based on their tunneling current signature. Our results are based on simulations of the nanopore tunneling current through DNA molecules, calculated using nonequilibrium electron-transport methodology within an effective multiorbital model derived from first-principles calculations, followed by a base-calling algorithm accounting for neighbor current-current correlations. This methodology can be integrated with existing experimental techniques to improve base-calling fidelity.

Facies associations, depositional environments and stratigraphic framework of the Early Miocene-Pleistocene successions of the Mukah-Balingian Area, Sarawak, Malaysia

Science.gov (United States)

Murtaza, Muhammad; Rahman, Abdul Hadi Abdul; Sum, Chow Weng; Konjing, Zainey

2018-02-01

Thirty-five stratigraphic section exposed along the Mukah-Selangau road in the Mukah-Balingian area have been studied. Sedimentological and palynological data have been integrated to gain a better insight into the depositional architecture of the area. Broadly, the Mukah-Balingian area is dominated by fluvial, floodplain and estuarine related coal-bearing deposits. The Balingian, Begrih and Liang formations have been described and interpreted in terms of seven facies association. These are: FA1 - Fluvial-dominated channel facies association; FA2 - Tide-influenced channel facies association; FA3 - Tide-dominated channel facies association; FA4 - Floodplain facies association; FA5 - Estuarine central basin-mud flats facies association; FA6 - Tidal flat facies association and FA7 - Coastal swamps and marshes facies association. The Balingian Formation is characterised by the transgressive phase in the base, followed by a regressive phase in the upper part. On the basis of the occurrence of Florscheutzia trilobata with Florscheutzia levipoli, the Early to Middle Miocene age has been assigned to the Balingian Formation. The distinct facies pattern and foraminifera species found from the samples taken from the Begrih outcrop imply deposition in the intertidal flats having pronounced fluvio-tidal interactions along the paleo-margin. Foraminiferal data combined with the pronounced occurrence of Stenochlaena laurifolia suggest at least the Late Miocene age for the Begrih Formation. The internal stratigraphic architecture of the Liang Formation is a function of a combination of sea level, stable tectonic and autogenic control. Based on stratigraphic position, the Middle Pliocene to Pleistocene age for the Liang Formation is probable. The Balingian, Begrih and Liang formations display deposits of multiple regressive-transgressive cycles while the sediments were derived from the uplifted Penian high and Rajang group.

Heavy mineral delineation of the Cretaceous, Paleocene, and Eocene stratigraphic sections at the Savannah River Site, Upper Coastal Plain of South Carolina

International Nuclear Information System (INIS)

Cathcart, E.M.; Sargent, K.A.

1994-01-01

The Upper Atlantic Coastal Plain of South Carolina consists of a fluvial-deltaic and shallow marine complex of unconsolidated sediments overlying the crystalline basement rocks of the North American continent. Because of the lateral and vertical variability of these sediments, stratigraphic boundaries have been difficult to distinguish. Portions of the Cretaceous, Paleocene, and eocene stratigraphic sections from cores recovered during the construction of two monitoring wells at the Savannah River Site were studied to determine if heavy mineral suites could be utilized to distinguish boundaries. The stratigraphic sections include: the Late Cretaceous Middendorf, Black Creek, and Steel Creek Formations, the Paleocene Snapp Formation, the late Paleocene-Early Eocene Fourmile Branch Formation, and the Early Eocene Congaree formation. In previous studies composite samples were taken over 2.5 ft. intervals along the cores and processed using a heavy liquid for heavy mineral recovery. During this study, heavy mineral distributions were determined by binocular microscope and the mineral identifications confirmed by x-ray diffraction analysis of hand-picked samples. The heavy mineral concentration data and grain size data were then compared to the stratigraphic boundary positions determined by other workers using more classical methods. These comparisons were used to establish the utility of this method for delineating the stratigraphic boundaries in the area of study

High-resolution sequence stratigraphic character and sandstone-type uranium ore formation. A case from Saihan Formation in Baiyinwula area, Erlian Basin

International Nuclear Information System (INIS)

He Zhongbo; Qin Mingkuan

2006-01-01

High-resolution sequence stratigraphy has been applied widely in the petroleum exploration and development, many achievements have been achieved. However, it is in the beginning stage that high-resolution sequence stratigraphy is applied to explore the sandstone-type uranium deposits in Erlian Basin. By applying principles of high-resolution sequence stratigraphy and taking typical boreholes as an example, sedimentary cycles of Saihan Formation, the ore-bearing formation in Baiyinwula area are divided and correlated through cross sections. One long-term cycle (LSC 1 ), two middle-term cycles (MSC 1 , MSC 2 ) have been identified in this study. Based on this and combined with the mineralization character of sandstone uranium deposits in this area, it is presented that the interlayer oxidation zone is developed mainly in the rising hemicycle of MSC 1 and uranium ore bodies predominantly in channel sand bodies that were developed in the system tract with low accommodation; furthermore, it is recognized that these sand bodies are moderate (10-15 m) in thickness, fairly good in interconnectivity, relatively thin (<3 m) with the argillaceous interbed, and good in permeability, abundant in the organic matter and thus it is favorable for the development of the interlayer oxidization zone. (authors)

High-resolution sequence stratigraphy and continental environmental evolution: An example from east-central Argentina

Science.gov (United States)

Beilinson, Elisa; Veiga, Gonzalo D.; Spalletti, Luis A.

2013-10-01

The aims of this contribution is to establish a high-resolution sequence stratigraphic scheme for the continental deposits that constitute the Punta San Andrés Alloformation (Plio-Pleistocene) in east-central Argentina, to analyze the basin fill evolution and to identify and assess the role that extrinsic factors such as climate and sea-level oscillations played during evolution of the unit. For the high-resolution sequence stratigraphical study of the Punta San Andrés Alloformation, high- and low-accommodation system tracts were defined mainly on the basis of the architectural elements present in the succession, also taking into account the relative degree of channel and floodplain deposits. Discontinuities and the nature of depositional systems generated during variations in accommodation helped identify two fourth-order high-accommodation system tracts and two fourth-order low-accommodation system tracts. At a third-order scale, the Punta San Andrés Alloformation may be interpreted as the progradation of continental depositional systems, characterized by a braided system in the proximal areas, and a low-sinuosity, single-channel system in the distal areas, defined by a high rate of sediment supply and discharge peaks which periodically flooded the plains and generated high aggradation rates during the late Pliocene and lower Pleistocene.

Highly accurate fluorogenic DNA sequencing with information theory-based error correction.

Science.gov (United States)

Chen, Zitian; Zhou, Wenxiong; Qiao, Shuo; Kang, Li; Duan, Haifeng; Xie, X Sunney; Huang, Yanyi

2017-12-01

Eliminating errors in next-generation DNA sequencing has proved challenging. Here we present error-correction code (ECC) sequencing, a method to greatly improve sequencing accuracy by combining fluorogenic sequencing-by-synthesis (SBS) with an information theory-based error-correction algorithm. ECC embeds redundancy in sequencing reads by creating three orthogonal degenerate sequences, generated by alternate dual-base reactions. This is similar to encoding and decoding strategies that have proved effective in detecting and correcting errors in information communication and storage. We show that, when combined with a fluorogenic SBS chemistry with raw accuracy of 98.1%, ECC sequencing provides single-end, error-free sequences up to 200 bp. ECC approaches should enable accurate identification of extremely rare genomic variations in various applications in biology and medicine.

Cultural conservatism and variability in the Acheulian sequence of Gesher Benot Ya'aqov.

Science.gov (United States)

Sharon, Gonen; Alperson-Afil, Nira; Goren-Inbar, Naama

2011-04-01

The Acheulian Technocomplex exhibits two phenomena: variability and conservatism. Variability is expressed in the composition and frequencies of tool types, particularly in the varying frequencies of bifaces (handaxes and cleavers). Conservatism is expressed in the continuous presence of bifaces along an immense time trajectory. The site of Gesher Benot Ya'aqov (GBY) offers a unique opportunity to study aspects of variability and conservatism as a result of its long cultural-stratigraphic sequence containing superimposed lithic assemblages. This study explores aspects of variability and conservatism within the Acheulian lithic assemblages of GBY, with emphasis placed on the bifacial tools. While variability has been studied through a comparison of typological frequencies in a series of assemblages from the site, evidence for conservatism was examined in the production modes expressed by the reduction sequence of the bifaces. We demonstrate that while pronounced typological variability is observed among the GBY assemblages, they were all manufactured by the same technology. The technology, size, and morphology of the bifaces throughout the entire stratigraphic sequence of GBY reflect the strong conservatism of their makers. We conclude that the biface frequency cannot be considered as a chrono/cultural marker that might otherwise allow us to distinguish between different phases within the Acheulian. The variability observed within the assemblages is explained as a result of different activities, tasks, and functions, which were carried out at specific localities along the shores of the paleo-Hula Lake in the early Middle Pleistocene. Copyright © 2010 Elsevier Ltd. All rights reserved.

Additional data to the stratigraphy and the chronology of the Kostenki 1 (Poliakov) sequence, Voronezh, Russia : Le Sungirien, Saint-Petersbourg 2016

NARCIS (Netherlands)

Haesaerts, P; Damblon, F; van der Plicht, Johannes; Otte, Marcel; Nigst, Phillip R.

2017-01-01

Kostenki 1 is one of the many sites of the Kostenki- Borshchevo site cluster south of Voronezh, which has a long sequence covering the Early and Mid Upper Palaeo- lithic, including the Streletskian Cultural Layer V. Here we present stratigraphic data from our 1994 eldwork (sections of the 1981-1982

Single-base resolution and long-coverage sequencing based on single-molecule nanomanipulation

International Nuclear Information System (INIS)

An Hongjie; Huang Jiehuan; Lue Ming; Li Xueling; Lue Junhong; Li Haikuo; Zhang Yi; Li Minqian; Hu Jun

2007-01-01

We show new approaches towards a novel single-molecule sequencing strategy which consists of high-resolution positioning isolation of overlapping DNA fragments with atomic force microscopy (AFM), subsequent single-molecule PCR amplification and conventional Sanger sequencing. In this study, a DNA labelling technique was used to guarantee the accuracy in positioning the target DNA. Single-molecule multiplex PCR was carried out to test the contamination. The results showed that the two overlapping DNA fragments isolated by AFM could be successfully sequenced with high quality and perfect contiguity, indicating that single-base resolution and long-coverage sequencing have been achieved simultaneously

Studies of base pair sequence effects on DNA solvation based on all

Indian Academy of Sciences (India)

Detailed analyses of the sequence-dependent solvation and ion atmosphere of DNA are presented based on molecular dynamics (MD) simulations on all the 136 unique tetranucleotide steps obtained by the ABC consortium using the AMBER suite of programs. Significant sequence effects on solvation and ion localization ...

Recent advances in nanopore-based nucleic acid analysis and sequencing

International Nuclear Information System (INIS)

Shi, Jidong; Fang, Ying; Hou, Junfeng

2016-01-01

Nanopore-based sequencing platforms are transforming the field of genomic science. This review (containing 116 references) highlights some recent progress on nanopore-based nucleic acid analysis and sequencing. These studies are classified into three categories, biological, solid-state, and hybrid nanopores, according to their nanoporous materials. We begin with a brief description of the translocation-based detection mechanism of nanopores. Next, specific examples are given in nanopore-based nucleic acid analysis and sequencing, with an emphasis on identifying strategies that can improve the resolution of nanopores. This review concludes with a discussion of future research directions that will advance the practical applications of nanopore technology. (author)

Proposed stratigraphic nomenclature and macroscopic identification of lithostratigraphic units of the Paintbrush Group exposed at Yucca Mountain, Nevada

Energy Technology Data Exchange (ETDEWEB)

Buesch, D.C.; Spengler, R.W.; Moyer, T.C.; Geslin, J.K.

1996-09-01

This paper describes the formations of the Paintbrush Group exposed at Yucca Mountain, Nevada, presents a detailed stratigraphic nomenclature for the Tiva Canyon and Topopah spring Tuffs, and discusses the criteria that define lithostratigraphic units. The Tiva Canyon and Topopah Spring Tuffs are divided into zones, subzones, and intervals on the basis of macroscopic features observed in surface exposures and borehole samples. Primary divisions reflect depositional and compositional zoning that is expressed by variations in crystal content, phenocryst assemblage, pumice content and composition, and lithic content. Secondary divisions define welding and crystlalization zones, depositional features, or fracture characteristics. Both formations are divided into crystal-rich and crystal-poor members that have an identical sequency of zones, although subzone designations vary slightly between the two units. The identified lithostratigraphic divisions can be used to approximate thermal-mechanical and hydrogeologic boundaries in the field. Linking these three systems of nomenclature provides a framework within which to correlate these properties through regions of sparse data.

Proposed stratigraphic nomenclature and macroscopic identification of lithostratigraphic units of the Paintbrush Group exposed at Yucca Mountain, Nevada

International Nuclear Information System (INIS)

Buesch, D.C.; Spengler, R.W.; Moyer, T.C.; Geslin, J.K.

1996-01-01

This paper describes the formations of the Paintbrush Group exposed at Yucca Mountain, Nevada, presents a detailed stratigraphic nomenclature for the Tiva Canyon and Topopah spring Tuffs, and discusses the criteria that define lithostratigraphic units. The Tiva Canyon and Topopah Spring Tuffs are divided into zones, subzones, and intervals on the basis of macroscopic features observed in surface exposures and borehole samples. Primary divisions reflect depositional and compositional zoning that is expressed by variations in crystal content, phenocryst assemblage, pumice content and composition, and lithic content. Secondary divisions define welding and crystlalization zones, depositional features, or fracture characteristics. Both formations are divided into crystal-rich and crystal-poor members that have an identical sequency of zones, although subzone designations vary slightly between the two units. The identified lithostratigraphic divisions can be used to approximate thermal-mechanical and hydrogeologic boundaries in the field. Linking these three systems of nomenclature provides a framework within which to correlate these properties through regions of sparse data

A Window Into Clinical Next-Generation Sequencing-Based Oncology Testing Practices.

Science.gov (United States)

Nagarajan, Rakesh; Bartley, Angela N; Bridge, Julia A; Jennings, Lawrence J; Kamel-Reid, Suzanne; Kim, Annette; Lazar, Alexander J; Lindeman, Neal I; Moncur, Joel; Rai, Alex J; Routbort, Mark J; Vasalos, Patricia; Merker, Jason D

2017-12-01

- Detection of acquired variants in cancer is a paradigm of precision medicine, yet little has been reported about clinical laboratory practices across a broad range of laboratories. - To use College of American Pathologists proficiency testing survey results to report on the results from surveys on next-generation sequencing-based oncology testing practices. - College of American Pathologists proficiency testing survey results from more than 250 laboratories currently performing molecular oncology testing were used to determine laboratory trends in next-generation sequencing-based oncology testing. - These presented data provide key information about the number of laboratories that currently offer or are planning to offer next-generation sequencing-based oncology testing. Furthermore, we present data from 60 laboratories performing next-generation sequencing-based oncology testing regarding specimen requirements and assay characteristics. The findings indicate that most laboratories are performing tumor-only targeted sequencing to detect single-nucleotide variants and small insertions and deletions, using desktop sequencers and predesigned commercial kits. Despite these trends, a diversity of approaches to testing exists. - This information should be useful to further inform a variety of topics, including national discussions involving clinical laboratory quality systems, regulation and oversight of next-generation sequencing-based oncology testing, and precision oncology efforts in a data-driven manner.

Protein Function Prediction Based on Sequence and Structure Information

KAUST Repository

Smaili, Fatima Z.

2016-05-25

The number of available protein sequences in public databases is increasing exponentially. However, a significant fraction of these sequences lack functional annotation which is essential to our understanding of how biological systems and processes operate. In this master thesis project, we worked on inferring protein functions based on the primary protein sequence. In the approach we follow, 3D models are first constructed using I-TASSER. Functions are then deduced by structurally matching these predicted models, using global and local similarities, through three independent enzyme commission (EC) and gene ontology (GO) function libraries. The method was tested on 250 “hard” proteins, which lack homologous templates in both structure and function libraries. The results show that this method outperforms the conventional prediction methods based on sequence similarity or threading. Additionally, our method could be improved even further by incorporating protein-protein interaction information. Overall, the method we use provides an efficient approach for automated functional annotation of non-homologous proteins, starting from their sequence.

Sequence stratigraphic and sedimentologic significance of biogenic structures from a late Paleozoic marginal- to open-marine reservoir, Morrow Sandstone, subsurface of southwest Kansas, USA

Science.gov (United States)

Buatois, L.A.; Mangano, M.G.; Alissa, A.; Carr, T.R.

2002-01-01

Integrated ichnologic, sedimentologic, and stratigraphic studies of cores and well logs from Lower Pennsylvanian oil and gas reservoirs (lower Morrow Sandstone, southwest Kansas) allow distinction between fluvio-estuarine and open marine deposits in the Gentzler and Arroyo fields. The fluvio-estuarine facies assemblage is composed of both interfluve and valley-fill deposits, encompassing a variety of depositional environments such as fluvial channel, interfluve paleosol, bay head delta, estuary bay, restricted tidal flat, intertidal channel, and estuary mouth. Deposition in a brackish-water estuarine valley is supported by the presence of a low diversity, opportunistic, impoverished marine ichnofaunal assemblage dominated by infaunal structures, representing an example of a mixed, depauperate Cruziana and Skolithos ichnofacies. Overall distribution of ichnofossils along the estuarine valley was mainly controlled by the salinity gradient, with other parameters, such as oxygenation, substrate and energy, acting at a more local scale. The lower Morrow estuarine system displays the classical tripartite division of wave-dominated estuaries (i.e. seaward-marine sand plug, fine-grained central bay, and sandy landward zone), but tidal action is also recorded. The estuarine valley displays a northwest-southeast trend, draining to the open sea in the southeast. Recognition of valley-fill sandstones in the lower Morrow has implications for reservoir characterization. While the open marine model predicts a "layer-cake" style of facies distribution as a consequence of strandline shoreline progradation, identification of valley-fill sequences points to more compartmentalized reservoirs, due to the heterogeneity created by valley incision and subsequent infill. The open-marine facies assemblage comprises upper, middle, and lower shoreface; offshore transition; offshore; and shelf deposits. In contrast to the estuarine assemblage, open marine ichnofaunas are characterized by a

Characteristics of Chinese petroleum geology. Geological features and exploration cases of stratigraphic, foreland and deep formation traps

Energy Technology Data Exchange (ETDEWEB)

Jia, Chengzao [PetroChina Company Limited, Beijing (China)

2012-07-01

The first book of this subject in the recent 10 years. ''Characteristics of Chinese Petroleum Geology: Geological Features and Exploration Cases of Stratigraphic, Foreland and Deep Formation Traps'' systematically presents the progress made in petroleum geology in China and highlights the latest advances and achievements in oil/gas exploration and research, especially in stratigraphic, foreland and deep formation traps. The book is intended for researchers, practitioners and students working in petroleum geology, and is also an authoritative reference work for foreign petroleum exploration experts who want to learn more about this field in China.

Chemical Contaminants as Stratigraphic Markers for the Anthropocene

Science.gov (United States)

Kruge, M. A.

2012-12-01

Thousands and even millions of years from now, widespread anthropogenic contaminants in sediments would likely persist, incorporated into the geological record. They would inadvertently preserve evidence of our present era (informally designated as the Anthropocene Epoch) characterized by large human populations engaged in intensive industrial and agricultural activities. Hypothetical geologists in the distant future would likely find unusually high concentrations of a wide variety of contaminants at stratigraphic levels corresponding to our present time, analogous to the iridium anomaly marking the bolide impact event at the close of the Cretaceous Period. These would include both organic and inorganic substances, such as industrially-derived heavy metals (e.g., Hg, Pb, Cr, Zn) and hydrocarbons, both petrogenic (derived directly from petroleum) and pyrogenic (combustion products). While there are natural sources for these materials, such as volcanic eruptions, wildfires, and oil seeps, their co-occurrence would provide a signature characteristic of human activity. Diagnostic assemblages of organic compounds would carry an anthropogenic imprint. The distribution of polycyclic aromatic hydrocarbons (PAHs) in a sediment sample could distinguish between natural and human sources. Stable isotopic signatures would provide additional evidence. Concentrations of contaminants in the sedimentary record would increase exponentially with increasing proximity to urban source areas, where at present billions of people are collectively consuming vast quantities of fossil fuels and generating large amounts of waste. Aolian and marine transport prior to deposition has been seen at present to globally redistribute detectable amounts of contaminants including Hg and PAHs, even at great distances from principal source areas. For organic contaminants, deposition in an anoxic sedimentary environment could insure their preservation, increasing the likelihood of their inclusion in the

Depositional History and Sequence Stratigraphy of the Middle Ordovician Yeongheung Formation (Yeongweol Group), Taebaeksan Basin, mid-east Korea

Science.gov (United States)

Kwon, Yoo Jin; Kwon, Yi Kyun

2017-04-01

The Middle Ordovician Yeongheung Formation consists of numerous meter-scale, shallowing-upward cycles which were deposited on a shallow-marine carbonate platform. Many diagnostic sedimentary textures and structures such as supratidal laminite, tepee structure, and solution-collapsed breccia are observed, which enable to infer the dry climate and high salinity conditions during deposition of the formation. In order to understand its depositional history, this study focuses on vertical and spatial stacking patterns of the second- to third-order sequences through the detailed outcrop description and geologic mapping. A total 19 lithofacies have been recognized, which can be grouped into 5 facies associations (FAs): FA1 (Supratidal flat), FA2 (Supratidal or dolomitization of peritidal facies), FA3 (Intertidal flat), FA4 (Shallow subtidal to peritidal platform), FA5 (Shallow subtidal shoal). Global mega-sequence boundary (Sauk-Tippecanoe) occurs in solution-collapsed breccia zone in the lower part of the formation. Correlation of the shallowing-upward cycle stacking pattern across the study area defines 6 transgressive-regressive depositional sequences. Each depositional sequences comprises a package of vertical and spatial staking of shallow subtidal cycles in the lower part and peritidal cycles in the upper part of the formation. According to sequence stratigraphic interpretation, the reconstructed relative sea-level curve of the Yeongweol platform is very similar to that of the Taebaek platform. Based on the absence of siliciclastic sequence such as the Jigunsan Formation and the lithologic & stratigraphic differences, however, the Yeongweol and Taebaek groups might not belong to a single depositional system within the North China platform. The Yeongweol Group can be divided by the four subunits into their unique lithologic successions and geographic distributions. The Eastern subunit of the Yeongweol Group is composed dominantly of carbonate rocks with a high

The Bero Volganic Group: New Lithological, Stratigraphic, and Geochemical Data of this Extension of the Parana-Etendeka Igneous Province into SW Angola with Implications

Science.gov (United States)

Marsh, J.; Swart, R.

2015-12-01

The Bero Volcanic Group, an extension of the Etendeka-Paraná Igneous Province into SW Angola, forms the eroded basement to the on-shore Namibe Basin, an Early Cretaceous-Cenozoic terrestrial and marine sedimentary sequence. The igneous suite outcrops between latitudes 14.68o and 15.25o S and comprises quartz latite rheoignimbrites/lavas, tholeiitic basaltic lavas, pyroclastic/volcaniclastic deposits, minor aeolian sandstones, and mafic tholeiitic dykes and gabbroic sheets. Quartz latite lithologies dominate. In the Rio Bero area in the S quartz latites are underlain by several thin flows of basalt interbedded with, and underlain by, thin discontinuous lenses of aeolian sandstone. This sequence is consistent with the general stratigraphic sequence in the northern Etendeka of Namibia. To the N basalts and aeolian sandstones are absent and the quartz latites lie directly on Precambrian basement rocks in places. To date, data for a quartz latite correlated with a Chapecó rhyolites of the Paraná are available from only one locality in Angola. This study's wider sampling and major and trace element and radiogenic isotope analysis reveals the following: (1) all mafic rocks are high-Ti, the lavas being equivalent to the Khumiba/Urubici type; (2) mafic dykes cutting the quartz latites having affinities to the Paranapanema-Ribeira mafic lavas; (3) five quartz latite geochemical types are present, three of which are known from Etendeka/Paraná (Sarusas/Guarapuava, Khoraseb/Ourinhos and Ventura) and their stratigraphic relationships in Angola are consistent with those in the Etendeka and Paraná; (4) their Angolan occurrence significantly extends the area covered by, and potential eruptive volumes of, these silicic types; (5) two other quartz latite types are unknown in the Etendeka and Paraná and are probably products of low-volume, local eruptions. The Chinguau type is geochemically similar to the low-Ti quartz lalites of the southern Etendeka but has lower Epsilon Nd

Geologic, stratigraphic, thermal, and mechanical factors which influence repository design in the bedded salt environment

International Nuclear Information System (INIS)

Ashby, J.P.; Nair, O.; Ortman, D.; Rowe, J.

1979-12-01

This report describes the geologic, stratigraphic, thermal, and mechanical considerations applicable to repository design. The topics discussed in the report include: tectonic activity; geologic structure; stratigraphy; rock mechanical properties; and hydrologic properties

Paleomagnetic constrains in the reconstruction of the recent stratigraphic evolution of the Po delta

Science.gov (United States)

Correggiari, Annamaria; Vigliotti, Luigi; Remia, Alessandro; Perini, Luisa; Calabrese, Lorenzo; Luciani, Paolo

2014-05-01

The delta and prodelta deposits are characterized by a complex stratigraphic architecture that can be approached with several multidisciplinary tools. We present an example from the Po delta system characterized by alternating phases of rapid advance and abandonment of its multiple deltaic lobes that has been investigated through: (1) a review of historical cartography extending back several centuries; (2) integrated surveys of VHR seismic profiles recorded offshore of the modern delta from water depths as shallow as 5 m to the toe of the prodelta in about 30 m; and (3) sedimentological and geochronological data from precisely positioned sediment cores. Within this well known stratigraphic framework we have acquired seismic data and sediment cores in the area of the post roman Po delta system. However a precise dating of the recent evolution of depositional delta lobes is difficult because of the lack of suitable dating methods. To constrain the emplacement timing of the Renaissance lobes a paleomagnetic studies was carried out on a sedimentary sequence representing a seismic facies well correlated in the cores by whole core magnetic susceptibility profile. Forty eight samples were collected from a core section (RER96-1) characterized by a fine grained lithology suitable for paleomagnetic investigations. The characteristic remanent magnetization (ChRM) of the sediments has been obtained by applying an AF cleaning between 10 and 30 millitesla. The results have been compared with the directions recorded by the historical lavas of the Etna and Vesuvius. The combination of the trends observed in the declination and inclination suggests that the results can be compatible with the directions of the secular variation of the earth magnetic field occurring during the XVII century. This allow to date the sismic unit as representative of the beginning of the new delta following the Porto Viro avulsion made by the Venice Republic in 1604 AD. This delta history reflects the

Sequence-based classification and identification of Fungi.

Science.gov (United States)

Hibbett, David; Abarenkov, Kessy; Kõljalg, Urmas; Öpik, Maarja; Chai, Benli; Cole, James; Wang, Qiong; Crous, Pedro; Robert, Vincent; Helgason, Thorunn; Herr, Joshua R; Kirk, Paul; Lueschow, Shiloh; O'Donnell, Kerry; Nilsson, R Henrik; Oono, Ryoko; Schoch, Conrad; Smyth, Christopher; Walker, Donald M; Porras-Alfaro, Andrea; Taylor, John W; Geiser, David M

Fungal taxonomy and ecology have been revolutionized by the application of molecular methods and both have increasing connections to genomics and functional biology. However, data streams from traditional specimen- and culture-based systematics are not yet fully integrated with those from metagenomic and metatranscriptomic studies, which limits understanding of the taxonomic diversity and metabolic properties of fungal communities. This article reviews current resources, needs, and opportunities for sequence-based classification and identification (SBCI) in fungi as well as related efforts in prokaryotes. To realize the full potential of fungal SBCI it will be necessary to make advances in multiple areas. Improvements in sequencing methods, including long-read and single-cell technologies, will empower fungal molecular ecologists to look beyond ITS and current shotgun metagenomics approaches. Data quality and accessibility will be enhanced by attention to data and metadata standards and rigorous enforcement of policies for deposition of data and workflows. Taxonomic communities will need to develop best practices for molecular characterization in their focal clades, while also contributing to globally useful datasets including ITS. Changes to nomenclatural rules are needed to enable validPUBLICation of sequence-based taxon descriptions. Finally, cultural shifts are necessary to promote adoption of SBCI and to accord professional credit to individuals who contribute to community resources.

Integrating seismic-reflection and sequence-stratigraphic methods to characterize the hydrogeology of the Floridan aquifer system in southeast Florida

Science.gov (United States)

Cunningham, Kevin J.

2013-01-01

The Floridan aquifer system (FAS) is receiving increased attention as a result of regulatory restrictions on water-supply withdrawals and treated wastewater management practices. The South Florida Water Management District’s Regional Water Availability Rule, adopted in 2007, restricts urban withdrawals from the shallower Biscayne aquifer to pre-April 2006 levels throughout southeast Florida. Legislation adopted by the State of Florida requires elimination of ocean outfalls of treated wastewater by 2025. These restrictions have necessitated the use of the more deeply buried FAS as an alternate water resource to meet projected water-supply shortfalls, and as a repository for the disposal of wastewater via Class I deep injection wells and injection of reclaimed water. Some resource managers in Broward County have expressed concern regarding the viability of the FAS as an alternative water supply due to a lack of technical data and information regarding its long-term sustainability. Sustainable development and management of the FAS for water supply is uncertain because of the potential risk posed by structural geologic anomalies (faults, fractures, and karst collapse structures) and knowledge gaps in the stratigraphy of the system. The integration of seismic-reflection and borehole data into an improved geologic and hydrogeologic framework will provide a better understanding of the structural and stratigraphic features that influence groundwater flow and contaminant transport.

C, Sr and Sr isotopic composition on probable vendian- tommotian carbonate sequences in Nw Argentina

International Nuclear Information System (INIS)

Sial, A. N.; Ferreira, V.P; Toselli, A.J.; Acenolaza, F.G; Pimentel, M.M; Parada, M.A; Alonso, R.N

2001-01-01

C-isotope stratigraphy is one of the most powerfool tools in Precambrian chronostratigraphy, especially when sediments lack recognizable animal fossils. The δ 13 C secular variation curves for marine carbonates in the Neoproterozoic-Cambrian interval show strong positive-negative excursions, several of them interpreted as the stratigraphic position of ancient ice ages (Hoffman et al. 1998). The Sr isotope composition of the seawater for this age interval is characterized by a continuous increase of 87 Sr/ 86 Sr that is interrupted, several times, by sharp rises, which represent important changes in the Earth history (Montanez et al. 2000). Only limited data on the behavior of C and Sr isotopes in carbonates are available in South America. We examine here carbonate sequences from the Argentine Precordillera, San Juan province, and from other carbonate sequences in NW Argentina that could be, potentially, proxies for the Precambrian-Cambrian transition. We have studied their δ 13 C and 87 Sr/ 86 Sr chemostratigraphy and compare it to global C and Sr isotope secular variation curves for this time span. This study aims to improve the relatively coarse stratigraphic resolution provided only by the study of the fossil record in some of the carbonate successions under consideration (au)

Thermodynamics-based models of transcriptional regulation with gene sequence.

Science.gov (United States)

Wang, Shuqiang; Shen, Yanyan; Hu, Jinxing

2015-12-01

Quantitative models of gene regulatory activity have the potential to improve our mechanistic understanding of transcriptional regulation. However, the few models available today have been based on simplistic assumptions about the sequences being modeled or heuristic approximations of the underlying regulatory mechanisms. In this work, we have developed a thermodynamics-based model to predict gene expression driven by any DNA sequence. The proposed model relies on a continuous time, differential equation description of transcriptional dynamics. The sequence features of the promoter are exploited to derive the binding affinity which is derived based on statistical molecular thermodynamics. Experimental results show that the proposed model can effectively identify the activity levels of transcription factors and the regulatory parameters. Comparing with the previous models, the proposed model can reveal more biological sense.

Disk-based compression of data from genome sequencing.

Science.gov (United States)

Grabowski, Szymon; Deorowicz, Sebastian; Roguski, Łukasz

2015-05-01

High-coverage sequencing data have significant, yet hard to exploit, redundancy. Most FASTQ compressors cannot efficiently compress the DNA stream of large datasets, since the redundancy between overlapping reads cannot be easily captured in the (relatively small) main memory. More interesting solutions for this problem are disk based, where the better of these two, from Cox et al. (2012), is based on the Burrows-Wheeler transform (BWT) and achieves 0.518 bits per base for a 134.0 Gbp human genome sequencing collection with almost 45-fold coverage. We propose overlapping reads compression with minimizers, a compression algorithm dedicated to sequencing reads (DNA only). Our method makes use of a conceptually simple and easily parallelizable idea of minimizers, to obtain 0.317 bits per base as the compression ratio, allowing to fit the 134.0 Gbp dataset into only 5.31 GB of space. http://sun.aei.polsl.pl/orcom under a free license. sebastian.deorowicz@polsl.pl Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Sequence memory based on coherent spin-interaction neural networks.

Science.gov (United States)

Xia, Min; Wong, W K; Wang, Zhijie

2014-12-01

Sequence information processing, for instance, the sequence memory, plays an important role on many functions of brain. In the workings of the human brain, the steady-state period is alterable. However, in the existing sequence memory models using heteroassociations, the steady-state period cannot be changed in the sequence recall. In this work, a novel neural network model for sequence memory with controllable steady-state period based on coherent spininteraction is proposed. In the proposed model, neurons fire collectively in a phase-coherent manner, which lets a neuron group respond differently to different patterns and also lets different neuron groups respond differently to one pattern. The simulation results demonstrating the performance of the sequence memory are presented. By introducing a new coherent spin-interaction sequence memory model, the steady-state period can be controlled by dimension parameters and the overlap between the input pattern and the stored patterns. The sequence storage capacity is enlarged by coherent spin interaction compared with the existing sequence memory models. Furthermore, the sequence storage capacity has an exponential relationship to the dimension of the neural network.

Aeolian sedimentary processes at the Bagnold Dunes, Mars: Implications for modern dune dynamics and sedimentary structures in the aeolian stratigraphic record of Mars

Science.gov (United States)

Ewing, Ryan C.; Bridges, Nathan T.; Sullivan, Rob; Lapotre, Mathieu G. A.; Fischer, Woodward W.; Lamb, Mike P.; Rubin, David M.; Lewis, Kevin W.; Gupta, Sanjeev

2016-04-01

Wind-blown sand dunes are ubiquitous on the surface of Mars and are a recognized component of the martian stratigraphic record. Our current knowledge of the aeolian sedimentary processes that determine dune morphology, drive dune dynamics, and create aeolian cross-stratification are based upon orbital studies of ripple and dune morphodynamics, rover observations of stratification on Mars, Earth analogs, and experimental and theoretical studies of sand movement under Martian conditions. In-situ observations of sand dunes (informally called the Bagnold Dunes) by Curiosity Rover in Gale Crater, Mars provide the first opportunity to make observations of dunes from the grain-to-dune scale thereby filling the gap in knowledge between theory and orbital observations and refining our understanding of the martian aeolian stratigraphic record. We use the suite of cameras on Curiosity, including Navigation Camera (Navcam), Mast Camera (Mastcam) and Mars Hand Lens Imager (MAHLI), to make observations of the Bagnold Dunes. Measurements of sedimentary structures are made where stereo images are available. Observations indicate that structures generated by gravity-driven processes on the dune lee slopes, such as grainflow and grainfall, are similar to the suite of aeolian sedimentary structures observed on Earth and should be present and recognizable in Mars' aeolian stratigraphic record. Structures formed by traction-driven processes deviate significantly from those found on Earth. The dune hosts centimeter-scale wind ripples and large, meter-scale ripples, which are not found on Earth. The large ripples migrate across the depositional, lee slopes of the dune, which implies that these structures should be present in Mars' stratigraphic record and may appear similar to compound-dune stratification.The Mars Science Laboratory Curiosity Rover Team is acknowledged for their support of this work.

Geochemical evaluation of a shale stratigraphic profile from Paraiba Valley (Tremembe)

International Nuclear Information System (INIS)

Loureiro, M.R.B.; Cardoso, J.N.

1987-01-01

The sedimentary core ranges 0-35m depth and covers three types of bituminous shales, intercalated by two layers of sterile clay. A systematic geochemical study of samples of most stratigraphic layers was undertaken for the first time in this work, including elemental analysis (C, H), carbonate content, type of organic matter, infrared spectrometry and molecular characterization of organic extracts (hight-resolution) gas chromatography, mass spectrometry). No consistent correlation between lithology and amount/type of organic matter was observed, contrary to literature data, pointing out the paper shale strata as richest in organic matter. Molecular stratigraphy of the core presented similar n-alkane profiles generally maximizing at n-C 27 attesting to a small variation in input along the sedimentary section. Characterization of the branched/cyclic hydrocarbons evidenced a continental input to the sediment, as revealed by the presence, in several layers, of isometric des-A-fernenes, presumed products of diagenesis of arborinone. A microbial input was also evidenced through the general occurrence of hopanoids, trace amounts of steroidal skeletons as well as atomic H/C ratios ca. 2. The sharp variations in biomarker profiles with depth showed great potential as correlation markers in a detailed stratigraphic study of the basin, as a valuable supplement to traditional lithological parameters. (author) [pt

Selected stratigraphic data for drill holes located in Frenchman Flat, Nevada Test Site. Rev. 1

International Nuclear Information System (INIS)

Drellack, S.L. Jr.

1997-02-01

Stratigraphic data are presented in tabular form for 72 holes drilled in Frenchman Flat, Nevada Test Site, between 1950 and 1993. Three pairs of data presentations are included for each hole: depth to formation tops, formation thicknesses, and formation elevations are presented in both field (English) and metric units. Also included for each hole, where available, are various construction data (hole depth, hole diameter, surface location coordinates) and certain information of hydrogeologic significance (depth to water level, top of zeolitization). The event name is given for holes associated with a particular nuclear test. An extensive set of footnotes is included, which indicates data sources and provides other information. The body of the report describes the stratigraphic setting of Frenchman Flat, gives drill-hole naming conventions and database terminology, and provides other background and reference material

Completed Ensemble Empirical Mode Decomposition: a Robust Signal Processing Tool to Identify Sequence Strata

Science.gov (United States)

Purba, H.; Musu, J. T.; Diria, S. A.; Permono, W.; Sadjati, O.; Sopandi, I.; Ruzi, F.

2018-03-01

Well logging data provide many geological information and its trends resemble nonlinear or non-stationary signals. As long well log data recorded, there will be external factors can interfere or influence its signal resolution. A sensitive signal analysis is required to improve the accuracy of logging interpretation which it becomes an important thing to determine sequence stratigraphy. Complete Ensemble Empirical Mode Decomposition (CEEMD) is one of nonlinear and non-stationary signal analysis method which decomposes complex signal into a series of intrinsic mode function (IMF). Gamma Ray and Spontaneous Potential well log parameters decomposed into IMF-1 up to IMF-10 and each of its combination and correlation makes physical meaning identification. It identifies the stratigraphy and cycle sequence and provides an effective signal treatment method for sequence interface. This method was applied to BRK- 30 and BRK-13 well logging data. The result shows that the combination of IMF-5, IMF-6, and IMF-7 pattern represent short-term and middle-term while IMF-9 and IMF-10 represent the long-term sedimentation which describe distal front and delta front facies, and inter-distributary mouth bar facies, respectively. Thus, CEEMD clearly can determine the different sedimentary layer interface and better identification of the cycle of stratigraphic base level.

The Influence of Stratigraphic History on Landscape Evolution

Science.gov (United States)

Forte, A. M.; Yanites, B.; Whipple, K. X.

2016-12-01

Variation in rock erodibility can play a significant role in landscape evolution. Using a version of the CHILD landscape evolution model that allows for variations in rock erodibility, we found surprisingly complex landscape evolution in simulations with simple, two unit stratigraphies with contrasting erodibility. This work indicated that the stratigraphic order of units in terms of erodibility, the orientation of the contact with respect to the main drainage direction, and the contact dip angle all have pronounced effects on landscape evolution. Here we expand that work to explore the implications of more complicated stratigraphies on landscape evolution. Introducing multiple units adds additional controls on landscape evolution, namely the thicknesses and relative erodibility of rock layers. In models with a sequence of five alternating hard and soft units embedded within arbitrarily thick over- and underlying units, the number of individual layers that noticeably influence landscape morphology decreases as the thickness of individual layers reduces. Contacts with soft rocks over hard produce the most noticeable effect in model output such as erosion rate and channel steepness. For large contrasts in erodibility of 25 m thick layers, only one soft over hard contact is clearly manifest in the landscape. Between 50 and 75 m, two such contacts are manifest, and by 100 m thickness, all three of these contacts are manifest. However, for a given thickness of layers, more units are manifest in the landscape as the erodibility contrast between units decreases. This is true even though the magnitude of landscape effects away from steady-state erosion rates or channel steepness also decrease with decreasing erodibility contrast. Finally, we explore suites of models with alternating layers reflecting either `hardening-' or `softening-upwards' stratigraphies and find that the two scenarios result in decidedly different landscape forms. Hardening-upwards sections produce a

On the geochemistry of the Kyra eruption sequence of Nisyros volcano on Nisyros and Tilos, Greece

International Nuclear Information System (INIS)

Sterba, Johannes H.; Steinhauser, Georg; Bichler, Max

2011-01-01

The Kyra sequence is a volcanic eruption sequence originating from the eastern flank of Nisyros volcano, Greece. Its eruptions products can be found not only on Nisyros itself but also on the nearby non-volcanic island of Tilos. In an extensive sampling campaign, outcrops of the Kyra eruption products on Nisyros were sampled and corresponding samples on Tilos were taken. The clear stratigraphical relationship between the different units within in the individual outcrops, combined with the chemical information gained by the application of instrumental neutron activation analysis (INAA) to the samples, made a detailed chemo-stratigraphy of the complete eruption sequence possible. It can be shown that the sequence is separated into eight distinguishable eruptions. Furthermore, no eruption products of the caldera-forming eruptions from Nisyros (Lower- and Upper Caldera Pumice) or from Santorin were found on Tilos.

On the geochemistry of the Kyra eruption sequence of Nisyros volcano on Nisyros and Tilos, Greece

Energy Technology Data Exchange (ETDEWEB)

Sterba, Johannes H., E-mail: jsterba@ati.ac.at [Atominstitut der oesterreichischen Universitaeten, Vienna University of Technology (Austria); Steinhauser, Georg; Bichler, Max [Atominstitut der oesterreichischen Universitaeten, Vienna University of Technology (Austria)

2011-11-15

The Kyra sequence is a volcanic eruption sequence originating from the eastern flank of Nisyros volcano, Greece. Its eruptions products can be found not only on Nisyros itself but also on the nearby non-volcanic island of Tilos. In an extensive sampling campaign, outcrops of the Kyra eruption products on Nisyros were sampled and corresponding samples on Tilos were taken. The clear stratigraphical relationship between the different units within in the individual outcrops, combined with the chemical information gained by the application of instrumental neutron activation analysis (INAA) to the samples, made a detailed chemo-stratigraphy of the complete eruption sequence possible. It can be shown that the sequence is separated into eight distinguishable eruptions. Furthermore, no eruption products of the caldera-forming eruptions from Nisyros (Lower- and Upper Caldera Pumice) or from Santorin were found on Tilos.

Swarm-based Sequencing Recommendations in E-learning

NARCIS (Netherlands)

Van den Berg, Bert; Tattersall, Colin; Janssen, José; Brouns, Francis; Kurvers, Hub; Koper, Rob

2005-01-01

Van den Berg, B., Tattersall, C., Janssen, J., Brouns, F., Kurvers, H., & Koper, R. (2006). Swarm-based Sequencing Recommendations in E-learning. International Journal of Computer Science & Applications, III(III), 1-11.

An optical CDMA system based on chaotic sequences

Science.gov (United States)

Liu, Xiao-lei; En, De; Wang, Li-guo

2014-03-01

In this paper, a coherent asynchronous optical code division multiple access (OCDMA) system is proposed, whose encoder/decoder is an all-optical generator. This all-optical generator can generate analog and bipolar chaotic sequences satisfying the logistic maps. The formula of bit error rate (BER) is derived, and the relationship of BER and the number of simultaneous transmissions is analyzed. Due to the good property of correlation, this coherent OCDMA system based on these bipolar chaotic sequences can support a large number of simultaneous users, which shows that these chaotic sequences are suitable for asynchronous OCDMA system.

T-R Cycle Characterization and Imaging: Advanced Diagnostic Methodology for Petroleum Reservoir and Trap Detection and Delineation

Energy Technology Data Exchange (ETDEWEB)

Ernest A. Mancini

2006-08-30

Characterization of stratigraphic sequences (T-R cycles or sequences) included outcrop studies, well log analysis and seismic reflection interpretation. These studies were performed by researchers at the University of Alabama, Wichita State University and McGill University. The outcrop, well log and seismic characterization studies were used to develop a depositional sequence model, a T-R cycle (sequence) model, and a sequence stratigraphy predictive model. The sequence stratigraphy predictive model developed in this study is based primarily on the modified T-R cycle (sequence) model. The T-R cycle (sequence) model using transgressive and regressive systems tracts and aggrading, backstepping, and infilling intervals or sections was found to be the most appropriate sequence stratigraphy model for the strata in the onshore interior salt basins of the Gulf of Mexico to improve petroleum stratigraphic trap and specific reservoir facies imaging, detection and delineation. The known petroleum reservoirs of the Mississippi Interior and North Louisiana Salt Basins were classified using T-R cycle (sequence) terminology. The transgressive backstepping reservoirs have been the most productive of oil, and the transgressive backstepping and regressive infilling reservoirs have been the most productive of gas. Exploration strategies were formulated using the sequence stratigraphy predictive model and the classification of the known petroleum reservoirs utilizing T-R cycle (sequence) terminology. The well log signatures and seismic reflector patterns were determined to be distinctive for the aggrading, backstepping and infilling sections of the T-R cycle (sequence) and as such, well log and seismic data are useful for recognizing and defining potential reservoir facies. The use of the sequence stratigraphy predictive model, in combination with the knowledge of how the distinctive characteristics of the T-R system tracts and their subdivisions are expressed in well log patterns

A sequence-dependent rigid-base model of DNA

Science.gov (United States)

Gonzalez, O.; Petkevičiutė, D.; Maddocks, J. H.

2013-02-01

A novel hierarchy of coarse-grain, sequence-dependent, rigid-base models of B-form DNA in solution is introduced. The hierarchy depends on both the assumed range of energetic couplings, and the extent of sequence dependence of the model parameters. A significant feature of the models is that they exhibit the phenomenon of frustration: each base cannot simultaneously minimize the energy of all of its interactions. As a consequence, an arbitrary DNA oligomer has an intrinsic or pre-existing stress, with the level of this frustration dependent on the particular sequence of the oligomer. Attention is focussed on the particular model in the hierarchy that has nearest-neighbor interactions and dimer sequence dependence of the model parameters. For a Gaussian version of this model, a complete coarse-grain parameter set is estimated. The parameterized model allows, for an oligomer of arbitrary length and sequence, a simple and explicit construction of an approximation to the configuration-space equilibrium probability density function for the oligomer in solution. The training set leading to the coarse-grain parameter set is itself extracted from a recent and extensive database of a large number of independent, atomic-resolution molecular dynamics (MD) simulations of short DNA oligomers immersed in explicit solvent. The Kullback-Leibler divergence between probability density functions is used to make several quantitative assessments of our nearest-neighbor, dimer-dependent model, which is compared against others in the hierarchy to assess various assumptions pertaining both to the locality of the energetic couplings and to the level of sequence dependence of its parameters. It is also compared directly against all-atom MD simulation to assess its predictive capabilities. The results show that the nearest-neighbor, dimer-dependent model can successfully resolve sequence effects both within and between oligomers. For example, due to the presence of frustration, the model can

A sequence-dependent rigid-base model of DNA.

Science.gov (United States)

Gonzalez, O; Petkevičiūtė, D; Maddocks, J H

2013-02-07

A novel hierarchy of coarse-grain, sequence-dependent, rigid-base models of B-form DNA in solution is introduced. The hierarchy depends on both the assumed range of energetic couplings, and the extent of sequence dependence of the model parameters. A significant feature of the models is that they exhibit the phenomenon of frustration: each base cannot simultaneously minimize the energy of all of its interactions. As a consequence, an arbitrary DNA oligomer has an intrinsic or pre-existing stress, with the level of this frustration dependent on the particular sequence of the oligomer. Attention is focussed on the particular model in the hierarchy that has nearest-neighbor interactions and dimer sequence dependence of the model parameters. For a Gaussian version of this model, a complete coarse-grain parameter set is estimated. The parameterized model allows, for an oligomer of arbitrary length and sequence, a simple and explicit construction of an approximation to the configuration-space equilibrium probability density function for the oligomer in solution. The training set leading to the coarse-grain parameter set is itself extracted from a recent and extensive database of a large number of independent, atomic-resolution molecular dynamics (MD) simulations of short DNA oligomers immersed in explicit solvent. The Kullback-Leibler divergence between probability density functions is used to make several quantitative assessments of our nearest-neighbor, dimer-dependent model, which is compared against others in the hierarchy to assess various assumptions pertaining both to the locality of the energetic couplings and to the level of sequence dependence of its parameters. It is also compared directly against all-atom MD simulation to assess its predictive capabilities. The results show that the nearest-neighbor, dimer-dependent model can successfully resolve sequence effects both within and between oligomers. For example, due to the presence of frustration, the model can

Stratigraphy, Sequence, and Crater Populations of Lunar Impact Basins from Lunar Orbiter Laser Altimeter (LOLA) Data: Implications for the Late Heavy Bombardment

Science.gov (United States)

Fassett, C. I.; Head, J. W.; Kadish, S. J.; Mazarico, E.; Neumann, G. A.; Smith, D. E.; Zuber, M. T.

2012-01-01

New measurements of the topography of the Moon from the Lunar Orbiter Laser Altimeter (LOLA)[1] provide an excellent base-map for analyzing the large crater population (D.20 km)of the lunar surface [2, 3]. We have recently used this data to calculate crater size-frequency distributions (CSFD) for 30 lunar impact basins, which have implications for their stratigraphy and sequence. These data provide an avenue for assessing the timing of the transitions between distinct crater populations characteristic of ancient and young lunar terrains, which has been linked to the late heavy bombardment (LHB). We also use LOLA data to re-examine relative stratigraphic relationships between key lunar basins.

antaRNA: ant colony-based RNA sequence design.

Science.gov (United States)

Kleinkauf, Robert; Mann, Martin; Backofen, Rolf

2015-10-01

RNA sequence design is studied at least as long as the classical folding problem. Although for the latter the functional fold of an RNA molecule is to be found ,: inverse folding tries to identify RNA sequences that fold into a function-specific target structure. In combination with RNA-based biotechnology and synthetic biology ,: reliable RNA sequence design becomes a crucial step to generate novel biochemical components. In this article ,: the computational tool antaRNA is presented. It is capable of compiling RNA sequences for a given structure that comply in addition with an adjustable full range objective GC-content distribution ,: specific sequence constraints and additional fuzzy structure constraints. antaRNA applies ant colony optimization meta-heuristics and its superior performance is shown on a biological datasets. http://www.bioinf.uni-freiburg.de/Software/antaRNA CONTACT: backofen@informatik.uni-freiburg.de Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press.

Lunar Impact Basins: Stratigraphy, Sequence and Ages from Superposed Impact Crater Populations Measured from Lunar Orbiter Laser Altimeter (LOLA) Data

Science.gov (United States)

Fassett, C. I.; Head, J. W.; Kadish, S. J.; Mazarico, E.; Neumann, G. A.; Smith, D. E.; Zuber, M. T.

2012-01-01

Impact basin formation is a fundamental process in the evolution of the Moon and records the history of impactors in the early solar system. In order to assess the stratigraphy, sequence, and ages of impact basins and the impactor population as a function of time, we have used topography from the Lunar Orbiter Laser Altimeter (LOLA) on the Lunar Reconnaissance Orbiter (LRO) to measure the superposed impact crater size-frequency distributions for 30 lunar basins (D = 300 km). These data generally support the widely used Wilhelms sequence of lunar basins, although we find significantly higher densities of superposed craters on many lunar basins than derived by Wilhelms (50% higher densities). Our data also provide new insight into the timing of the transition between distinct crater populations characteristic of ancient and young lunar terrains. The transition from a lunar impact flux dominated by Population 1 to Population 2 occurred before the mid-Nectarian. This is before the end of the period of rapid cratering, and potentially before the end of the hypothesized Late Heavy Bombardment. LOLA-derived crater densities also suggest that many Pre-Nectarian basins, such as South Pole-Aitken, have been cratered to saturation equilibrium. Finally, both crater counts and stratigraphic observations based on LOLA data are applicable to specific basin stratigraphic problems of interest; for example, using these data, we suggest that Serenitatis is older than Nectaris, and Humboldtianum is younger than Crisium. Sample return missions to specific basins can anchor these measurements to a Pre-Imbrian absolute chronology.

Automation tools for accelerator control a network based sequencer

International Nuclear Information System (INIS)

Clout, P.; Geib, M.; Westervelt, R.

1991-01-01

In conjunction with a major client, Vista Control Systems has developed a sequencer for control systems which works in conjunction with its realtime, distributed Vsystem database. Vsystem is a network-based data acquisition, monitoring and control system which has been applied successfully to both accelerator projects and projects outside this realm of research. The network-based sequencer allows a user to simply define a thread of execution in any supported computer on the network. The script defining a sequence has a simple syntax designed for non-programmers, with facilities for selectively abbreviating the channel names for easy reference. The semantics of the script contains most of the familiar capabilities of conventional programming languages, including standard stream I/O and the ability to start other processes with parameters passed. The script is compiled to threaded code for execution efficiency. The implementation is described in some detail and examples are given of applications for which the sequencer has been used

Stratigraphic architecture of bedrock reference section, Victoria Crater, Meridiani Planum, Mars

Science.gov (United States)

Edgar, Lauren A.; Grotzinger, John P.; Hayes, Alex G.; Rubin, David M.; Squyres, Steve W.; Bell, James F.; Herkenhoff, Ken E.

2012-01-01

The Mars Exploration Rover Opportunity has investigated bedrock outcrops exposed in several craters at Meridiani Planum, Mars, in an effort to better understand the role of surface processes in its geologic history. Opportunity has recently completed its observations of Victoria crater, which is 750 m in diameter and exposes cliffs up to ~15 m high. The plains surrounding Victoria crater are ~10 m higher in elevation than those surrounding the previously explored Endurance crater, indicating that the Victoria crater exposes a stratigraphically higher section than does the Endurance crater; however, Victoria strata overlap in elevation with the rocks exposed at the Erebus crater. Victoria crater has a well-developed geomorphic pattern of promontories and embayments that define the crater wall and that reveal thick bedsets (3–7m) of large-scale cross-bedding, interpreted as fossil eolian dunes. Opportunity was able to drive into the crater at Duck Bay, located on the western margin of Victoria crater. Data from the Microscopic Imager and Panoramic Camera reveal details about the structures, textures, and depositional and diagenetic events that influenced the Victoria bedrock. A lithostratigraphic subdivision of bedrock units was enabled by the presence of a light-toned band that lines much of the upper rim of the crater. In ascending order, three stratigraphic units are named Lyell, Smith, and Steno; Smith is the light-toned band. In the Reference Section exposed along the ingress path at Duck Bay, Smith is interpreted to represent a zone of diagenetic recrystallization; however, its upper contact also coincides with a primary erosional surface. Elsewhere in the crater the diagenetic band crosscuts the physical stratigraphy. Correlation with strata present at nearby promontory Cape Verde indicates that there is an erosional surface at the base of the cliff face that corresponds to the erosional contact below Steno. The erosional contact at the base of Cape Verde

RESEARCH NOTE Genome-based exome-sequencing analysis ...

Indian Academy of Sciences (India)

Navya

2017-02-22

Feb 22, 2017 ... Genome-based exome-sequencing analysis identifies GYG1, DIS3L, DDRGK1 genes ... Cardiology Division, Department of Internal Medicine, Severance .... with p values of <0.05 byanalyzing differences in allele distribution.

Characterizing Structural and Stratigraphic Heterogeneities in a Faulted Aquifer Using Pump Tests with an Array of Westbay Multilevel Monitoring Wells

Science.gov (United States)

Johnson, B.; Zhurina, E. N.

2001-12-01

We are developing and assessing field testing and analysis methodologies for quantitative characterization of aquifer heterogenities using data measured in an array of multilevel monitoring wells (MLW) during pumping and recovery well tests. We have developed a unique field laboratory to determine the permeability field in a 20m by 40m by 70m volume in the fault partitioned, siliciclastic Hickory aquifer system in central Texas. The site incorporates both stratigraphic variations and a normal fault system that partially offsets the aquifer and impedes cross-fault flow. We constructed a high-resolution geologic model of the site based upon 1050 m of core and a suite of geophysical logs from eleven, closely spaced (3-10m), continuously cored boreholes to depths of 125 m. Westbay multilevel monitoring systems installed in eight holes provide 94 hydraulically isolated measurement zones and 25 injection zones. A good geologic model is critical to proper installation of the MLW. Packers are positioned at all significant fault piercements and selected, laterally extensive, clay-rich strata. Packers in adjacent MLW bracket selected hydrostratigraphic intervals. Pump tests utilized two, uncased, fully penetrating irrigation wells that straddle the fault system and are in close proximity (7 to 65 m) to the MLW. Pumping and recovery transient pressure histories were measured in 85 zones using pressure transducers with a resolution of 55 Pa (0.008 psi). The hydraulic response is that of an anisotropic, unconfined aquifer. The transient pressure histories vary significantly from zone to zone in a single MLW as well as between adjacent MLW. Derivative plots are especially useful for differentiating details of pressure histories. Based on the geologic model, the derivative curve of a zone reflects its absolute vertical position, vertical stratigraphic position, and proximity to either a fault or significant stratigraphic heterogeneity. Additional forward modeling is needed to

Unlocking the hydrocarbon potential of the eastern Black Sea basin. Prospectivity of middle Miocene submarine fan reservoirs by seismic sequence stratigraphy

International Nuclear Information System (INIS)

Gundogan, Coskun; Galip, Ozbek; Ali, Demirer

2002-01-01

Full text : The objective of this paper is to present present depositional characteristics and hydrocarbon prospectivity of the middle Miocene submarine basin floor fan deposits from the exploration stand point of view by using seismic data available in the offshore eastern Black Sea basin. This basin is a Tertiary trough formed as a continuation of the Mesozoic oceanic basin. The hydrocarbon potential of the basin is believed to be high in the Tertiary section because of the existence of the elements necessary for generation, migration and entrapment of hydrocarbon. A sequence stratigraphic study has been carried out by using 2-d seismic data in the Turkish portion of the eastern Black Sea basin. The objective of the study was to determine periods of major clastic sediment influxes which might lead to identify good reservoir intervals and their spatial distribution in this basin. All basic seismic sequence stratigraphic interpretation techniques and seismic facies analysis were used to identify times of these sand rich deposition periods. Sequence stratigraphy and seismic facies analysis indicate that the basinal areas of the middle Miocene sequences were dominated mainly by submarine fan complexes introduced in the lowstand stages and pelagic sediments deposited during the transgressive and highstand stages. It was proposed that Turkish portion of this basin which is one of the best frontier exploration area with its high potential left in the world, is glimpsing to those looking for good future exploration opportunities.

Assessment of bauxite, clay, and laterite deposits in Afghanistan

Science.gov (United States)

Renaud, Karine M.; Wardlaw, Bruce R.; Hubbard, Bernard E.

2015-01-01

Bauxite-bearing rocks are present in several regions of Afghanistan; specifically, the southeast segment of the North Afghanistan Platform, the eastern parts of South Afghanistan, and within the Afghanistan-North and -South Pamir Fold Regions. Bauxite-bearing rocks occur at various stratigraphic levels, in lithologically different sequences of sedimentary rocks. The bauxites are paleosols and represent previous, rather than recent, weathering events. Bauxites and bauxite-type horizons are most common at the base of carbonate rock units, where they form the basal horizons of sedimentary rock sequences separated by erosion and stratigraphic unconformity surfaces. Less common are zones in redeposited weathering developed on igneous rocks. At present there are five known stratigraphic intervals with significant bauxite and bauxite-type deposits and occurrences: the lower Permian, the upper Permian, the Upper Triassic, the Lower Jurassic, and the base of the Upper Jurassic.

An accurate clone-based haplotyping method by overlapping pool sequencing.

Science.gov (United States)

Li, Cheng; Cao, Changchang; Tu, Jing; Sun, Xiao

2016-07-08

Chromosome-long haplotyping of human genomes is important to identify genetic variants with differing gene expression, in human evolution studies, clinical diagnosis, and other biological and medical fields. Although several methods have realized haplotyping based on sequencing technologies or population statistics, accuracy and cost are factors that prohibit their wide use. Borrowing ideas from group testing theories, we proposed a clone-based haplotyping method by overlapping pool sequencing. The clones from a single individual were pooled combinatorially and then sequenced. According to the distinct pooling pattern for each clone in the overlapping pool sequencing, alleles for the recovered variants could be assigned to their original clones precisely. Subsequently, the clone sequences could be reconstructed by linking these alleles accordingly and assembling them into haplotypes with high accuracy. To verify the utility of our method, we constructed 130 110 clones in silico for the individual NA12878 and simulated the pooling and sequencing process. Ultimately, 99.9% of variants on chromosome 1 that were covered by clones from both parental chromosomes were recovered correctly, and 112 haplotype contigs were assembled with an N50 length of 3.4 Mb and no switch errors. A comparison with current clone-based haplotyping methods indicated our method was more accurate. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

SPARSE: quadratic time simultaneous alignment and folding of RNAs without sequence-based heuristics.

Science.gov (United States)

Will, Sebastian; Otto, Christina; Miladi, Milad; Möhl, Mathias; Backofen, Rolf

2015-08-01

RNA-Seq experiments have revealed a multitude of novel ncRNAs. The gold standard for their analysis based on simultaneous alignment and folding suffers from extreme time complexity of [Formula: see text]. Subsequently, numerous faster 'Sankoff-style' approaches have been suggested. Commonly, the performance of such methods relies on sequence-based heuristics that restrict the search space to optimal or near-optimal sequence alignments; however, the accuracy of sequence-based methods breaks down for RNAs with sequence identities below 60%. Alignment approaches like LocARNA that do not require sequence-based heuristics, have been limited to high complexity ([Formula: see text] quartic time). Breaking this barrier, we introduce the novel Sankoff-style algorithm 'sparsified prediction and alignment of RNAs based on their structure ensembles (SPARSE)', which runs in quadratic time without sequence-based heuristics. To achieve this low complexity, on par with sequence alignment algorithms, SPARSE features strong sparsification based on structural properties of the RNA ensembles. Following PMcomp, SPARSE gains further speed-up from lightweight energy computation. Although all existing lightweight Sankoff-style methods restrict Sankoff's original model by disallowing loop deletions and insertions, SPARSE transfers the Sankoff algorithm to the lightweight energy model completely for the first time. Compared with LocARNA, SPARSE achieves similar alignment and better folding quality in significantly less time (speedup: 3.7). At similar run-time, it aligns low sequence identity instances substantially more accurate than RAF, which uses sequence-based heuristics. © The Author 2015. Published by Oxford University Press.

SNBRFinder: A Sequence-Based Hybrid Algorithm for Enhanced Prediction of Nucleic Acid-Binding Residues.

Directory of Open Access Journals (Sweden)

Xiaoxia Yang

Full Text Available Protein-nucleic acid interactions are central to various fundamental biological processes. Automated methods capable of reliably identifying DNA- and RNA-binding residues in protein sequence are assuming ever-increasing importance. The majority of current algorithms rely on feature-based prediction, but their accuracy remains to be further improved. Here we propose a sequence-based hybrid algorithm SNBRFinder (Sequence-based Nucleic acid-Binding Residue Finder by merging a feature predictor SNBRFinderF and a template predictor SNBRFinderT. SNBRFinderF was established using the support vector machine whose inputs include sequence profile and other complementary sequence descriptors, while SNBRFinderT was implemented with the sequence alignment algorithm based on profile hidden Markov models to capture the weakly homologous template of query sequence. Experimental results show that SNBRFinderF was clearly superior to the commonly used sequence profile-based predictor and SNBRFinderT can achieve comparable performance to the structure-based template methods. Leveraging the complementary relationship between these two predictors, SNBRFinder reasonably improved the performance of both DNA- and RNA-binding residue predictions. More importantly, the sequence-based hybrid prediction reached competitive performance relative to our previous structure-based counterpart. Our extensive and stringent comparisons show that SNBRFinder has obvious advantages over the existing sequence-based prediction algorithms. The value of our algorithm is highlighted by establishing an easy-to-use web server that is freely accessible at http://ibi.hzau.edu.cn/SNBRFinder.

SNBRFinder: A Sequence-Based Hybrid Algorithm for Enhanced Prediction of Nucleic Acid-Binding Residues.

Science.gov (United States)

Yang, Xiaoxia; Wang, Jia; Sun, Jun; Liu, Rong

2015-01-01

Protein-nucleic acid interactions are central to various fundamental biological processes. Automated methods capable of reliably identifying DNA- and RNA-binding residues in protein sequence are assuming ever-increasing importance. The majority of current algorithms rely on feature-based prediction, but their accuracy remains to be further improved. Here we propose a sequence-based hybrid algorithm SNBRFinder (Sequence-based Nucleic acid-Binding Residue Finder) by merging a feature predictor SNBRFinderF and a template predictor SNBRFinderT. SNBRFinderF was established using the support vector machine whose inputs include sequence profile and other complementary sequence descriptors, while SNBRFinderT was implemented with the sequence alignment algorithm based on profile hidden Markov models to capture the weakly homologous template of query sequence. Experimental results show that SNBRFinderF was clearly superior to the commonly used sequence profile-based predictor and SNBRFinderT can achieve comparable performance to the structure-based template methods. Leveraging the complementary relationship between these two predictors, SNBRFinder reasonably improved the performance of both DNA- and RNA-binding residue predictions. More importantly, the sequence-based hybrid prediction reached competitive performance relative to our previous structure-based counterpart. Our extensive and stringent comparisons show that SNBRFinder has obvious advantages over the existing sequence-based prediction algorithms. The value of our algorithm is highlighted by establishing an easy-to-use web server that is freely accessible at http://ibi.hzau.edu.cn/SNBRFinder.

Crash sequence based risk matrix for motorcycle crashes.

Science.gov (United States)

Wu, Kun-Feng; Sasidharan, Lekshmi; Thor, Craig P; Chen, Sheng-Yin

2018-04-05

Considerable research has been conducted related to motorcycle and other powered-two-wheeler (PTW) crashes; however, it always has been controversial among practitioners concerning with types of crashes should be first targeted and how to prioritize resources for the implementation of mitigating actions. Therefore, there is a need to identify types of motorcycle crashes that constitute the greatest safety risk to riders - most frequent and most severe crashes. This pilot study seeks exhibit the efficacy of a new approach for prioritizing PTW crash causation sequences as they relate to injury severity to better inform the application of mitigating countermeasures. To accomplish this, the present study constructed a crash sequence-based risk matrix to identify most frequent and most severe motorcycle crashes in an attempt to better connect causes and countermeasures of PTW crashes. Although the frequency of each crash sequence can be computed from crash data, a crash severity model is needed to compare the levels of crash severity among different crash sequences, while controlling for other factors that also have effects on crash severity such drivers' age, use of helmet, etc. The construction of risk matrix based on crash sequences involve two tasks: formulation of crash sequence and the estimation of a mixed-effects (ME) model to adjust the levels of severities for each crash sequence to account for other crash contributing factors that would have an effect on the maximum level of crash severity in a crash. Three data elements from the National Automotive Sampling System - General Estimating System (NASS-GES) data were utilized to form a crash sequence: critical event, crash types, and sequence of events. A mixed-effects model was constructed to model the severity levels for each crash sequence while accounting for the effects of those crash contributing factors on crash severity. A total of 8039 crashes involving 8208 motorcycles occurred during 2011 and 2013 were

SPARSE: quadratic time simultaneous alignment and folding of RNAs without sequence-based heuristics

Science.gov (United States)

Will, Sebastian; Otto, Christina; Miladi, Milad; Möhl, Mathias; Backofen, Rolf

2015-01-01

Motivation: RNA-Seq experiments have revealed a multitude of novel ncRNAs. The gold standard for their analysis based on simultaneous alignment and folding suffers from extreme time complexity of O(n6). Subsequently, numerous faster ‘Sankoff-style’ approaches have been suggested. Commonly, the performance of such methods relies on sequence-based heuristics that restrict the search space to optimal or near-optimal sequence alignments; however, the accuracy of sequence-based methods breaks down for RNAs with sequence identities below 60%. Alignment approaches like LocARNA that do not require sequence-based heuristics, have been limited to high complexity (≥ quartic time). Results: Breaking this barrier, we introduce the novel Sankoff-style algorithm ‘sparsified prediction and alignment of RNAs based on their structure ensembles (SPARSE)’, which runs in quadratic time without sequence-based heuristics. To achieve this low complexity, on par with sequence alignment algorithms, SPARSE features strong sparsification based on structural properties of the RNA ensembles. Following PMcomp, SPARSE gains further speed-up from lightweight energy computation. Although all existing lightweight Sankoff-style methods restrict Sankoff’s original model by disallowing loop deletions and insertions, SPARSE transfers the Sankoff algorithm to the lightweight energy model completely for the first time. Compared with LocARNA, SPARSE achieves similar alignment and better folding quality in significantly less time (speedup: 3.7). At similar run-time, it aligns low sequence identity instances substantially more accurate than RAF, which uses sequence-based heuristics. Availability and implementation: SPARSE is freely available at http://www.bioinf.uni-freiburg.de/Software/SPARSE. Contact: backofen@informatik.uni-freiburg.de Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25838465

Devonian and Lower Carboniferous Conodonts of the Cantabrian Mountains (Spain) and their stratigraphic application

NARCIS (Netherlands)

Adrichem Boogaert, van H.A.

1967-01-01

A short review of the literature on the stratigraphy of the Devonian and the Lower Carboniferous of the Cantabrian Mountains precedes the report of the author's stratigraphic and palaeontologic observations in León: the Río Esla area (Gedinnian to Viséan), the central Cantabrian area (Famennian to

SEQUENCE STRATIGRAPHIC ANALYSIS AND FACIES ARCHITECTURE OF THE CRETACEOUS MANCOS SHALE ON AND NEAR THE JICARILLA APACHE INDIAN RESERVATION, NEW MEXICO-THEIR RELATION TO SITES OF OIL ACCUMULATION

International Nuclear Information System (INIS)

Jennie Ridgley

2000-01-01

Oil distribution in the lower part of the Mancos Shale seems to be mainly controlled by fractures and by sandier facies that are dolomite-cemented. Structure in the area of the Jicarilla Apache Indian Reservation consists of the broad northwest- to southeast-trending Chaco slope, the deep central basin, and the monocline that forms the eastern boundary of the San Juan Basin. Superimposed on the regional structure are broad low-amplitude folds. Fractures seem best developed in the areas of these folds. Using sequence stratigraphic principals, the lower part of the Mancos Shale has been subdivided into four main regressive and transgressive components. These include facies that are the basinal time equivalents to the Gallup Sandstone, an overlying interbedded sandstone and shale sequence time equivalent to the transgressive Mulatto Tongue of the Mancos Shale, the El Vado Sandstone Member which is time equivalent to part of the Dalton Sandstone, and an unnamed interbedded sandstone and shale succession time equivalent to the regressive Dalton Sandstone and transgressive Hosta Tongue of the Mesaverde Group. Facies time equivalent to the Gallup Sandstone underlie an unconformity of regional extent. These facies are gradually truncated from south to north across the Reservation. The best potential for additional oil resources in these facies is in the southern part of the Reservation where the top sandier part of these facies is preserved. The overlying unnamed wedge of transgressive rocks produces some oil but is underexplored, except for sandstones equivalent to the Tocito Sandstone. This wedge of rocks is divided into from two to five units. The highest sand content in this wedge occurs where each of the four subdivisions above the Tocito terminates to the south and is overstepped by the next youngest unit. These terminal areas should offer the best targets for future oil exploration. The El Vado Sandstone Member overlies the transgressive wedge. It produces most of

ABI Base Recall: Automatic Correction and Ends Trimming of DNA Sequences.

Science.gov (United States)

Elyazghi, Zakaria; Yazouli, Loubna El; Sadki, Khalid; Radouani, Fouzia

2017-12-01

Automated DNA sequencers produce chromatogram files in ABI format. When viewing chromatograms, some ambiguities are shown at various sites along the DNA sequences, because the program implemented in the sequencing machine and used to call bases cannot always precisely determine the right nucleotide, especially when it is represented by either a broad peak or a set of overlaying peaks. In such cases, a letter other than A, C, G, or T is recorded, most commonly N. Thus, DNA sequencing chromatograms need manual examination: checking for mis-calls and truncating the sequence when errors become too frequent. The purpose of this paper is to develop a program allowing the automatic correction of these ambiguities. This application is a Web-based program powered by Shiny and runs under R platform for an easy exploitation. As a part of the interface, we added the automatic ends clipping option, alignment against reference sequences, and BLAST. To develop and test our tool, we collected several bacterial DNA sequences from different laboratories within Institut Pasteur du Maroc and performed both manual and automatic correction. The comparison between the two methods was carried out. As a result, we note that our program, ABI base recall, accomplishes good correction with a high accuracy. Indeed, it increases the rate of identity and coverage and minimizes the number of mismatches and gaps, hence it provides solution to sequencing ambiguities and saves biologists' time and labor.

Depositional setting analysis using seismic sedimentology: Example from the Paleogene Lishagang sequence in the Fushan depression, South China Sea

Directory of Open Access Journals (Sweden)

Yuan Li

2017-09-01

Full Text Available The Fushan depression is a classic lacustrine rifted sub-basin in the Beibuwan Basin, South China Sea. The Paleogene Liushagang sequence is the main hydrocarbon-bearing stratigraphic unit in the depression. Using three-dimensional (3-D seismic data and logging data, we analyzed depositional setting of the Liushagang sequence. We use wave impedance inversion to describe progradational directions of provenance and the general distribution of sand body. The seismic facies was analyzed by using the seismic sedimentology approach based on 3-D seismic data, and summed into eight types of seismic facies which could be well related to sedimentary facies. Seismic attributes with six objective sequence boundaries were extracted. Consequently, four provenance system of Liushagang sequence in the study area were confirmed by the corresponding relationship between the geologic information and the warm color and higher value area of seismic attributes: (i the Hainan uplift provenance area in the south, (ii the Linggao uplift provenance area in the west, (iii the Yunlong uplift provenance area in the east and (iv the northern provenance area. The seismic sedimentology used in this study may provide new insights into a better understanding of depositional setting in continental lacustrine rifted basins.

A priori Considerations When Conducting High-Throughput Amplicon-Based Sequence Analysis

Directory of Open Access Journals (Sweden)

Aditi Sengupta

2016-03-01

Full Text Available Amplicon-based sequencing strategies that include 16S rRNA and functional genes, alongside “meta-omics” analyses of communities of microorganisms, have allowed researchers to pose questions and find answers to “who” is present in the environment and “what” they are doing. Next-generation sequencing approaches that aid microbial ecology studies of agricultural systems are fast gaining popularity among agronomy, crop, soil, and environmental science researchers. Given the rapid development of these high-throughput sequencing techniques, researchers with no prior experience will desire information about the best practices that can be used before actually starting high-throughput amplicon-based sequence analyses. We have outlined items that need to be carefully considered in experimental design, sampling, basic bioinformatics, sequencing of mock communities and negative controls, acquisition of metadata, and in standardization of reaction conditions as per experimental requirements. Not all considerations mentioned here may pertain to a particular study. The overall goal is to inform researchers about considerations that must be taken into account when conducting high-throughput microbial DNA sequencing and sequences analysis.

Sequencing-based breast cancer diagnostics as an alternative to routine biomarkers.

Science.gov (United States)

Rantalainen, Mattias; Klevebring, Daniel; Lindberg, Johan; Ivansson, Emma; Rosin, Gustaf; Kis, Lorand; Celebioglu, Fuat; Fredriksson, Irma; Czene, Kamila; Frisell, Jan; Hartman, Johan; Bergh, Jonas; Grönberg, Henrik

2016-11-30

Sequencing-based breast cancer diagnostics have the potential to replace routine biomarkers and provide molecular characterization that enable personalized precision medicine. Here we investigate the concordance between sequencing-based and routine diagnostic biomarkers and to what extent tumor sequencing contributes clinically actionable information. We applied DNA- and RNA-sequencing to characterize tumors from 307 breast cancer patients with replication in up to 739 patients. We developed models to predict status of routine biomarkers (ER, HER2,Ki-67, histological grade) from sequencing data. Non-routine biomarkers, including mutations in BRCA1, BRCA2 and ERBB2(HER2), and additional clinically actionable somatic alterations were also investigated. Concordance with routine diagnostic biomarkers was high for ER status (AUC = 0.95;AUC(replication) = 0.97) and HER2 status (AUC = 0.97;AUC(replication) = 0.92). The transcriptomic grade model enabled classification of histological grade 1 and histological grade 3 tumors with high accuracy (AUC = 0.98;AUC(replication) = 0.94). Clinically actionable mutations in BRCA1, BRCA2 and ERBB2(HER2) were detected in 5.5% of patients, while 53% had genomic alterations matching ongoing or concluded breast cancer studies. Sequencing-based molecular profiling can be applied as an alternative to histopathology to determine ER and HER2 status, in addition to providing improved tumor grading and clinically actionable mutations and molecular subtypes. Our results suggest that sequencing-based breast cancer diagnostics in a near future can replace routine biomarkers.

Cluster-Based Multipolling Sequencing Algorithm for Collecting RFID Data in Wireless LANs

Science.gov (United States)

Choi, Woo-Yong; Chatterjee, Mainak

2015-03-01

With the growing use of RFID (Radio Frequency Identification), it is becoming important to devise ways to read RFID tags in real time. Access points (APs) of IEEE 802.11-based wireless Local Area Networks (LANs) are being integrated with RFID networks that can efficiently collect real-time RFID data. Several schemes, such as multipolling methods based on the dynamic search algorithm and random sequencing, have been proposed. However, as the number of RFID readers associated with an AP increases, it becomes difficult for the dynamic search algorithm to derive the multipolling sequence in real time. Though multipolling methods can eliminate the polling overhead, we still need to enhance the performance of the multipolling methods based on random sequencing. To that extent, we propose a real-time cluster-based multipolling sequencing algorithm that drastically eliminates more than 90% of the polling overhead, particularly so when the dynamic search algorithm fails to derive the multipolling sequence in real time.

A base composition analysis of natural patterns for the preprocessing of metagenome sequences.

Science.gov (United States)

Bonham-Carter, Oliver; Ali, Hesham; Bastola, Dhundy

2013-01-01

On the pretext that sequence reads and contigs often exhibit the same kinds of base usage that is also observed in the sequences from which they are derived, we offer a base composition analysis tool. Our tool uses these natural patterns to determine relatedness across sequence data. We introduce spectrum sets (sets of motifs) which are permutations of bacterial restriction sites and the base composition analysis framework to measure their proportional content in sequence data. We suggest that this framework will increase the efficiency during the pre-processing stages of metagenome sequencing and assembly projects. Our method is able to differentiate organisms and their reads or contigs. The framework shows how to successfully determine the relatedness between these reads or contigs by comparison of base composition. In particular, we show that two types of organismal-sequence data are fundamentally different by analyzing their spectrum set motif proportions (coverage). By the application of one of the four possible spectrum sets, encompassing all known restriction sites, we provide the evidence to claim that each set has a different ability to differentiate sequence data. Furthermore, we show that the spectrum set selection having relevance to one organism, but not to the others of the data set, will greatly improve performance of sequence differentiation even if the fragment size of the read, contig or sequence is not lengthy. We show the proof of concept of our method by its application to ten trials of two or three freshly selected sequence fragments (reads and contigs) for each experiment across the six organisms of our set. Here we describe a novel and computationally effective pre-processing step for metagenome sequencing and assembly tasks. Furthermore, our base composition method has applications in phylogeny where it can be used to infer evolutionary distances between organisms based on the notion that related organisms often have much conserved code.

MR-based attenuation correction in brain PET based on UTE sequences

Energy Technology Data Exchange (ETDEWEB)

Cabello, Jorge; Nekolla, Stephan G; Ziegler, Sibylle I [Department of Nuclear Medicine, Klinikum rechts der Isar, Technische Universität München (Germany)

2014-07-29

Attenuation correction (AC) in brain PET/MR has recently emerged as one of the challenging tasks in the PET/MR field. It has been shown that to ignore the attenuation produced by bone can lead to errors ranging from 5-30% in regions close to bone structures. Since the information provided by the MR signal is not directly related to tissue attenuation, alternative methods have to be developed. Signal from bone tissue is difficult to measure given its short transverse relaxation time (T2). Ultrashort-echo time (UTE) pulse sequences were developed to measure signal from tissues with short T2. A combination of two consecutive UTE echoes has been used in several works to measure signal from bone tissue. The first echo is able to measure signal from bone tissue in addition to soft tissue, while the second echo contains most of the soft tissue contained in the first echo but not bone. In this work we extract the attenuation information from the difference between the logarithm of two images obtained after applying two consecutive UTE pulse sequences using the mMR scanner (Siemens Healthcare). Subsequently, image processing techniques are applied to reduce the noise and extract air cavities within the head. The resulting image is converted to linear attenuation coefficients, generating what is known as µ-map, to be used during reconstruction. For comparison purposes PET/CT scans of the same patients were acquired prior to the PET/MR scan. Additional µ-maps obtained for comparison were extracted from a Dixon sequence (used in clinical routine) and an additional µ-map calculated by the scanner based on UTE pulse sequences. Preliminary quantitative results measured in the cerebellum, using the value obtained with CT-based AC as reference, show differences of 34% without AC, 13% using the Dixon-based and UTE-based provided by the scanner, and 0.8% with the AC strategy presented here.

An assembly sequence planning method based on composite algorithm

Directory of Open Access Journals (Sweden)

Enfu LIU

2016-02-01

Full Text Available To solve the combination explosion problem and the blind searching problem in assembly sequence planning of complex products, an assembly sequence planning method based on composite algorithm is proposed. In the composite algorithm, a sufficient number of feasible assembly sequences are generated using formalization reasoning algorithm as the initial population of genetic algorithm. Then fuzzy knowledge of assembly is integrated into the planning process of genetic algorithm and ant algorithm to get the accurate solution. At last, an example is conducted to verify the feasibility of composite algorithm.

Mitochondrial DNA sequence-based phylogenetic relationship ...

Indian Academy of Sciences (India)

cophaga ranges from 0.037–0.106 and 0.049–0.207 for COI and ND5 genes, respectively (tables 2 and 3). Analysis of genetic distance on the basis of sequence difference for both the mitochondrial genes shows very little genetic difference. The discrepancy in the phylogenetic trees based on individ- ual genes may be due ...

Application of genotyping-by-sequencing on semiconductor sequencing platforms: a comparison of genetic and reference-based marker ordering in barley.

Directory of Open Access Journals (Sweden)

Martin Mascher

Full Text Available The rapid development of next-generation sequencing platforms has enabled the use of sequencing for routine genotyping across a range of genetics studies and breeding applications. Genotyping-by-sequencing (GBS, a low-cost, reduced representation sequencing method, is becoming a common approach for whole-genome marker profiling in many species. With quickly developing sequencing technologies, adapting current GBS methodologies to new platforms will leverage these advancements for future studies. To test new semiconductor sequencing platforms for GBS, we genotyped a barley recombinant inbred line (RIL population. Based on a previous GBS approach, we designed bar code and adapter sets for the Ion Torrent platforms. Four sets of 24-plex libraries were constructed consisting of 94 RILs and the two parents and sequenced on two Ion platforms. In parallel, a 96-plex library of the same RILs was sequenced on the Illumina HiSeq 2000. We applied two different computational pipelines to analyze sequencing data; the reference-independent TASSEL pipeline and a reference-based pipeline using SAMtools. Sequence contigs positioned on the integrated physical and genetic map were used for read mapping and variant calling. We found high agreement in genotype calls between the different platforms and high concordance between genetic and reference-based marker order. There was, however, paucity in the number of SNP that were jointly discovered by the different pipelines indicating a strong effect of alignment and filtering parameters on SNP discovery. We show the utility of the current barley genome assembly as a framework for developing very low-cost genetic maps, facilitating high resolution genetic mapping and negating the need for developing de novo genetic maps for future studies in barley. Through demonstration of GBS on semiconductor sequencing platforms, we conclude that the GBS approach is amenable to a range of platforms and can easily be modified as new

Prehistoric floods on the Tennessee River—Assessing the use of stratigraphic records of past floods for improved flood-frequency analysis

Science.gov (United States)

Harden, Tessa M.; O'Connor, Jim E.

2017-06-14

Stratigraphic analysis, coupled with geochronologic techniques, indicates that a rich history of large Tennessee River floods is preserved in the Tennessee River Gorge area. Deposits of flood sediment from the 1867 peak discharge of record (460,000 cubic feet per second at Chattanooga, Tennessee) are preserved at many locations throughout the study area at sites with flood-sediment accumulation. Small exposures at two boulder overhangs reveal evidence of three to four other floods similar in size, or larger, than the 1867 flood in the last 3,000 years—one possibly as much or more than 50 percent larger. Records of floods also are preserved in stratigraphic sections at the mouth of the gorge at Williams Island and near Eaves Ferry, about 70 river miles upstream of the gorge. These stratigraphic records may extend as far back as about 9,000 years ago, giving a long history of Tennessee River floods. Although more evidence is needed to confirm these findings, a more in-depth comprehensive paleoflood study is feasible for the Tennessee River.

An efficient binomial model-based measure for sequence comparison and its application.

Science.gov (United States)

Liu, Xiaoqing; Dai, Qi; Li, Lihua; He, Zerong

2011-04-01

Sequence comparison is one of the major tasks in bioinformatics, which could serve as evidence of structural and functional conservation, as well as of evolutionary relations. There are several similarity/dissimilarity measures for sequence comparison, but challenges remains. This paper presented a binomial model-based measure to analyze biological sequences. With help of a random indicator, the occurrence of a word at any position of sequence can be regarded as a random Bernoulli variable, and the distribution of a sum of the word occurrence is well known to be a binomial one. By using a recursive formula, we computed the binomial probability of the word count and proposed a binomial model-based measure based on the relative entropy. The proposed measure was tested by extensive experiments including classification of HEV genotypes and phylogenetic analysis, and further compared with alignment-based and alignment-free measures. The results demonstrate that the proposed measure based on binomial model is more efficient.

Treinta y Tres stratigraphic terrain: ex Cuchilla Dionisio terrain. Uruguay

International Nuclear Information System (INIS)

Bossi, J.

2010-01-01

From 1998 we are discussing if the eastern area of ZCSB is an allochtonous block named TCD or if it belongs to Dom Feliciano belt with an age of 500 - 700 Ma. This crustal block is difficult to study because Laguna Merin Graben cut it in two around 4000 k m2 crustal fragments distant s more de 100 km between them. Southern block which was named T PE by Masquelín (2006) was demonstrated as allochtonous by Bossi and Gaucher (2004) destroying the Cdf model but seriously complicating the stratigraphic terminology. It is proposed to do some changes in order to profit the general agreement about allochtomy. The CDT with change by Treinta y Tres terrane; T PE become sub - terrain Punta del Este; sub - terrain Cuchilla Dionisio for the septetrional block. From 1998 we are discussing if the eastern area of ZCSB is an allochtonous block named TCD or if it belongs to Dom Feliciano belt with an age of 500 - 700 Ma. This crustal block is difficult to study because Laguna Merín Graben cut it in two around 4000 k m2 crustal fragments distant s more de 100 km between them. Southern block which was named T PE by Masquelín (2006) was demonstrated as allochtonous by Bossi and Gaucher (2004) destroying the CDF model but seriously complicating the stratigraphic terminology. It is proposed to do some changes in order to profit the general agreement about allochtomy. The CDT with change by Treinta y Tres terrain; TPE become sub - terrain Punta del Este; sub - terrain Cuchilla Dionisio for the septetrional block

Sequence stratigraphy as a scientific enterprise: the evolution and persistence of conflicting paradigms

Science.gov (United States)

Miall, Andrew D.; Miall, Charlene E.

2001-08-01

In the 1970s, seismic stratigraphy represented a new paradigm in geological thought. The development of new techniques for analyzing seismic-reflection data constituted a "crisis," as conceptualized by T.S. Kuhn, and stimulated a revolution in stratigraphy. We analyze here a specific subset of the new ideas, that pertaining to the concept of global-eustasy and the global cycle chart published by Vail et al. [Vail, P.R., Mitchum, R.M., Jr., Todd, R.G., Widmier, J.M., Thompson, S., III, Sangree, J.B., Bubb, J.N., Hatlelid, W.G., 1977. Seismic stratigraphy and global changes of sea-level. In: Payton, C.E. (Ed.), Seismic Stratigraphy—Applications to Hydrocarbon Exploration, Am. Assoc. Pet. Geol. Mem. 26, pp. 49-212.] The global-eustasy model posed two challenges to the "normal science" of stratigraphy then underway: (1) that sequence stratigraphy, as exemplified by the global cycle chart, constitutes a superior standard of geologic time to that assembled from conventional chronostratigraphic evidence, and (2) that stratigraphic processes are dominated by the effects of eustasy, to the exclusion of other allogenic mechanisms, including tectonism. While many stratigraphers now doubt the universal validity of the model of global-eustasy, what we term the global-eustasy paradigm, a group of sequence researchers led by Vail still adheres to it, and the two conceptual approaches have evolved into two conflicting paradigms. Those who assert that there are multiple processes generating stratigraphic sequences (possibly including eustatic processes) are adherents of what we term the complexity paradigm. Followers of this paradigm argue that tests of the global cycle chart amount to little more than circular reasoning. A new body of work documenting the European sequence record was published in 1998 by de Graciansky et al. These workers largely follow the global-eustasy paradigm. Citation and textual analysis of this work indicates that they have not responded to any of the

Morphodynamics and stratigraphic architecture of shelf-edge deltas subject to constant vs. dynamic environmental forcings

Science.gov (United States)

Straub, K. M.

2017-12-01

When deltas dock at the edge of continental margins they generally construct thick stratigraphic intervals and activate channelized continental slope systems. Deposits of shelf-edge deltas have the capacity to store detailed paleo-environmental records, given their location in the source to sink system. However, present day highstand sea-level conditions have pushed most deltaic systems well inbound of their shelf-edges, making it difficult to study their space-time dynamics and resulting stratigraphic products. Several competing theories describe how deltas and their downslope environments respond to sea-level cycles of varying magnitude and periodicity. We explore these hypotheses in a physical experiment where the topographic evolution of a coupled delta and downdip slope system was monitored at high temporal and spatial resolution. The experiment had three stages. In the first stage a delta aggraded at the shelf-edge under constant water and sediment supply, in addition to a constant generation of accommodation through a sea-level rise. In the second stage the sediment transport system responded to low magnitude and high frequency sea-level cycles. Finally, in the third stage the transport system responded to a high magnitude and long period sea-level cycle. In each stage, fine sediment from the input grain size distribution and dissolved salt in the input water supply promoted plunging hyperpycnal flows. Specifically, we compare the mean and temporal variability of the sediment delivered to the slope system between stages. In addition, we compare stratigraphic architecture and sediment sizes delivered to the slope system in each stage. These results are used to improve inversion of slope deposits for paleo-environmental forcings.

Using Outcrop Exposures on the Road to Yellowknife Bay to Build a Stratigraphic Column, Gale Crater, Mars

Science.gov (United States)

Stack, K. M.; Grotzinger, J. P.; Sumner, D.; Ehlmann, B. L.; Milliken, R. E.; Eigenbrode, J. L.; Gupta, S.; Williams, R. M. E.; Kah, L. C.; Lewis, K. W.

2013-01-01

Since landing in Gale Crater on August 5, 2012, the Curiosity rover has driven 450 m east, descending approximately 15 m in elevation from the Bradbury landing site to Yellowknife Bay. Outcrop exposure along this drive has been discontinuous, but isolated outcrops may represent windows into underlying inplace stratigraphy. This study presents an inventory of outcrops targeted by Curiosity (Figs. 1-2), grouped by lithological properties observed in Mastcam and Navcam imagery. Outcrop locations are placed in a stratigraphic context using orbital imagery and first principles of stratigraphy. The stratigraphic models presented here represent an essential first step in understanding the relative age relationships of lithological units encountered at the Curiosity landing site. Such observations will provide crucial context for assessing habitability potential of ancient Gale crater environments and organic matter preservation.

LookSeq: A browser-based viewer for deep sequencing data

OpenAIRE

Manske, Heinrich Magnus; Kwiatkowski, Dominic P.

2009-01-01

Sequencing a genome to great depth can be highly informative about heterogeneity within an individual or a population. Here we address the problem of how to visualize the multiple layers of information contained in deep sequencing data. We propose an interactive AJAX-based web viewer for browsing large data sets of aligned sequence reads. By enabling seamless browsing and fast zooming, the LookSeq program assists the user to assimilate information at different levels of resolution, from an ov...

Transitions in Lava Emplacement Recorded in the Deccan Traps Sequence (India)

Science.gov (United States)

Vanderkluysen, L.; Self, S.; Jay, A. E.; Sheth, H. C.; Clarke, A. B.

2015-12-01

Transitions in the style of lava flow emplacement are recognized in the stratigraphic sequence of several mafic large igneous provinces (LIPs), including the Etendeka (Namibia), the Faeroe Islands (North Atlantic LIP), the Ethiopian Traps, and the Deccan Traps (India). These transitions, from units dominated by meter-sized pāhoehoe toes and lobes to those dominated by inflated sheet lobes tens to hundreds of meters in width and meters to tens of meters in height, seems to be a fundamental feature of LIP emplacement. In the Deccan, this volcanological transition is thought to coincide with deeper changes to the volcano-magmatic system expressed, notably, in the trace element and isotopic signature of erupted flows. We investigated this transition in the Deccan Traps by logging eight sequences along the Western Ghats, an escarpment in western India where the Deccan province is thickest and best exposed. The Deccan province, which once covered ~1 million km2 of west-central India, is subdivided in eleven chemo-stratigraphic formations in the type sections of the Western Ghats. Where the lower Deccan formations are exposed, we found that as much as 65% of the exposed thickness (below the Khandala Formation) is made up of sheet lobes, from 40% in the Bhimashankar Formation to 75% in the Thakurvadi Formation. Near the bottom of the sequence, 25% of the Neral Formation is composed of sheet lobes ≥15 m in thickness. On this basis, the traditional view that inflated sheet lobes are an exclusive feature of the upper part of the stratigraphy must be challenged. Several mechanisms have been proposed to explain the development of compound flows and inflated sheet lobes, involving one or more of the following factors: underlying slope, varying effusion rate, and source geometry. Analogue experiments are currently under way to test the relative influence of each of these factors in the development of different lava flow morphologies in LIPs.

Hydrodynamism, crude oil distribution and geochemistry of the stratigraphic column in a transect of the Eastern Venezuelan Basin

Energy Technology Data Exchange (ETDEWEB)

Gallango, O.; Escandon, M.; Alberdi, M. (Intevep, S.A. Caracas (Venezuela)); Parnaud, F.; Pascual, J.C. (Beicip, Rueil Malmaison (France))

1992-01-01

The hydrocarbon accumulation history in a transect of the Eastern Venezuelan Basin is closely related to the generation and migration process as a consequence of the stratigraphic, structural and tectonic evolution of the basin during the Cretaceous and Cenozoic times. Thermal maturity assessment based on kinetic parameters using the appropriate software indicates that the generation of oil from the marine facies of the Querecual and San Antonio source rocks in the northern part of the basin took place during early Paleocene to early Miocene times prior to the start of thrusting, while the second and third phase occurred during middle Miocene to recent times in zones beneath the principal thrust in the Maturing area. The third phase of oil generation is associated with the latter thrusts which are out of sequence. Taking into consideration the development of the oil and gas kitchen through time, the hydrodynamism, the characteristics and distribution of the hydrocarbons, the migration of oil and gas have been outlined. The major differences observed among the oils, are due to maturity and post-accumulation processes such as oil mixing and biodegradation. A wide range of thermal maturity was observed in the oils, which is mainly due to the thermal stress experienced by the source rock. Association of light crudes with meteoric waters have been observed, as well as heavy to extra-heavy crudes with connate waters at greater depth. These unusual associations of crudes and formation waters are related to the hydrodynamical regime in the basin.

Spatio-temporal variation in groundwater head affected by stratigraphic heterogeneity of the alluvial aquifer in Northwest India

Science.gov (United States)

van Dijk, W. M.; Joshi, S. K.; Densmore, A. L.; Jackson, C. R.; Sutanudjaja, E.; Lafare, A. E. A.; Gupta, S.; Mackay, J. D.; Mason, P. J.; Sinha, R.

2017-12-01

Groundwater is a primary source of freshwater in the alluvial aquifer system of northwestern India. Unsustainable exploitation of the groundwater resources has led to a regional hotspot in groundwater depletion. Rapid groundwater-level decline shows spatial variation, as the effects of various stresses, including precipitation, potential evapotranspiration and abstraction, are likely to be influenced by the stratigraphic and geomorphic heterogeneity between sediment fan and interfan areas (see Geomorphological map in Figure A). We used a transfer function-noise (TFN) time series approach to quantify the effect of the various stress components in the period 1974-2010, based on predefined impulse response functions (IRFs) of von Asmuth et al. (2008). The objective of this study was 1) to acquire the impulse response function of various stresses, 2) assess the spatial estimation parameter (the zeroth moment, M0) of the spatial development of the groundwater head and 3) relate the spatial M0 to the observed stratigraphic and geomorphic heterogeneity. We collected information on the groundwater head pre- and post-monsoon, the district-wise monthly precipitation and potential evapotranspiration, and we modeled the monthly abstraction rate using land-use information. The TFN identified the IRF of precipitation as well as abstraction. The IRF, summarized in the parameter M0, identified a hotspot for the abstraction stress (see M0 spatial map for abstraction in Figure B) at the margins of the Sutlej and Yamuna fans. No hotspot is observed for the precipitation stress, but the M0 for precipitation increases with distance from the Himalayan front. At larger distances from the Himalayan front, observed groundwater head rises cannot be explained by the IRFs for the abstraction and precipitation stresses. This is likely because the current TFN models do not account for other stresses, such as recharge by canal leakage, which are locally important. We conclude that the spatial

Stratigraphic distribution, taphonomy and paleoenvironments of Spinicaudata in the Triassic and Jurassic of the Paraná Basin

Science.gov (United States)

Jenisch, Alan Gregory; Lehn, Ilana; Gallego, Oscar Florencio; Monferran, Mateo Daniel; Horodyski, Rodrigo Scalise; Faccini, Ubiratan Ferrucio

2017-12-01

Due to the chitino-phosphatic nature of Spinicaudata conchostracan exoskeletons, their carapaces exhibit a low preservational potential compared to other bivalve groups. However, the recent studies point towards the increased tolerance of the carapace against the physical processes. Due to this peculiar characteristic, conchostracan carapace have been utilized as precise temporal markers in estimating stratigraphic and taphonomic parameters. The same characteristic also makes the spinicaudatans useful in evaluating the depositional processes and environments. The present work aims at providing a paleoenvironmental and stratigraphic analysis of conchostracans (Spinicaudata) from the Triassic-Jurassic of the Paraná Basin (Santa Maria and Caturrita formations) in terms of the sedimentary facies analysis, depositional system characterization, and analysis of the taphonomic signatures of the fossiliferous horizons within these formations. The results from the taphonomic study delineates the presence of 4 distinct fossil assemblages based on the causative mechanism and fundamental characteristics of the fossil concentrations: two taphonomic assemblages in the laminated mudstone beds deposited from the decanting fine-grained sediments in floodplains; the sandstone beds with plane parallel laminations and dune- and ripple-cross-stratifications deposited from the flooding-related overflow in the floodplains; and the association of laminated mudstone and massive sandstone beds deposited as the river mouth bars. The results show that the taphonomic signatures, e.g., closed valves, may indicate the various patterns of autochthony and allochthony. In the fine-grained floodplain assemblages, the high degree of preservation can be attributed to autochthony in the conchostracans, whereas the preservational condition of floodplain sandstone sheet and mouth bar assemblages point toward parautochthony and even allochthony. Therefore, the preservational quality of conchostracan

Study design requirements for RNA sequencing-based breast cancer diagnostics.

Science.gov (United States)

Mer, Arvind Singh; Klevebring, Daniel; Grönberg, Henrik; Rantalainen, Mattias

2016-02-01

Sequencing-based molecular characterization of tumors provides information required for individualized cancer treatment. There are well-defined molecular subtypes of breast cancer that provide improved prognostication compared to routine biomarkers. However, molecular subtyping is not yet implemented in routine breast cancer care. Clinical translation is dependent on subtype prediction models providing high sensitivity and specificity. In this study we evaluate sample size and RNA-sequencing read requirements for breast cancer subtyping to facilitate rational design of translational studies. We applied subsampling to ascertain the effect of training sample size and the number of RNA sequencing reads on classification accuracy of molecular subtype and routine biomarker prediction models (unsupervised and supervised). Subtype classification accuracy improved with increasing sample size up to N = 750 (accuracy = 0.93), although with a modest improvement beyond N = 350 (accuracy = 0.92). Prediction of routine biomarkers achieved accuracy of 0.94 (ER) and 0.92 (Her2) at N = 200. Subtype classification improved with RNA-sequencing library size up to 5 million reads. Development of molecular subtyping models for cancer diagnostics requires well-designed studies. Sample size and the number of RNA sequencing reads directly influence accuracy of molecular subtyping. Results in this study provide key information for rational design of translational studies aiming to bring sequencing-based diagnostics to the clinic.

Autonomously generating operations sequences for a Mars Rover using AI-based planning

Science.gov (United States)

Sherwood, Rob; Mishkin, Andrew; Estlin, Tara; Chien, Steve; Backes, Paul; Cooper, Brian; Maxwell, Scott; Rabideau, Gregg

2001-01-01

This paper discusses a proof-of-concept prototype for ground-based automatic generation of validated rover command sequences from highlevel science and engineering activities. This prototype is based on ASPEN, the Automated Scheduling and Planning Environment. This Artificial Intelligence (AI) based planning and scheduling system will automatically generate a command sequence that will execute within resource constraints and satisfy flight rules.

The necessity and application of stratigraphic borings in hydrogeologic site assessments

International Nuclear Information System (INIS)

Sciacca, J.

1991-01-01

The siting and placement of monitoring wells is one of the most critical elements in hydrogeologic assessments of contaminated sites. Monitoring wells are placed to collect hydraulic and chemical concentration data to: (1) determine potential groundwater flow paths and rates: (2) analyze the nature and extent of chemical constituents in groundwater; and (3) estimate contaminant fate and transport. In many instances monitoring wells provide inappropriate or erroneous hydraulic data, do not provide coverage of potential high permeability flow pathways (such as channel sands) or may themselves create (through improper construction) a vertical conduit for contaminant flow from low permeability to high permeability units. This problem is commonly due to installing monitoring wells before conducting essential stratigraphic analysis and formulating a depositional model for the site area. This paper presents case examples where stratigraphic borings were drilled and logged in the vicinity of proposed well locations to effectively design and install the monitoring well network. The borings were continuously sampled or geophysically logged to provide a vertical profile of the borehole. In addition, the geophysical logs provided curve signatures which allowed interpretation of depositional facies. These data were used to interpret subsurface stratigraphy and effectively position monitoring wells that achieve the above objectives and prevent problems associated with faulty well positioning. This method may cost more initially. However, these initial costs are cheaper than long-term project expenses for abandoning improperly completed wells. subsequently installing supplemental monitoring wells or modifying poorly designed treatment systems which resulted from improper or insufficient data generated from the initial monitoring network

SUGAR: graphical user interface-based data refiner for high-throughput DNA sequencing.

Science.gov (United States)

Sato, Yukuto; Kojima, Kaname; Nariai, Naoki; Yamaguchi-Kabata, Yumi; Kawai, Yosuke; Takahashi, Mamoru; Mimori, Takahiro; Nagasaki, Masao

2014-08-08

Next-generation sequencers (NGSs) have become one of the main tools for current biology. To obtain useful insights from the NGS data, it is essential to control low-quality portions of the data affected by technical errors such as air bubbles in sequencing fluidics. We develop a software SUGAR (subtile-based GUI-assisted refiner) which can handle ultra-high-throughput data with user-friendly graphical user interface (GUI) and interactive analysis capability. The SUGAR generates high-resolution quality heatmaps of the flowcell, enabling users to find possible signals of technical errors during the sequencing. The sequencing data generated from the error-affected regions of a flowcell can be selectively removed by automated analysis or GUI-assisted operations implemented in the SUGAR. The automated data-cleaning function based on sequence read quality (Phred) scores was applied to a public whole human genome sequencing data and we proved the overall mapping quality was improved. The detailed data evaluation and cleaning enabled by SUGAR would reduce technical problems in sequence read mapping, improving subsequent variant analysis that require high-quality sequence data and mapping results. Therefore, the software will be especially useful to control the quality of variant calls to the low population cells, e.g., cancers, in a sample with technical errors of sequencing procedures.

Radioisotope investigations on the stratigraphic distribution of poly/methyl methacrylate/grafted onto leather

International Nuclear Information System (INIS)

Pietrucha, K.; Kroh, J.

1984-01-01

Investigations on the stratigraphic distribution of poly/methyl methacrylate/ in leather follow our earlier experiments on radiation grafting of vinyl monomers in situ. Polymer distribution was determined for pigskins and cattlehides tanned with basic sulphates of chromium/III/. 14 C-labelled methyl methacrylate was used in present experiments. Precision slicing technique was employed to cut consecutive slices parallel to the grain surface of the radiation modified leather. Quantative analysis of polymer distribution in leather was based on radioactivity measurements. Each layer was burned in Oxymat apparatus and resulting 14 CO 2 was analysed by liquid scintillation method. On the basis of radioactivity measurements and visual observations with light microscope conclusion on desirable distribution of polymer was reached. In the midcorium part of leather polymer is evenly distributed and its content is much higher than for outer layers next to surface and flesh. Mechanism of relevant processes as well as formation and role played by peroxide compounds is discussed

Radioisotope investigations on the stratigraphic distribution of poly(methyl methacrylate) grafted onto leather

International Nuclear Information System (INIS)

Pietrucha, K.; Kroh, J.

1985-01-01

Investigations on the stratigraphic distribution of poly(methyl methacrylate) in leather follow our earlier experiments on radiation grafting of vinyl monomers in situ. Polymer distribution was determined for pigskins and cattlehides tanned with basic sulphates of chromium (III). 14 C-labelled methyl methacrylate was used in present experiments. Precision slicing technique was employed to cut consecutive slices parallel to the grain surface of the radiation modified leather. Quantitative analysis of polymer distribution in leather was based on radioactivity measurements. Each layer was burned in Oxymat apparatus and resulting 14 CO 2 was analysed by liquid scintillation method. On the basis of radioactivity measurements and visual observations with light microscope conclusion on desirable distribution of polymer was reached. In the midcorium part of leather polymer is evenly distributed and its content is much higher than for outer layers next to surface and flesh. Mechanism of relevant processes as well as formation and role played by peroxide compounds are discussed. (author)

Elman RNN based classification of proteins sequences on account of their mutual information.

Science.gov (United States)

Mishra, Pooja; Nath Pandey, Paras

2012-10-21

In the present work we have employed the method of estimating residue correlation within the protein sequences, by using the mutual information (MI) of adjacent residues, based on structural and solvent accessibility properties of amino acids. The long range correlation between nonadjacent residues is improved by constructing a mutual information vector (MIV) for a single protein sequence, like this each protein sequence is associated with its corresponding MIVs. These MIVs are given to Elman RNN to obtain the classification of protein sequences. The modeling power of MIV was shown to be significantly better, giving a new approach towards alignment free classification of protein sequences. We also conclude that sequence structural and solvent accessible property based MIVs are better predictor. Copyright © 2012 Elsevier Ltd. All rights reserved.

Speeding disease gene discovery by sequence based candidate prioritization

Directory of Open Access Journals (Sweden)

Porteous David J

2005-03-01

Full Text Available Abstract Background Regions of interest identified through genetic linkage studies regularly exceed 30 centimorgans in size and can contain hundreds of genes. Traditionally this number is reduced by matching functional annotation to knowledge of the disease or phenotype in question. However, here we show that disease genes share patterns of sequence-based features that can provide a good basis for automatic prioritization of candidates by machine learning. Results We examined a variety of sequence-based features and found that for many of them there are significant differences between the sets of genes known to be involved in human hereditary disease and those not known to be involved in disease. We have created an automatic classifier called PROSPECTR based on those features using the alternating decision tree algorithm which ranks genes in the order of likelihood of involvement in disease. On average, PROSPECTR enriches lists for disease genes two-fold 77% of the time, five-fold 37% of the time and twenty-fold 11% of the time. Conclusion PROSPECTR is a simple and effective way to identify genes involved in Mendelian and oligogenic disorders. It performs markedly better than the single existing sequence-based classifier on novel data. PROSPECTR could save investigators looking at large regions of interest time and effort by prioritizing positional candidate genes for mutation detection and case-control association studies.

HLA class I sequence-based typing using DNA recovered from frozen plasma.

Science.gov (United States)

Cotton, Laura A; Abdur Rahman, Manal; Ng, Carmond; Le, Anh Q; Milloy, M-J; Mo, Theresa; Brumme, Zabrina L

2012-08-31

We describe a rapid, reliable and cost-effective method for intermediate-to-high-resolution sequence-based HLA class I typing using frozen plasma as a source of genomic DNA. The plasma samples investigated had a median age of 8.5 years. Total nucleic acids were isolated from matched frozen PBMC (~2.5 million) and plasma (500 μl) samples from a panel of 25 individuals using commercial silica-based kits. Extractions yielded median [IQR] nucleic acid concentrations of 85.7 [47.0-130.0]ng/μl and 2.2 [1.7-2.6]ng/μl from PBMC and plasma, respectively. Following extraction, ~1000 base pair regions spanning exons 2 and 3 of HLA-A, -B and -C were amplified independently via nested PCR using universal, locus-specific primers and sequenced directly. Chromatogram analysis was performed using commercial DNA sequence analysis software and allele interpretation was performed using a free web-based tool. HLA-A, -B and -C amplification rates were 100% and chromatograms were of uniformly high quality with clearly distinguishable mixed bases regardless of DNA source. Concordance between PBMC and plasma-derived HLA types was 100% at the allele and protein levels. At the nucleotide level, a single partially discordant base (resulting from a failure to call both peaks in a mixed base) was observed out of >46,975 bases sequenced (>99.9% concordance). This protocol has previously been used to perform HLA class I typing from a variety of genomic DNA sources including PBMC, whole blood, granulocyte pellets and serum, from specimens up to 30 years old. This method provides comparable specificity to conventional sequence-based approaches and could be applied in situations where cell samples are unavailable or DNA quantities are limiting. Copyright © 2012 Elsevier B.V. All rights reserved.

Complex programmable logic device based alarm sequencer for nuclear power plants

International Nuclear Information System (INIS)

Khedkar, Ravindra; Solomon, J. Selva; KrishnaKumar, B.

2001-01-01

Complex Programmable Logic Device based Alarm Sequencer is an instrument, which detects alarms, memorizes them and displays the sequences of occurrence of alarms. It caters to sixteen alarm signals and distinguishes the sequence among any two alarms with a time resolution of 1 ms. The system described has been designed for continuous operation in process plants, nuclear power plants etc. The system has been tested and found to be working satisfactorily. (author)

High resolution seismic stratigraphic analysis. An integrated approach to the subsurface geology of the SE Persian Gulf[Paper 2 is not open for the public

Energy Technology Data Exchange (ETDEWEB)

Farzadi, Pourdad

2006-07-01

Dariyan. The traditional surface based seismic interpretation only gives insights into variability at the top and base of this formation and not from within it. To enhance internal stratigraphic relations a multivariate seismic analysis, combined with a data reduction algorithm, enabled interpretation in an integrated fashion to construct a sequence stratigraphic framework. Six seismic attribute volumes were used, and Principal Component Analysis (PCA) reduced noise and redundant data. Three eustatically-controlled depositional units are recognized in the Dariyan Formation from well data. By analogy with the Shu'aiba, isolated rudist-dominated build-ups in the middle fining-upward unit probably have the best reservoir potential. The extent of platforms and shelf flooding such as the Mishrif and Dariyan reservoirs discussed in this study is generally greatest during sea-level high stands. The carbonate factory is most robust and carbonate sedimentation is greatest at such times. The studied depositional processes result in a variety of stratal geometries, ranging from parallel platform-interior beds to gently- to steeply-dipping fore slope beds, and complex-massive- to chaotically-bedded platform margin facies. The shingled geometry of the reservoir intervals is expressed as a series of bas inward inclined clinoforms. Turonian subaerial exposure of massive carbonates of the Mishrif Formation led to extensive karst formation. Karstification disrupted the normal bedding patterns at the top of the Mishrif Formation making chaotic stratal patterns, and dissolution expanded and enhanced fractures. This provides opportunity for complex raypaths, dispersion of wavefronts, and multiple diffraction points causing a lowered seismic resolution. Distinctive chaotic seismic facies with circular sinkhole and collapse features, discovered by integrated attribute analysis of the Mishrif Formation, clearly correlate with the production rates of existing wells. Pro grading high stand

Studies of base pair sequence effects on DNA solvation based on all-atom molecular dynamics simulations.

Science.gov (United States)

Dixit, Surjit B; Mezei, Mihaly; Beveridge, David L

2012-07-01

Detailed analyses of the sequence-dependent solvation and ion atmosphere of DNA are presented based on molecular dynamics (MD) simulations on all the 136 unique tetranucleotide steps obtained by the ABC consortium using the AMBER suite of programs. Significant sequence effects on solvation and ion localization were observed in these simulations. The results were compared to essentially all known experimental data on the subject. Proximity analysis was employed to highlight the sequence dependent differences in solvation and ion localization properties in the grooves of DNA. Comparison of the MD-calculated DNA structure with canonical A- and B-forms supports the idea that the G/C-rich sequences are closer to canonical A- than B-form structures, while the reverse is true for the poly A sequences, with the exception of the alternating ATAT sequence. Analysis of hydration density maps reveals that the flexibility of solute molecule has a significant effect on the nature of observed hydration. Energetic analysis of solute-solvent interactions based on proximity analysis of solvent reveals that the GC or CG base pairs interact more strongly with water molecules in the minor groove of DNA that the AT or TA base pairs, while the interactions of the AT or TA pairs in the major groove are stronger than those of the GC or CG pairs. Computation of solvent-accessible surface area of the nucleotide units in the simulated trajectories reveals that the similarity with results derived from analysis of a database of crystallographic structures is excellent. The MD trajectories tend to follow Manning's counterion condensation theory, presenting a region of condensed counterions within a radius of about 17 A from the DNA surface independent of sequence. The GC and CG pairs tend to associate with cations in the major groove of the DNA structure to a greater extent than the AT and TA pairs. Cation association is more frequent in the minor groove of AT than the GC pairs. In general, the

Protein sequencing via nanopore based devices: a nanofluidics perspective

Science.gov (United States)

Chinappi, Mauro; Cecconi, Fabio

2018-05-01

Proteins perform a huge number of central functions in living organisms, thus all the new techniques allowing their precise, fast and accurate characterization at single-molecule level certainly represent a burst in proteomics with important biomedical impact. In this review, we describe the recent progresses in the developing of nanopore based devices for protein sequencing. We start with a critical analysis of the main technical requirements for nanopore protein sequencing, summarizing some ideas and methodologies that have recently appeared in the literature. In the last sections, we focus on the physical modelling of the transport phenomena occurring in nanopore based devices. The multiscale nature of the problem is discussed and, in this respect, some of the main possible computational approaches are illustrated.

LookSeq: a browser-based viewer for deep sequencing data.

Science.gov (United States)

Manske, Heinrich Magnus; Kwiatkowski, Dominic P

2009-11-01

Sequencing a genome to great depth can be highly informative about heterogeneity within an individual or a population. Here we address the problem of how to visualize the multiple layers of information contained in deep sequencing data. We propose an interactive AJAX-based web viewer for browsing large data sets of aligned sequence reads. By enabling seamless browsing and fast zooming, the LookSeq program assists the user to assimilate information at different levels of resolution, from an overview of a genomic region to fine details such as heterogeneity within the sample. A specific problem, particularly if the sample is heterogeneous, is how to depict information about structural variation. LookSeq provides a simple graphical representation of paired sequence reads that is more revealing about potential insertions and deletions than are conventional methods.

Discovery of Jurassic ammonite-bearing series in Jebel Bou Hedma (South-Central Tunisian Atlas): Implications for stratigraphic correlations and paleogeographic reconstruction

Science.gov (United States)

Bahrouni, Néjib; Houla, Yassine; Soussi, Mohamed; Boughdiri, Mabrouk; Ali, Walid Ben; Nasri, Ahmed; Bouaziz, Samir

2016-01-01

Recent geological mapping undertaken in the Southern-Central Atlas of Tunisia led to the discovery of Jurassic ammonite-bearing series in the Jebel Bou Hedma E-W anticline structure. These series represent the Southernmost Jurassic rocks ever documented in the outcrops of the Tunisian Atlas. These series which outcrop in a transitional zone between the Southern Tunisian Atlas and the Chott basin offer a valuable benchmark for new stratigraphic correlation with the well-known Jurassic series of the North-South Axis of Central Tunisia and also with the Jurassic subsurface successions transected by petroleum wells in the study area. The preliminary investigations allowed the identification, within the most complete section outcropping in the center of the structure, of numerous useful biochronological and sedimentological markers helping in the establishment of an updated Jurassic stratigraphic framework chart of South-Western Tunisia. Additionally, the Late Jurassic succession documents syn-sedimentary features such as slumping, erosion and reworking of sediments and ammonite faunas that can be considered as strong witnesses of an important geodynamic event around the Jurassic-Cretaceous boundary. These stratigraphic and geodynamic new data make of the Jurassic of Jebel Bou Hedma a key succession for stratigraphic correlation attempt between Atlas Tunisian series and those currently buried in the Chott basin or outcropping in the Saharan platform. Furthermore, the several rich-ammonite identified horizons within the Middle and Upper Jurassic series constitute reliable time lines that can be useful for both paleogeographic and geodynamic reconstructions of this part of the North African Tethyan margin but also in the refinement of the potential migration routes for ammonite populations from the Maghrebian Southern Tethys to Arabia.

Luminescence chronology of loess-paleosol sequences from Canterbury, South Island, New Zealand

International Nuclear Information System (INIS)

Berger, G.W.; Pillans, B.J.; Tonkin, P.J.

2001-01-01

The extensive Quaternary loess-paleosol deposits of South Island, New Zealand, represent one of the major proxy records of paleoclimatic changes in the Southern Hemisphere. We attempted to produce the first numeric chronology of these subaerial sequences in the Canterbury region by using thermoluminescence and infrared-stimulated luminescence dating methods. We examined five exposures: a 6 m thick section at Cust, north of Christchurch; two thicker (c. 14 m) sequences on Banks Peninsula (Barrys Bay and Onawe sites); farther south, a c. 12 m sequence in Timaru; and a c. 7 m sequence on the coast at the Normanby site near Timaru. Our results are largely based on single experiments per sample, and therefore provide imprecise ages for several of the older samples. The most satisfactory results are those from the youngest site (Cust), for which three samples were dated. Here, phases of maximum loess deposition are dated at 73 +/- 13 ka (basal loess-paleosol unit L3), 41 +/- 5 ka (basal L2), and 27 +/- 3 ka (basal L1). At Barrys Bay an age of 70 +/- 15 ka was obtained in the basal L1, and at Timaru two separate samples in the base of L1 also yielded ages of c. 70 ka, thus correlating the entire Cust loess sequence with the L1 loess unit at these two other study sites. Only at Barrys Bay were ages (c. 130-250 ka) in stratigraphic order obtained for older samples (units L2 and deeper). At the other sites, some samples in the sub-L1 units gave age reversals, and some (including the oldest sample at Barrys Bay) yielded poor precision (e.g., 20%). Units L2 at Timaru and Barrys Bay may correlate to all or part of MIS 6; however, the poor precision and some age reversals in other units at these sites and at Normanby and Onawe preclude any unambiguous correlations between sites or to the MIS time-scale. Nevertheless, in the absence of any prior numeric ages, these first results serve as a basis for more precise future dating of these units. Although these reconnaissance dating

Sequence Stratigraphy of lower zones of Asmari Formation in Marun Oilfield by using of microfacies analysis, isolith maps and γ- Ray log

Directory of Open Access Journals (Sweden)

Ahmad Mirmarghabi

2015-02-01

Full Text Available The Oligo- Miocene Asmari Formation is one of the most important reservoir units of the Marun Oilfield in Dezful Embayment SW Iran, deposited in Zagros foreland basin. The goal of this study is to interpret depositional environment and sequence stratigraphy of lower zones of the Asmari Formation in Well No.281, 342 and 312in Marun Oilfield based on changes in the shape of γ- Ray, isolith maps and microfacies properties. Accordingly, identification of 9 carbonate microfacies and 2 siliciclastic petrofacies were identified that are deposited in four depositional environment including open marine, barrier, lagoon and tidal flat in a homoclinal ramp (consisting of outer, middle and inner ramp. Also, based on the shape of γ- Ray log, There sediment were deposited in marine environment. In open marine and barrier environments, The shape of γ- Ray log is serrated bell-shaped, serrated funnel-shaped, left bow-shaped, serrated shape and right boxcar shape, Whole in the beach environment it is cylinder and funnel shape and in lagoon and tidal flat environment can be seen on right bow to cylinder-shaped. Based on the isolith maps, sandstone of lower zones of the Asmari Formation in Marun Oilfield expanded by deltaic system along the southwestern margin of the basin and influenced by changes in sea level constantly. Sequence stratigraphic analysis led to identification of three third- order (DS1, DS2 and DS3 depositional sequences.

Spike-Based Bayesian-Hebbian Learning of Temporal Sequences.

Directory of Open Access Journals (Sweden)

Philip J Tully

2016-05-01

Full Text Available Many cognitive and motor functions are enabled by the temporal representation and processing of stimuli, but it remains an open issue how neocortical microcircuits can reliably encode and replay such sequences of information. To better understand this, a modular attractor memory network is proposed in which meta-stable sequential attractor transitions are learned through changes to synaptic weights and intrinsic excitabilities via the spike-based Bayesian Confidence Propagation Neural Network (BCPNN learning rule. We find that the formation of distributed memories, embodied by increased periods of firing in pools of excitatory neurons, together with asymmetrical associations between these distinct network states, can be acquired through plasticity. The model's feasibility is demonstrated using simulations of adaptive exponential integrate-and-fire model neurons (AdEx. We show that the learning and speed of sequence replay depends on a confluence of biophysically relevant parameters including stimulus duration, level of background noise, ratio of synaptic currents, and strengths of short-term depression and adaptation. Moreover, sequence elements are shown to flexibly participate multiple times in the sequence, suggesting that spiking attractor networks of this type can support an efficient combinatorial code. The model provides a principled approach towards understanding how multiple interacting plasticity mechanisms can coordinate hetero-associative learning in unison.

DNA cross-linking by dehydromonocrotaline lacks apparent base sequence preference.

Science.gov (United States)

Rieben, W Kurt; Coulombe, Roger A

2004-12-01

Pyrrolizidine alkaloids (PAs) are ubiquitous plant toxins, many of which, upon oxidation by hepatic mixed-function oxidases, become reactive bifunctional pyrrolic electrophiles that form DNA-DNA and DNA-protein cross-links. The anti-mitotic, toxic, and carcinogenic action of PAs is thought to be caused, at least in part, by these cross-links. We wished to determine whether the activated PA pyrrole dehydromonocrotaline (DHMO) exhibits base sequence preferences when cross-linked to a set of model duplex poly A-T 14-mer oligonucleotides with varying internal and/or end 5'-d(CG), 5'-d(GC), 5'-d(TA), 5'-d(CGCG), or 5'-d(GCGC) sequences. DHMO-DNA cross-links were assessed by electrophoretic mobility shift assay (EMSA) of 32P endlabeled oligonucleotides and by HPLC analysis of cross-linked DNAs enzymatically digested to their constituent deoxynucleosides. The degree of DNA cross-links depended upon the concentration of the pyrrole, but not on the base sequence of the oligonucleotide target. Likewise, HPLC chromatograms of cross-linked and digested DNAs showed no discernible sequence preference for any nucleotide. Added glutathione, tyrosine, cysteine, and aspartic acid, but not phenylalanine, threonine, serine, lysine, or methionine competed with DNA as alternate nucleophiles for cross-linking by DHMO. From these data it appears that DHMO exhibits no strong base preference when forming cross-links with DNA, and that some cellular nucleophiles can inhibit DNA cross-link formation.

Skeleton-based human action recognition using multiple sequence alignment

Science.gov (United States)

Ding, Wenwen; Liu, Kai; Cheng, Fei; Zhang, Jin; Li, YunSong

2015-05-01

Human action recognition and analysis is an active research topic in computer vision for many years. This paper presents a method to represent human actions based on trajectories consisting of 3D joint positions. This method first decompose action into a sequence of meaningful atomic actions (actionlets), and then label actionlets with English alphabets according to the Davies-Bouldin index value. Therefore, an action can be represented using a sequence of actionlet symbols, which will preserve the temporal order of occurrence of each of the actionlets. Finally, we employ sequence comparison to classify multiple actions through using string matching algorithms (Needleman-Wunsch). The effectiveness of the proposed method is evaluated on datasets captured by commodity depth cameras. Experiments of the proposed method on three challenging 3D action datasets show promising results.

Economics of Developing Hot Stratigraphic Reservoirs

Energy Technology Data Exchange (ETDEWEB)

Greg Mines; Hillary Hanson; Rick Allis; Joseph Moore

2014-09-01

Stratigraphic geothermal reservoirs at 3 – 4 km depth in high heat-flow basins are capable of sustaining 100 MW-scale power plants at about 10 c/kWh. This paper examines the impacts on the levelized cost of electricity (LCOE) of reservoir depth and temperature, reservoir productivity, and drillhole/casing options. For a reservoir at 3 km depth with a moderate productivity index by hydrothermal reservoir standards (about 50 L/s/MPa, 5.6 gpm/psi), an LCOE of 10c/kWh requires the reservoir to be at about 200°C. This is the upper temperature limit for pumps. The calculations assume standard hydrothermal drilling costs, with the production interval completed with a 7 inch liner in an 8.5 inch hole. If a reservoir at 4 km depth has excellent permeability characteristics with a productivity index of 100 L/s/MPa (11.3 gpm/psi), then the LCOE is about 11 c/kWh assuming the temperature decline rate with development is not excessive (< 1%/y, with first thermal breakthrough delayed by about 10 years). Completing wells with modest horizontal legs (e.g. several hundred meters) may be important for improving well productivity because of the naturally high, sub-horizontal permeability in this type of reservoir. Reducing the injector/producer well ratio may also be cost-effective if the injectors are drilled as larger holes.

The Lower Cambrian of Scandinavia: Depositional environment, sequence stratigraphy and palaeogeography

Science.gov (United States)

Nielsen, Arne Thorshøj; Schovsbo, Niels Hemmingsen

2011-08-01

Lower Cambrian successions described from Scandinavia are reviewed and subjected to sequence stratigraphical analysis; comparisons are also made with successions described from northeast Poland, Estonia, Latvia and Lithuania. The treated stratigraphic interval is bounded upwards by a regional unconformity ascribed to the Hawke Bay Event. The East European regional stage classification, comprising the Rovnian, Lontovan, Dominopolian, Ljubomlian, Vergalian, Rausvian and Kibartian, is adopted for the Lower Cambrian of Scandinavia. These units are approximately equivalent to the Terreneuvian and Cambrian provisional series 2. The Rovnian and Lontovan stages are pre-trilobitic. The Dominopolian and 'Ljubomlian' stages encompass the ' Rusophycus' and Schmidtiellus mickwitzi zones; whether the former zone is of pre-trilobitic age is uncertain but possible. The 'Ljubomlian' is treated informally because the definition adopted in this paper does not correspond to the original concept of the stage. The Vergalian and Rausvian are for the time being classified as one combined stage. The lower main part of the Vergalian-Rausvian corresponds to the new informal Holmia kjerulfi- 'Ornamentaspis' linnarssoni zone, whereas the upper part is separated as the new informal Comluella?-Ellipsocephalus lunatus zone. This zone also includes the Kibartian Stage. Volborthella and poorly known olenellid trilobites range into the Kibartian and the stage is considered of Early Cambrian age. The Holmia inusitata Zone is abandoned; it is contemporaneous with the traditional ' O.' linnarssoni Zone. The autochthonous strata underlying the Hawke Bay unconformity in the Laisvall sector, Swedish Lapland, are assigned to the Laisberg and Grammajukku formations and it is proposed to abandon the Laisvall and Såvvare formations. The Laisberg Fm can locally be divided into the Ackerselet, Saivatj, Maiva, Kautsky Ore, Tjalek, Nadok Ore and Assjatj members. The Vakkejokk Breccia near Luopakte is likely

(Brassicaceae) based on nuclear ribosomal ITS DNA sequences

Indian Academy of Sciences (India)

Home; Journals; Journal of Genetics; Volume 93; Issue 2. Phylogeny and biogeography of Alyssum (Brassicaceae) based on nuclear ribosomal ITS DNA sequences. Yan Li Yan Kong Zhe Zhang Yanqiang Yin Bin Liu Guanghui Lv Xiyong Wang. Research Article Volume 93 Issue 2 August 2014 pp 313-323 ...

Genome Sequencing

DEFF Research Database (Denmark)

Sato, Shusei; Andersen, Stig Uggerhøj

2014-01-01

The current Lotus japonicus reference genome sequence is based on a hybrid assembly of Sanger TAC/BAC, Sanger shotgun and Illumina shotgun sequencing data generated from the Miyakojima-MG20 accession. It covers nearly all expressed L. japonicus genes and has been annotated mainly based on transcr......The current Lotus japonicus reference genome sequence is based on a hybrid assembly of Sanger TAC/BAC, Sanger shotgun and Illumina shotgun sequencing data generated from the Miyakojima-MG20 accession. It covers nearly all expressed L. japonicus genes and has been annotated mainly based...

Correlation of proterozoic sediments of Western and Central Africa and South America based upon radiochronological and paleontological data

International Nuclear Information System (INIS)

Bonhomme, M.G.

1982-01-01

Nearly 70 new Rb-Sr isochron ages and many K-Ar conventional ages have been determined between 1975 and 1980 on Proterozoic sedimentary or metasedimentary sequences in western and Central Africa and South America. Some stratigraphic results have been established: (1) five formations have been dated of the Lower Proterozoic; (2) a long sedimentation gap occurs, mainly in western Africa and in some regions of Central Africa and South America between nearly 1600 and 1100 Ma; (3) the upper Riphean assemblages of stromatolites have been dated and compared to those of the Eurasian craton; (4) two main glacial events have been dated, the first one placed at ca. 950 Ma, the second during the Vendian, at ca. 650-620 Ma; (5) it can be stated that, when applied to Precambrian sequences, all stratigraphic methods must be used together. (Auth.)

A New Images Hiding Scheme Based on Chaotic Sequences

Institute of Scientific and Technical Information of China (English)

LIU Nian-sheng; GUO Dong-hui; WU Bo-xi; Parr G

2005-01-01

We propose a data hidding technique in a still image. This technique is based on chaotic sequence in the transform domain of covert image. We use different chaotic random sequences multiplied by multiple sensitive images, respectively, to spread the spectrum of sensitive images. Multiple sensitive images are hidden in a covert image as a form of noise. The results of theoretical analysis and computer simulation show the new hiding technique have better properties with high security, imperceptibility and capacity for hidden information in comparison with the conventional scheme such as LSB (Least Significance Bit).

Visual Localization across Seasons Using Sequence Matching Based on Multi-Feature Combination.

Science.gov (United States)

Qiao, Yongliang

2017-10-25

Visual localization is widely used in autonomous navigation system and Advanced Driver Assistance Systems (ADAS). However, visual-based localization in seasonal changing situations is one of the most challenging topics in computer vision and the intelligent vehicle community. The difficulty of this task is related to the strong appearance changes that occur in scenes due to weather or season changes. In this paper, a place recognition based visual localization method is proposed, which realizes the localization by identifying previously visited places using the sequence matching method. It operates by matching query image sequences to an image database acquired previously (video acquired during traveling period). In this method, in order to improve matching accuracy, multi-feature is constructed by combining a global GIST descriptor and local binary feature CSLBP (Center-symmetric local binary patterns) to represent image sequence. Then, similarity measurement according to Chi-square distance is used for effective sequences matching. For experimental evaluation, the relationship between image sequence length and sequences matching performance is studied. To show its effectiveness, the proposed method is tested and evaluated in four seasons outdoor environments. The results have shown improved precision-recall performance against the state-of-the-art SeqSLAM algorithm.

CodonLogo: a sequence logo-based viewer for codon patterns.

Science.gov (United States)

Sharma, Virag; Murphy, David P; Provan, Gregory; Baranov, Pavel V

2012-07-15

Conserved patterns across a multiple sequence alignment can be visualized by generating sequence logos. Sequence logos show each column in the alignment as stacks of symbol(s) where the height of a stack is proportional to its informational content, whereas the height of each symbol within the stack is proportional to its frequency in the column. Sequence logos use symbols of either nucleotide or amino acid alphabets. However, certain regulatory signals in messenger RNA (mRNA) act as combinations of codons. Yet no tool is available for visualization of conserved codon patterns. We present the first application which allows visualization of conserved regions in a multiple sequence alignment in the context of codons. CodonLogo is based on WebLogo3 and uses the same heuristics but treats codons as inseparable units of a 64-letter alphabet. CodonLogo can discriminate patterns of codon conservation from patterns of nucleotide conservation that appear indistinguishable in standard sequence logos. The CodonLogo source code and its implementation (in a local version of the Galaxy Browser) are available at http://recode.ucc.ie/CodonLogo and through the Galaxy Tool Shed at http://toolshed.g2.bx.psu.edu/.

SEQUENCE STRATIGRAPHY AND PALEONTOLOGY OF THE UPPER MIOCENE PISCO FORMATION ALONG THE WESTERN SIDE OF THE LOWER ICA VALLEY (ICA DESERT, PERU

Directory of Open Access Journals (Sweden)

CLAUDIO DI CELMA

2017-04-01

Full Text Available The sequence stratigraphic framework and a summary of the fossil fauna of the upper Miocene portion of the Pisco Formation exposed along the western side of the Ica River (southern Peru is presented through a new geological map encompassing an area of about 200 km2 and detailed chronostratigraphic analyses. Extensive field mapping and sedimentological study of outcrop sections have shown that the Pisco Formation is a cyclical sediment unit composed of at least three fining-upward, unconformity-bounded depositional sequences, designated P0, P1, and P2 from oldest to youngest. In the study area, these sequences progressively onlap a composite basal unconformity from southwest to northeast. Integration of biostratigraphic and tephrochronologic age determinations constrains the ages of the three Pisco sequences within the study area. Based on the age of surrounding sediments, a conservative estimate of the age of P0 suggests deposition of these strata between 17.99 ± 0.10 Ma and 9.00 ± 0.02 Ma, whereas diatom biostratigraphy and calculated 40Ar/39Ar ages converge to indicate that strata of the P1 sequence were deposited sometime between 9.5 Ma and 8.9 Ma and that those of the P2 sequence are younger than 8.5 Ma and older than 6.71 ± 0.02 Ma. Our survey for both vertebrate and macro-invertebrate remains in the three sequences confirms the outstanding paleontological value of the Pisco Formation and contributes to depict regional faunal shifts in the fossil assemblage.

Digital chaotic sequence generator based on coupled chaotic systems

International Nuclear Information System (INIS)

Shu-Bo, Liu; Jing, Sun; Jin-Shuo, Liu; Zheng-Quan, Xu

2009-01-01

Chaotic systems perform well as a new rich source of cryptography and pseudo-random coding. Unfortunately their digital dynamical properties would degrade due to the finite computing precision. Proposed in this paper is a modified digital chaotic sequence generator based on chaotic logistic systems with a coupling structure where one chaotic subsystem generates perturbation signals to disturb the control parameter of the other one. The numerical simulations show that the length of chaotic orbits, the output distribution of chaotic system, and the security of chaotic sequences have been greatly improved. Moreover the chaotic sequence period can be extended at least by one order of magnitude longer than that of the uncoupled logistic system and the difficulty in decrypting increases 2 128 *2 128 times indicating that the dynamical degradation of digital chaos is effectively improved. A field programmable gate array (FPGA) implementation of an algorithm is given and the corresponding experiment shows that the output speed of the generated chaotic sequences can reach 571.4 Mbps indicating that the designed generator can be applied to the real-time video image encryption. (general)

A trace display and editing program for data from fluorescence based sequencing machines.

Science.gov (United States)

Gleeson, T; Hillier, L

1991-12-11

'Ted' (Trace editor) is a graphical editor for sequence and trace data from automated fluorescence sequencing machines. It provides facilities for viewing sequence and trace data (in top or bottom strand orientation), for editing the base sequence, for automated or manual trimming of the head (vector) and tail (uncertain data) from the sequence, for vertical and horizontal trace scaling, for keeping a history of sequence editing, and for output of the edited sequence. Ted has been used extensively in the C.elegans genome sequencing project, both as a stand-alone program and integrated into the Staden sequence assembly package, and has greatly aided in the efficiency and accuracy of sequence editing. It runs in the X windows environment on Sun workstations and is available from the authors. Ted currently supports sequence and trace data from the ABI 373A and Pharmacia A.L.F. sequencers.

Predicting effects of noncoding variants with deep learning-based sequence model.

Science.gov (United States)

Zhou, Jian; Troyanskaya, Olga G

2015-10-01

Identifying functional effects of noncoding variants is a major challenge in human genetics. To predict the noncoding-variant effects de novo from sequence, we developed a deep learning-based algorithmic framework, DeepSEA (http://deepsea.princeton.edu/), that directly learns a regulatory sequence code from large-scale chromatin-profiling data, enabling prediction of chromatin effects of sequence alterations with single-nucleotide sensitivity. We further used this capability to improve prioritization of functional variants including expression quantitative trait loci (eQTLs) and disease-associated variants.

Sequence Stratigraphy of lower zones of Asmari Formation in Marun Oilfield by using of microfacies analysis, isolith maps and γ- Ray log

Directory of Open Access Journals (Sweden)

Jalil Jafari

2015-01-01

Full Text Available The Oligo- Miocene Asmari Formation is one of the most important reservoir units of the Marun Oilfield in Dezful Embayment SW Iran, deposited in Zagros foreland basin. The goal of this study is to interpret depositional environment and sequence stratigraphy of lower zones of the Asmari Formation in Well No.281, 342 and 312in Marun Oilfield based on changes in the shape of γ- Ray, isolith maps and microfacies properties. Accordingly, identification of 9 carbonate microfacies and 2 siliciclastic petrofacies were identified that are deposited in four depositional environment including open marine, barrier, lagoon and tidal flat in a homoclinal ramp (consisting of outer, middle and inner ramp. Also, based on the shape of γ- Ray log, There sediment were deposited in marine environment. In open marine and barrier environments, The shape of γ- Ray log is serrated bell-shaped, serrated funnel-shaped, left bow-shaped, serrated shape and right boxcar shape, Whole in the beach environment it is cylinder and funnel shape and in lagoon and tidal flat environment can be seen on right bow to cylinder-shaped. Based on the isolith maps, sandstone of lower zones of the Asmari Formation in Marun Oilfield expanded by deltaic system along the southwestern margin of the basin and influenced by changes in sea level constantly. Sequence stratigraphic analysis led to identification of three third- order (DS1, DS2 and DS3 depositional sequences.

Robust Automatic Target Recognition via HRRP Sequence Based on Scatterer Matching

Directory of Open Access Journals (Sweden)

Yuan Jiang

2018-02-01

Full Text Available High resolution range profile (HRRP plays an important role in wideband radar automatic target recognition (ATR. In order to alleviate the sensitivity to clutter and target aspect, employing a sequence of HRRP is a promising approach to enhance the ATR performance. In this paper, a novel HRRP sequence-matching method based on singular value decomposition (SVD is proposed. First, the HRRP sequence is decoupled into the angle space and the range space via SVD, which correspond to the span of the left and the right singular vectors, respectively. Second, atomic norm minimization (ANM is utilized to estimate dominant scatterers in the range space and the Hausdorff distance is employed to measure the scatter similarity between the test and training data. Next, the angle space similarity between the test and training data is evaluated based on the left singular vector correlations. Finally, the range space matching result and the angle space correlation are fused with the singular values as weights. Simulation and outfield experimental results demonstrate that the proposed matching metric is a robust similarity measure for HRRP sequence recognition.

Stratigraphic and structural compartmentalization observed within a model turbidite reservoir, Pennsylvanian Upper Jackfork Formation, Hollywood Quarry, Arkansas

Energy Technology Data Exchange (ETDEWEB)

Slatt, R. [Colorado School of Mines, Golden, CO (United States); Jordan, D. [Arco International Oil and Gas Co., Plano, TX (United States); Stone, C. [Arkansas Geological Commission, Little Rock, AR (United States)] [and others

1995-08-01

Hollywood Quarry is a 600 x 375 x 150 ft. (200 x 125 x 50m) excavation which provides a window into lower Pennsylvanian Jackfork Formation turbidite stratal architecture along the crest of a faulted anticlinal fold. A variety of turbidite facies are present, including: (a) lenticular, channelized sandstones, pebbly sandstones, and conglomerates within shale, (b) laterally continuous, interbedded thin sandstones and shales, and (c) thicker, laterally continuous shales. The sandstone and shale layers we broken by several strike-slip and reverse faults, with vertical displacements of up to several feet. This combination of facies and structural elements has resulted in a highly compartmentalized stratigraphic interval, both horizontally and vertically, along the anticlinal flexure. The quarry can be considered analogous to a scaled-down turbidite reservoir. Outcrop gamma-ray logs, measured sections, a fault map, and cross sections provide a database which is analogous to what would be available for a subsurface reservoir. Thus, the quarry provides an ideal outdoor geologic and engineering {open_quote}workshop{close_quote} venue for visualizing the potential complexities of a combination structural-stratigraphic (turbidite) reservoir. Since all forms of compartmentalization are readily visible in the quarry, problems related to management of compartmentalized reservoirs can be discussed and analyzed first-hand while standing in the quarry, within this {open_quote}model reservoir{close_quotes}. These problems include: (a) the high degree of stratigraphic and structural complexity that may be encountered, even at close well spacings, (b) uncertainty in well log correlations and log-shape interpretations, (c) variations in volumetric calculations as a function of amount of data available, and (d) potential production problems associated with specific {open_quote}field{close_quote} development plans.

Protein Function Prediction Based on Sequence and Structure Information

KAUST Repository

Smaili, Fatima Z.

2016-01-01

operate. In this master thesis project, we worked on inferring protein functions based on the primary protein sequence. In the approach we follow, 3D models are first constructed using I-TASSER. Functions are then deduced by structurally matching

Implication of the cause of differences in 3D structures of proteins with high sequence identity based on analyses of amino acid sequences and 3D structures.

Science.gov (United States)

Matsuoka, Masanari; Sugita, Masatake; Kikuchi, Takeshi

2014-09-18

Proteins that share a high sequence homology while exhibiting drastically different 3D structures are investigated in this study. Recently, artificial proteins related to the sequences of the GA and IgG binding GB domains of human serum albumin have been designed. These artificial proteins, referred to as GA and GB, share 98% amino acid sequence identity but exhibit different 3D structures, namely, a 3α bundle versus a 4β + α structure. Discriminating between their 3D structures based on their amino acid sequences is a very difficult problem. In the present work, in addition to using bioinformatics techniques, an analysis based on inter-residue average distance statistics is used to address this problem. It was hard to distinguish which structure a given sequence would take only with the results of ordinary analyses like BLAST and conservation analyses. However, in addition to these analyses, with the analysis based on the inter-residue average distance statistics and our sequence tendency analysis, we could infer which part would play an important role in its structural formation. The results suggest possible determinants of the different 3D structures for sequences with high sequence identity. The possibility of discriminating between the 3D structures based on the given sequences is also discussed.

A coherent high-precision radiocarbon chronology for the Late-glacial sequence at Sluggan Bog, Co. Antrim, Northern Ireland

Science.gov (United States)

Lowe, J. J.; Walker, M. J. C.; Scott, E. M.; Harkness, D. D.; Bryant, C. L.; Davies, S. M.

2004-02-01

Seventy-five radiocarbon dates are presented from Sluggan Bog in Co. Antrim, Northern Ireland. The Holocene peats are underlain by Late-glacial sediments, which also appear to have accumulated largely in a mire environment. The radiocarbon dates, from the Late-glacial and early Holocene part of the profile, were obtained from the humic and humin fractions of the sedimentary matrix, and from plant macrofossils. The last-named were dated by AMS and the sediment samples by radiometric (beta counting) methods. Age-depth models for the three dating series show a very high level of agreement between the two fractions and the macrofossils. No statistically significant difference is found between the beta counting and AMS results. Three tephras were located in the profile, the uppermost of which is in a stratigraphical position suggestive of the Vedde Ash, but the geochemical and radiocarbon evidence do not support this interpretation. The lower ashes are in the correct stratigraphical position for the Laacher See and Borrobol tephras, attributions substantiated by the radiocarbon evidence, but not by the geochemical data. The Sluggan sequence has generated one of the most internally consistent radiocarbon chronologies for any Late-glacial site in the British Isles, and it is suggested that in future more effort should be devoted to the search for, and analysis of, Late-glacial mire sequences, rather than the limnic records that have formed the principal focus of Late-glacial investigations hitherto. Copyright

Visual Localization across Seasons Using Sequence Matching Based on Multi-Feature Combination

Directory of Open Access Journals (Sweden)

Yongliang Qiao

2017-10-01

Full Text Available Visual localization is widely used in autonomous navigation system and Advanced Driver Assistance Systems (ADAS. However, visual-based localization in seasonal changing situations is one of the most challenging topics in computer vision and the intelligent vehicle community. The difficulty of this task is related to the strong appearance changes that occur in scenes due to weather or season changes. In this paper, a place recognition based visual localization method is proposed, which realizes the localization by identifying previously visited places using the sequence matching method. It operates by matching query image sequences to an image database acquired previously (video acquired during traveling period. In this method, in order to improve matching accuracy, multi-feature is constructed by combining a global GIST descriptor and local binary feature CSLBP (Center-symmetric local binary patterns to represent image sequence. Then, similarity measurement according to Chi-square distance is used for effective sequences matching. For experimental evaluation, the relationship between image sequence length and sequences matching performance is studied. To show its effectiveness, the proposed method is tested and evaluated in four seasons outdoor environments. The results have shown improved precision–recall performance against the state-of-the-art SeqSLAM algorithm.

Constraining controls on carbonate sequences with high-resolution chronostratigraphy: Upper Miocene, Cabo de Gata region, SE Spain

Science.gov (United States)

Montgomery, P.; Farr, M.R.; Franseen, E.K.; Goldstein, R.H.

2001-01-01

A high-resolution chronostratigraphy has been developed for Miocene shallow-water carbonate strata in the Cabo de Gata region of SE Spain for evaluation of local, regional and global factors that controlled platform architecture prior to and during the Messinian salinity crisis. Paleomagnetic data were collected from strata at three localities. Mean natural remanent magnetization (NRM) ranges between 1.53 ?? 10-8 and 5.2 ?? 10-3 Am2/kg. Incremental thermal and alternating field demagnetization isolated the characteristic remanent magnetization (ChRM). Rock magnetic studies show that the dominant magnetic mineral is magnetite, but mixtures of magnetite and hematite occur. A composite chronostratigraphy was derived from five stratigraphic sections. Regional stratigraphic data, biostratigraphic data, and an 40Ar/39Ar date of 8.5 ?? 0.1 Ma, for an interbedded volcanic flow, place the strata in geomagnetic polarity Chrons C4r to C3r. Sequence-stratigraphic and diagenetic evidence indicate a major unconformity at the base of depositional sequence (DS)3 that contains a prograding reef complex, suggesting that approximately 250 000 yr of record (Subchrons C3Br.2r to 3Br.1r) are missing near the Messinian-Tortonian boundary. Correlation to the GPTS shows that the studied strata represent five third- to fourth-order DSs. Basal units are temperate to subtropical ramps (DS1A, DS1B, DS2); these are overlain by subtropical to tropical reefal platforms (DS3), which are capped by subtropical to tropical cyclic carbonates (Terminal Carbonate Complex, TCC). Correlation of the Cabo de Gata record to the Melilla area of Morocco, and the Sorbas basin of Spain indicate that early - Late Tortonian ramp strata from these areas are partially time-equivalent. Similar strata are extensively developed in the Western Mediterranean and likely were influenced by a cool climate or influx of nutrients during an overall rise in global sea-level. After ramp deposition, a sequence boundary (SB3) in

Revision of Begomovirus taxonomy based on pairwise sequence comparisons

KAUST Repository

Brown, Judith K.; Zerbini, F. Murilo; Navas-Castillo, Jesú s; Moriones, Enrique; Ramos-Sobrinho, Roberto; Silva, José C. F.; Fiallo-Olivé , Elvira; Briddon, Rob W.; Herná ndez-Zepeda, Cecilia; Idris, Ali; Malathi, V. G.; Martin, Darren P.; Rivera-Bustamante, Rafael; Ueda, Shigenori; Varsani, Arvind

2015-01-01

Viruses of the genus Begomovirus (family Geminiviridae) are emergent pathogens of crops throughout the tropical and subtropical regions of the world. By virtue of having a small DNA genome that is easily cloned, and due to the recent innovations in cloning and low-cost sequencing, there has been a dramatic increase in the number of available begomovirus genome sequences. Even so, most of the available sequences have been obtained from cultivated plants and are likely a small and phylogenetically unrepresentative sample of begomovirus diversity, a factor constraining taxonomic decisions such as the establishment of operationally useful species demarcation criteria. In addition, problems in assigning new viruses to established species have highlighted shortcomings in the previously recommended mechanism of species demarcation. Based on the analysis of 3,123 full-length begomovirus genome (or DNA-A component) sequences available in public databases as of December 2012, a set of revised guidelines for the classification and nomenclature of begomoviruses are proposed. The guidelines primarily consider a) genus-level biological characteristics and b) results obtained using a standardized classification tool, Sequence Demarcation Tool, which performs pairwise sequence alignments and identity calculations. These guidelines are consistent with the recently published recommendations for the genera Mastrevirus and Curtovirus of the family Geminiviridae. Genome-wide pairwise identities of 91 % and 94 % are proposed as the demarcation threshold for begomoviruses belonging to different species and strains, respectively. Procedures and guidelines are outlined for resolving conflicts that may arise when assigning species and strains to categories wherever the pairwise identity falls on or very near the demarcation threshold value.

Revision of Begomovirus taxonomy based on pairwise sequence comparisons

KAUST Repository

Brown, Judith K.

2015-04-18

Viruses of the genus Begomovirus (family Geminiviridae) are emergent pathogens of crops throughout the tropical and subtropical regions of the world. By virtue of having a small DNA genome that is easily cloned, and due to the recent innovations in cloning and low-cost sequencing, there has been a dramatic increase in the number of available begomovirus genome sequences. Even so, most of the available sequences have been obtained from cultivated plants and are likely a small and phylogenetically unrepresentative sample of begomovirus diversity, a factor constraining taxonomic decisions such as the establishment of operationally useful species demarcation criteria. In addition, problems in assigning new viruses to established species have highlighted shortcomings in the previously recommended mechanism of species demarcation. Based on the analysis of 3,123 full-length begomovirus genome (or DNA-A component) sequences available in public databases as of December 2012, a set of revised guidelines for the classification and nomenclature of begomoviruses are proposed. The guidelines primarily consider a) genus-level biological characteristics and b) results obtained using a standardized classification tool, Sequence Demarcation Tool, which performs pairwise sequence alignments and identity calculations. These guidelines are consistent with the recently published recommendations for the genera Mastrevirus and Curtovirus of the family Geminiviridae. Genome-wide pairwise identities of 91 % and 94 % are proposed as the demarcation threshold for begomoviruses belonging to different species and strains, respectively. Procedures and guidelines are outlined for resolving conflicts that may arise when assigning species and strains to categories wherever the pairwise identity falls on or very near the demarcation threshold value.

Sparc: a sparsity-based consensus algorithm for long erroneous sequencing reads

Directory of Open Access Journals (Sweden)

Chengxi Ye

2016-06-01

Full Text Available Motivation. The third generation sequencing (3GS technology generates long sequences of thousands of bases. However, its current error rates are estimated in the range of 15–40%, significantly higher than those of the prevalent next generation sequencing (NGS technologies (less than 1%. Fundamental bioinformatics tasks such as de novo genome assembly and variant calling require high-quality sequences that need to be extracted from these long but erroneous 3GS sequences. Results. We describe a versatile and efficient linear complexity consensus algorithm Sparc to facilitate de novo genome assembly. Sparc builds a sparse k-mer graph using a collection of sequences from a targeted genomic region. The heaviest path which approximates the most likely genome sequence is searched through a sparsity-induced reweighted graph as the consensus sequence. Sparc supports using NGS and 3GS data together, which leads to significant improvements in both cost efficiency and computational efficiency. Experiments with Sparc show that our algorithm can efficiently provide high-quality consensus sequences using both PacBio and Oxford Nanopore sequencing technologies. With only 30× PacBio data, Sparc can reach a consensus with error rate <0.5%. With the more challenging Oxford Nanopore data, Sparc can also achieve similar error rate when combined with NGS data. Compared with the existing approaches, Sparc calculates the consensus with higher accuracy, and uses approximately 80% less memory and time. Availability. The source code is available for download at https://github.com/yechengxi/Sparc.

Neoproterozoic–Cambrian stratigraphic framework of the Anti-Atlas and Ouzellagh promontory (High Atlas), Morocco

Science.gov (United States)

Alvaro, Jose Javier; Benziane, Fouad; Thomas, Robert; Walsh, Gregory J.; Yazidi, Abdelaziz

2014-01-01

In the last two decades, great progress has been made in the geochronological, chrono- and chemostratigraphic control of the Neoproterozoic and Cambrian from the Anti-Atlas Ranges and the Ouzellagh promontory (High Atlas). As a result, the Neoproterozoic is lithostratigraphically subdivided into: (i) the Lkest-Taghdout Group (broadly interpreted at c. 800–690 Ma) representative of rift-to-passive margin conditions on the northern West African craton; (ii) the Iriri (c. 760–740 Ma), Bou Azzer (c. 762–697 Ma) and Saghro (c. 760?–610 Ma) groups, the overlying Anezi, Bou Salda, Dadès and Tiddiline formations localized in fault-grabens, and the Ouarzazate Supergroup (c. 615–548 Ma), which form a succession of volcanosedimentary complexes recording the onset of the Pan-African orogeny and its aftermath; and (iii) the Taroudant (the Ediacaran–Cambrian boundary lying in the Tifnout Member of the Adoudou Formation), Tata, Feijas Internes and Tabanite groups that have recorded development of the late Ediacaran–Cambrian Atlas Rift. Recent discussions of Moroccan strata to select new global GSSPs by the International Subcommissions on Ediacaran and Cambrian Stratigraphy have raised the stratigraphic interest in this region. A revised and updated stratigraphic framework is proposed here to assist the tasks of both subcommissions and to fuel future discussions focused on different geological aspects of the Neoproterozoic–Cambrian time span.

Parallel algorithms for large-scale biological sequence alignment on Xeon-Phi based clusters.

Science.gov (United States)

Lan, Haidong; Chan, Yuandong; Xu, Kai; Schmidt, Bertil; Peng, Shaoliang; Liu, Weiguo

2016-07-19

Computing alignments between two or more sequences are common operations frequently performed in computational molecular biology. The continuing growth of biological sequence databases establishes the need for their efficient parallel implementation on modern accelerators. This paper presents new approaches to high performance biological sequence database scanning with the Smith-Waterman algorithm and the first stage of progressive multiple sequence alignment based on the ClustalW heuristic on a Xeon Phi-based compute cluster. Our approach uses a three-level parallelization scheme to take full advantage of the compute power available on this type of architecture; i.e. cluster-level data parallelism, thread-level coarse-grained parallelism, and vector-level fine-grained parallelism. Furthermore, we re-organize the sequence datasets and use Xeon Phi shuffle operations to improve I/O efficiency. Evaluations show that our method achieves a peak overall performance up to 220 GCUPS for scanning real protein sequence databanks on a single node consisting of two Intel E5-2620 CPUs and two Intel Xeon Phi 7110P cards. It also exhibits good scalability in terms of sequence length and size, and number of compute nodes for both database scanning and multiple sequence alignment. Furthermore, the achieved performance is highly competitive in comparison to optimized Xeon Phi and GPU implementations. Our implementation is available at https://github.com/turbo0628/LSDBS-mpi .

pyPaSWAS : Python-based multi-core CPU and GPU sequence alignment

NARCIS (Netherlands)

Warris, Sven; Timal, N Roshan N; Kempenaar, Marcel; Poortinga, Arne M; van de Geest, Henri; Varbanescu, Ana L; Nap, Jan-Peter

2018-01-01

BACKGROUND: Our previously published CUDA-only application PaSWAS for Smith-Waterman (SW) sequence alignment of any type of sequence on NVIDIA-based GPUs is platform-specific and therefore adopted less than could be. The OpenCL language is supported more widely and allows use on a variety of

The use of handheld radiometry for the identification of stratigraphic characteristics of Paraiba Basin units

International Nuclear Information System (INIS)

Souza, Ebenezer Moreno de; Villar, Heldio Pereira; Lima, Ricardo de Andrade; Lima Filho, Mario

2000-01-01

A study on the use of radiometric techniques for the identification of stratigraphic characteristics of Paraiba Basin units was carried out with handheld instrumentation. The area chosen ran from north Pernambuco to south Paraiba. The presence of radioactive material had been previously determined. For this work a portable scintillometer was fixed to the door of a vehicle, on the outside, with the probe directed downwards. Background radiation was measured as 40 cps (counts per second). The scintillometer has an alarm which sounds whenever the measured count rate rises above a pre-established figure, 100 cps in the present case. Monitoring then proceeded manually. In sites where the count rate was much higher than 100 cps, the probe was lowered to the soil surface. Local coordinates were obtained by GPS. Therefore, an isoradioactivity map of the area could be drawn. The comparison between this map and local geological charts showed significant correlation between observed count rates and geologic formations. Low count rates were indicative of the Barreiras formation, whereas the highest rates were obtained for the Gramame formation (with urano-phosphatic lythotypes). It is concluded that handheld radiometry is a useful tool in geological charting, is special in areas where stratigraphic units have been masked by environmental changes and human activities. (author)

Sea-level changes vs. organic productivity as controls on Early and Middle Devonian bioevents: Facies- and gamma-ray based sequence-stratigraphic correlation of the Prague Basin, Czech Republic

Czech Academy of Sciences Publication Activity Database

Bábek, O.; Faměra, M.; Šimíček, D.; Weinerová, H.; Hladil, Jindřich; Kalvoda, J.

2018-01-01

Roč. 160, January (2018), s. 75-95 ISSN 0921-8181 R&D Projects: GA ČR GA14-18183S Institutional support: RVO:67985831 Keywords : Devonian * carbonates * sequence stratigraphy * bioevents * eustatic cyclicity * palaeoclimatology Subject RIV: DB - Geology ; Mineralogy OBOR OECD: Paleontology Impact factor: 3.915, year: 2016

Context-dependent motor skill: perceptual processing in memory-based sequence production.

Science.gov (United States)

Ruitenberg, Marit F L; Abrahamse, Elger L; De Kleine, Elian; Verwey, Willem B

2012-10-01

Previous studies have shown that motor sequencing skill can benefit from the reinstatement of the learning context-even with respect to features that are formally not required for appropriate task performance. The present study explored whether such context-dependence develops when sequence execution is fully memory-based-and thus no longer assisted by stimulus-response translations. Specifically, we aimed to distinguish between preparation and execution processes. Participants performed two keying sequences in a go/no-go version of the discrete sequence production task in which the context consisted of the color in which the target keys of a particular sequence were displayed. In a subsequent test phase, these colors either were the same as during practice, were reversed for the two sequences or were novel. Results showed that, irrespective of the amount of practice, performance across all key presses in the reversed context condition was impaired relative to performance in the same and novel contexts. This suggests that the online preparation and/or execution of single key presses of the sequence is context-dependent. We propose that a cognitive processor is responsible both for these online processes and for advance sequence preparation and that combined findings from the current and previous studies build toward the notion that the cognitive processor is highly sensitive to changes in context across the various roles that it performs.

HIV-1 envelope sequence-based diversity measures for identifying recent infections.

Directory of Open Access Journals (Sweden)

Alexis Kafando

Full Text Available Identifying recent HIV-1 infections is crucial for monitoring HIV-1 incidence and optimizing public health prevention efforts. To identify recent HIV-1 infections, we evaluated and compared the performance of 4 sequence-based diversity measures including percent diversity, percent complexity, Shannon entropy and number of haplotypes targeting 13 genetic segments within the env gene of HIV-1. A total of 597 diagnostic samples obtained in 2013 and 2015 from recently and chronically HIV-1 infected individuals were selected. From the selected samples, 249 (134 from recent versus 115 from chronic infections env coding regions, including V1-C5 of gp120 and the gp41 ectodomain of HIV-1, were successfully amplified and sequenced by next generation sequencing (NGS using the Illumina MiSeq platform. The ability of the four sequence-based diversity measures to correctly identify recent HIV infections was evaluated using the frequency distribution curves, median and interquartile range and area under the curve (AUC of the receiver operating characteristic (ROC. Comparing the median and interquartile range and evaluating the frequency distribution curves associated with the 4 sequence-based diversity measures, we observed that the percent diversity, number of haplotypes and Shannon entropy demonstrated significant potential to discriminate recent from chronic infections (p<0.0001. Using the AUC of ROC analysis, only the Shannon entropy measure within three HIV-1 env segments could accurately identify recent infections at a satisfactory level. The env segments were gp120 C2_1 (AUC = 0.806, gp120 C2_3 (AUC = 0.805 and gp120 V3 (AUC = 0.812. Our results clearly indicate that the Shannon entropy measure represents a useful tool for predicting HIV-1 infection recency.

Geostatistical and stratigraphic analysis of deltaic reservoirs from the Reconcavo Basin, Brazil; Analise estratigrafica e geoestatistica de reservatorios deltaicos da Bacia do Reconcavo (BA)

Energy Technology Data Exchange (ETDEWEB)

Soares, Carlos Moreira

1997-07-01

This study presents the characterization of the external geometry of deltaic oil reservoirs, including the description of their areal distribution using geo statistic tools, such as variography and kriging. A high-resolution stratigraphic study was developed over a 25 km{sup 2} area, by using data from 276 closely-spaced wells of an oil-producer field from the Reconcavo Basin, northeastern Brazil. The studied succession records the progressive lacustrine transgression of a deltaic environment. Core data and stratigraphic cross sections suggest that the oil reservoirs are mostly amalgamated, delta-front lobes, and subordinately, crevasse deposits. Some important geometrical elements were recognized by the detailed variographic analysis developed for each stratigraphic unit (zone). The average width for the groups of deltaic lobes of one zone was measured from the variographic feature informally named as hole effect. This procedure was not possible for the other zones due to the intense lateral amalgamation of sandstones, indicated by many variographic nested structures. Net sand krigged maps for the main zones suggest a NNW-SSE orientation for the deltaic lobes, as also their common amalgamation and compensation arrangements. High-resolution stratigraphic analyses should include a more regional characterization of the depositional system that comprises the studied succession. On the other hand, geostatistical studies should be developed only after the recognition of the depositional processes acting in the study area and the geological meaning of the variable to be treated, including its spatial variability scales as a function of sand body thickness, orientation and amalgamation. (author)

Comparison of ompP5 sequence-based typing and pulsed-filed gel ...

African Journals Online (AJOL)

In this study, comparison of the outer membrane protein P5 gene (ompP5) sequence-based typing with pulsed-field gel electrophoresis (PFGE) for the genotyping of Haemophilus parasuis, the 15 serovar reference strains and 43 isolates were investigated. When comparing the two methods, 31 ompP5 sequence types ...

A Chaos-Based Secure Direct-Sequence/Spread-Spectrum Communication System

Directory of Open Access Journals (Sweden)

Nguyen Xuan Quyen

2013-01-01

Full Text Available This paper proposes a chaos-based secure direct-sequence/spread-spectrum (DS/SS communication system which is based on a novel combination of the conventional DS/SS and chaos techniques. In the proposed system, bit duration is varied according to a chaotic behavior but is always equal to a multiple of the fixed chip duration in the communication process. Data bits with variable duration are spectrum-spread by multiplying directly with a pseudonoise (PN sequence and then modulated onto a sinusoidal carrier by means of binary phase-shift keying (BPSK. To recover exactly the data bits, the receiver needs an identical regeneration of not only the PN sequence but also the chaotic behavior, and hence data security is improved significantly. Structure and operation of the proposed system are analyzed in detail. Theoretical evaluation of bit-error rate (BER performance in presence of additive white Gaussian noise (AWGN is provided. Parameter choice for different cases of simulation is also considered. Simulation and theoretical results are shown to verify the reliability and feasibility of the proposed system. Security of the proposed system is also discussed.

Improving the Hydro-stratigraphic Model of the Oxnard Forebay, Ventura County, California, using Transient Electromagnetic Surveying

Science.gov (United States)

Quady, Maura Colleen

2013-01-01

To characterize the hydro-stratigraphy of an area, drilling and well logs provide high resolution electrical resistivity data, albeit for limited areas (points). The expense of drilling indirectly leads to sparse data and it is necessary to assume lateral homogeneity between wells when creating stratigraphic maps. Unfortunately, this assumption may not apply to areas in complex depositional and tectonically active settings. The goal of this study is to fill in data gaps between wells in a groundwater basin in order to better characterize the hydro-stratigraphy under existing and potential sites for managed aquifer recharge. Basins in the southern California study area have been used for decades to recharge surface water to an upper aquifer system; this work also addresses whether the local hydro-stratigraphy favors surface infiltration as a means to recharge water to the lower aquifer system. Here, soundings of transient electromagnetism (TEM), a surface geophysical method, are correlated with nearby down-hole resistivity and lithology well logs for grain size interpretations of the subsurface in unsaturated conditions. Grain size is used as a proxy for permeability (hydraulic conductivity), with resistivity contrasts highlighting variations in the media, which would affect groundwater flow in both vertical and horizontal directions. Results suggest a nearly horizontal, extensive, low permeability layer exists in the area and only a few noted locations are favorable for surface -to-lower aquifer system recharge. Furthermore, zones of higher permeability deeper than the upper aquifer system are discontinuous and isolated among lower permeability zones. However, the TEM profiles show areas where lower permeability zones are thin, and where alternatives to surface percolation methods could be explored. In addition, the survey adds information about the transition between the upper and lower aquifer systems, and adds detail to the topography of the base of freshwater

Prediction of potential drug targets based on simple sequence properties

Directory of Open Access Journals (Sweden)

Lai Luhua

2007-09-01

Full Text Available Abstract Background During the past decades, research and development in drug discovery have attracted much attention and efforts. However, only 324 drug targets are known for clinical drugs up to now. Identifying potential drug targets is the first step in the process of modern drug discovery for developing novel therapeutic agents. Therefore, the identification and validation of new and effective drug targets are of great value for drug discovery in both academia and pharmaceutical industry. If a protein can be predicted in advance for its potential application as a drug target, the drug discovery process targeting this protein will be greatly speeded up. In the current study, based on the properties of known drug targets, we have developed a sequence-based drug target prediction method for fast identification of novel drug targets. Results Based on simple physicochemical properties extracted from protein sequences of known drug targets, several support vector machine models have been constructed in this study. The best model can distinguish currently known drug targets from non drug targets at an accuracy of 84%. Using this model, potential protein drug targets of human origin from Swiss-Prot were predicted, some of which have already attracted much attention as potential drug targets in pharmaceutical research. Conclusion We have developed a drug target prediction method based solely on protein sequence information without the knowledge of family/domain annotation, or the protein 3D structure. This method can be applied in novel drug target identification and validation, as well as genome scale drug target predictions.

DNA sequence modeling based on context trees

NARCIS (Netherlands)

Kusters, C.J.; Ignatenko, T.; Roland, J.; Horlin, F.

2015-01-01

Genomic sequences contain instructions for protein and cell production. Therefore understanding and identification of biologically and functionally meaningful patterns in DNA sequences is of paramount importance. Modeling of DNA sequences in its turn can help to better understand and identify such

Typing of canine parvovirus isolates using mini-sequencing based single nucleotide polymorphism analysis.

Science.gov (United States)

Naidu, Hariprasad; Subramanian, B Mohana; Chinchkar, Shankar Ramchandra; Sriraman, Rajan; Rana, Samir Kumar; Srinivasan, V A

2012-05-01

The antigenic types of canine parvovirus (CPV) are defined based on differences in the amino acids of the major capsid protein VP2. Type specificity is conferred by a limited number of amino acid changes and in particular by few nucleotide substitutions. PCR based methods are not particularly suitable for typing circulating variants which differ in a few specific nucleotide substitutions. Assays for determining SNPs can detect efficiently nucleotide substitutions and can thus be adapted to identify CPV types. In the present study, CPV typing was performed by single nucleotide extension using the mini-sequencing technique. A mini-sequencing signature was established for all the four CPV types (CPV2, 2a, 2b and 2c) and feline panleukopenia virus. The CPV typing using the mini-sequencing reaction was performed for 13 CPV field isolates and the two vaccine strains available in our repository. All the isolates had been typed earlier by full-length sequencing of the VP2 gene. The typing results obtained from mini-sequencing matched completely with that of sequencing. Typing could be achieved with less than 100 copies of standard plasmid DNA constructs or ≤10¹ FAID₅₀ of virus by mini-sequencing technique. The technique was also efficient for detecting multiple types in mixed infections. Copyright © 2012 Elsevier B.V. All rights reserved.

The Brazilian marginal basins: current state of knowledge; As bacias marginais brasileiras: estagio atual de conhecimento

Energy Technology Data Exchange (ETDEWEB)

Ponte, Francisco Celso; Asmus, Haroldo Erwin

2004-11-01

Based on distinctive stratigraphic and/or structural characteristics, the brazilian continental margin can be divided into two main provinces : (1)The southeastern-eastern province, extending from the Pelotas to the Recife - Joao Pessoa Basin, presents a tensional tectonic style of Late Jurassic - Early Cretaceous age, paralleling the structural alignments of the Precambrian basement, except in the northeastern segment where the Mesozoic faults of the Recife - Joao Pessoa Basin cut across the east west basement directions. The basin-fill, Upper Jurassic through Recent, consists, where complete, of three stratigraphic sequences, each of a distinct depositional environment: (a) a lower clastic non-marine sequence; (b) a middle evaporitic sequence, and (c) an upper clastic paralic and open marine sequence. (2)The northern province, extending from the Potiguar Basin to the Amazon Submarine Basin, displays both tensional and compressional tectonic styles of Upper Jurassic (?) to Upper Cretaceous age either paralleling or cutting transversally the basement alignments. The stratigraphic column differs from the southeastern - eastern province in lacking the Lower Cretaceous evaporitic rocks. The integration of the stratigraphic and structural data allows one to determine in the eastern Brazilian marginal basins the main evolutionary stages of a typical pull-apart continental margin: a continental pre-rift and rift stage, an evaporitic proto-ocean stage, and a normal open ocean stage. In the northern province it is possible to infer a continental rift valley stage, a marine transform - movement stage and an open ocean stage. The relationship between the rift valley and transform movement stages is not clear. (author)

The Brahmaputra River: a stratigraphic analysis of Holocene avulsion and fluvial valley reoccupation history

Science.gov (United States)

Hartzog, T. R.; Goodbred, S. L.

2011-12-01

The Brahmaputra River, one of the world's largest braided streams, is a major component of commerce, agriculture, and transportation in India and Bangladesh. Hence any significant change in course, morphology, or behavior would be likely to influence the regional culture and economy that relies on this major river system. The history of such changes is recorded in the stratigraphy deposited by the Brahmaputra River during the Holocene. Here we present stratigraphic analysis of sediment samples from the boring of 41 tube wells over a 120 km transect in the upper Bengal Basin of northern Bangladesh. The transect crosses both the modern fluvial valley and an abandoned fluvial valley about 60 km downstream of a major avulsion node. Although the modern Brahmaputra does not transport gravel, gravel strata are common below 20 m with fluvial sand deposits dominating most of the stratigraphy. Furthermore, the stratigraphy preserves very few floodplain mud strata below the modern floodplain mud cap. These preliminary findings will be assessed to determine their importance in defining past channel migration, avulsion frequency, and the reoccupation of abandoned fluvial valleys. Understanding the avulsion and valley reoccupation history of the Brahmaputra River is important to assess the risk involved with developing agriculture, business, and infrastructure on the banks of modern and abandoned channels. Based on the correlation of stratigraphy and digital surface elevation data, we hypothesize that the towns of Jamalpur and Sherpur in northern Bangladesh were once major ports on the Brahmaputra River even though they now lie on the banks of small underfit stream channels. If Jamalpur and Sherpur represent the outer extent of the Brahmaputra River braid-belt before the last major avulsion, these cities and any communities developed in the abandoned braid-belt assume a high risk of devastation if the next major avulsion reoccupies this fluvial valley. It is important to

Unearthing The Eruptive Personality Of El Salvador's Santa Ana (Ilamatepec) Volcano Though In-depth Stratigraphic Analysis Of Pre-1904 Deposits

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Gallant, E.; Martinez-Hackert, B.

2011-12-01

The Santa Ana (Ilamatepec) volcano (2384 m) in densely populated El Salvador Central America presents serious volcanic hazard potential. The volcano is a prevalent part of every day life in El Salvador; the sugarcane and coffee belt of the country are to its Southern and Western flanks, recreational areas lies to its East, and second and third largest cities of El Salvador exist within its 25 km radius. Understanding the eruptive characteristics and history is imperative due to the volcano's relative size (the highest in the country) and it's explosive, composite nature. Historical records indicate at least 9 potential VEI 3 eruptions since 1521 AD. The volcano's relative inaccessibility and potential hazards do not promote a vast reservoir of research activity, as can be seen in the scarcity of published papers on topics prior to the 1904 eruption. This research represents the first steps towards creating a comprehensive stratigraphic record of the crater and characterizing its eruptive history, with an eventual goal of recreating the volcanic structure prior to its collapse. Samples of pre-1904 eruptive material were taken from the southern wall of an E-W oriented fluvial gully located within the SSW of the tertiary crater. These were analyzed using thin sections and optical microscopy, grain size distribution techniques, and scanning electron microscopy. The 15-layer sequence indicates an explosive history characterized by intense phreatomagmatic phases, plinian, sub-plinian and basaltic/andesitic composition strombolian activity. Another poster within the session will discuss an older sequence within the walls of the secondary crater. Further detailed studies will be required to gain a better understanding of the characteristics of Santa Ana Volcano.

SDT: a virus classification tool based on pairwise sequence alignment and identity calculation.

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Brejnev Muhizi Muhire

Full Text Available The perpetually increasing rate at which viral full-genome sequences are being determined is creating a pressing demand for computational tools that will aid the objective classification of these genome sequences. Taxonomic classification approaches that are based on pairwise genetic identity measures are potentially highly automatable and are progressively gaining favour with the International Committee on Taxonomy of Viruses (ICTV. There are, however, various issues with the calculation of such measures that could potentially undermine the accuracy and consistency with which they can be applied to virus classification. Firstly, pairwise sequence identities computed based on multiple sequence alignments rather than on multiple independent pairwise alignments can lead to the deflation of identity scores with increasing dataset sizes. Also, when gap-characters need to be introduced during sequence alignments to account for insertions and deletions, methodological variations in the way that these characters are introduced and handled during pairwise genetic identity calculations can cause high degrees of inconsistency in the way that different methods classify the same sets of sequences. Here we present Sequence Demarcation Tool (SDT, a free user-friendly computer program that aims to provide a robust and highly reproducible means of objectively using pairwise genetic identity calculations to classify any set of nucleotide or amino acid sequences. SDT can produce publication quality pairwise identity plots and colour-coded distance matrices to further aid the classification of sequences according to ICTV approved taxonomic demarcation criteria. Besides a graphical interface version of the program for Windows computers, command-line versions of the program are available for a variety of different operating systems (including a parallel version for cluster computing platforms.

Structural protein descriptors in 1-dimension and their sequence-based predictions.

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Kurgan, Lukasz; Disfani, Fatemeh Miri

2011-09-01

The last few decades observed an increasing interest in development and application of 1-dimensional (1D) descriptors of protein structure. These descriptors project 3D structural features onto 1D strings of residue-wise structural assignments. They cover a wide-range of structural aspects including conformation of the backbone, burying depth/solvent exposure and flexibility of residues, and inter-chain residue-residue contacts. We perform first-of-its-kind comprehensive comparative review of the existing 1D structural descriptors. We define, review and categorize ten structural descriptors and we also describe, summarize and contrast over eighty computational models that are used to predict these descriptors from the protein sequences. We show that the majority of the recent sequence-based predictors utilize machine learning models, with the most popular being neural networks, support vector machines, hidden Markov models, and support vector and linear regressions. These methods provide high-throughput predictions and most of them are accessible to a non-expert user via web servers and/or stand-alone software packages. We empirically evaluate several recent sequence-based predictors of secondary structure, disorder, and solvent accessibility descriptors using a benchmark set based on CASP8 targets. Our analysis shows that the secondary structure can be predicted with over 80% accuracy and segment overlap (SOV), disorder with over 0.9 AUC, 0.6 Matthews Correlation Coefficient (MCC), and 75% SOV, and relative solvent accessibility with PCC of 0.7 and MCC of 0.6 (0.86 when homology is used). We demonstrate that the secondary structure predicted from sequence without the use of homology modeling is as good as the structure extracted from the 3D folds predicted by top-performing template-based methods.

Investigation of next-generation sequencing data of Klebsiella pneumoniae using web-based tools.

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Brhelova, Eva; Antonova, Mariya; Pardy, Filip; Kocmanova, Iva; Mayer, Jiri; Racil, Zdenek; Lengerova, Martina

2017-11-01

Rapid identification and characterization of multidrug-resistant Klebsiella pneumoniae strains is necessary due to the increasing frequency of severe infections in patients. The decreasing cost of next-generation sequencing enables us to obtain a comprehensive overview of genetic information in one step. The aim of this study is to demonstrate and evaluate the utility and scope of the application of web-based databases to next-generation sequenced (NGS) data. The whole genomes of 11 clinical Klebsiella pneumoniae isolates were sequenced using Illumina MiSeq. Selected web-based tools were used to identify a variety of genetic characteristics, such as acquired antimicrobial resistance genes, multilocus sequence types, plasmid replicons, and identify virulence factors, such as virulence genes, cps clusters, urease-nickel clusters and efflux systems. Using web-based tools hosted by the Center for Genomic Epidemiology, we detected resistance to 8 main antimicrobial groups with at least 11 acquired resistance genes. The isolates were divided into eight sequence types (ST11, 23, 37, 323, 433, 495 and 562, and a new one, ST1646). All of the isolates carried replicons of large plasmids. Capsular types, virulence factors and genes coding AcrAB and OqxAB efflux pumps were detected using BIGSdb-Kp, whereas the selected virulence genes, identified in almost all of the isolates, were detected using CLC Genomic Workbench software. Applying appropriate web-based online tools to NGS data enables the rapid extraction of comprehensive information that can be used for more efficient diagnosis and treatment of patients, while data processing is free of charge, easy and time-efficient.

Neogene and Quaternary geology of a stratigraphic test hole on Horn Island, Mississippi Sound

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Gohn, Gregory S.; Brewster-Wingard, G. Lynn; Cronin, Thomas M.; Edwards, Lucy E.; Gibson, Thomas G.; Rubin, Meyer; Willard, Debra A.

1996-01-01

During April and May, 1991, the U.S. Geological Survey (USGS) drilled a 510-ft-deep, continuously cored, stratigraphic test hole on Horn Island, Mississippi Sound, as part of a field study of the Neogene and Quaternary geology of the Mississippi coastal area. The USGS drilled two new holes at the Horn Island site. The first hole was continuously cored to a depth of 510 ft; coring stopped at this depth due to mechanical problems. To facilitate geophysical logging, an unsampled second hole was drilled to a depth of 519 ft at the same location.

MGmapper: Reference based mapping and taxonomy annotation of metagenomics sequence reads

DEFF Research Database (Denmark)

Petersen, Thomas Nordahl; Lukjancenko, Oksana; Thomsen, Martin Christen Frølund

2017-01-01

number of false positive species annotations are a problem unless thresholds or post-processing are applied to differentiate between correct and false annotations. MGmapper is a package to process raw next generation sequence data and perform reference based sequence assignment, followed by a post...... pipeline is freely available as a bitbucked package (https://bitbucket.org/genomicepidemiology/mgmapper). A web-version (https://cge.cbs.dtu.dk/services/MGmapper) provides the basic functionality for analysis of small fastq datasets....

Extracting flat-field images from scene-based image sequences using phase correlation

Energy Technology Data Exchange (ETDEWEB)

Caron, James N., E-mail: Caron@RSImd.com [Research Support Instruments, 4325-B Forbes Boulevard, Lanham, Maryland 20706 (United States); Montes, Marcos J. [Naval Research Laboratory, Code 7231, 4555 Overlook Avenue, SW, Washington, DC 20375 (United States); Obermark, Jerome L. [Naval Research Laboratory, Code 8231, 4555 Overlook Avenue, SW, Washington, DC 20375 (United States)

2016-06-15

Flat-field image processing is an essential step in producing high-quality and radiometrically calibrated images. Flat-fielding corrects for variations in the gain of focal plane array electronics and unequal illumination from the system optics. Typically, a flat-field image is captured by imaging a radiometrically uniform surface. The flat-field image is normalized and removed from the images. There are circumstances, such as with remote sensing, where a flat-field image cannot be acquired in this manner. For these cases, we developed a phase-correlation method that allows the extraction of an effective flat-field image from a sequence of scene-based displaced images. The method uses sub-pixel phase correlation image registration to align the sequence to estimate the static scene. The scene is removed from sequence producing a sequence of misaligned flat-field images. An average flat-field image is derived from the realigned flat-field sequence.

pyPaSWAS: Python-based multi-core CPU and GPU sequence alignment.

Science.gov (United States)

Warris, Sven; Timal, N Roshan N; Kempenaar, Marcel; Poortinga, Arne M; van de Geest, Henri; Varbanescu, Ana L; Nap, Jan-Peter

2018-01-01

Our previously published CUDA-only application PaSWAS for Smith-Waterman (SW) sequence alignment of any type of sequence on NVIDIA-based GPUs is platform-specific and therefore adopted less than could be. The OpenCL language is supported more widely and allows use on a variety of hardware platforms. Moreover, there is a need to promote the adoption of parallel computing in bioinformatics by making its use and extension more simple through more and better application of high-level languages commonly used in bioinformatics, such as Python. The novel application pyPaSWAS presents the parallel SW sequence alignment code fully packed in Python. It is a generic SW implementation running on several hardware platforms with multi-core systems and/or GPUs that provides accurate sequence alignments that also can be inspected for alignment details. Additionally, pyPaSWAS support the affine gap penalty. Python libraries are used for automated system configuration, I/O and logging. This way, the Python environment will stimulate further extension and use of pyPaSWAS. pyPaSWAS presents an easy Python-based environment for accurate and retrievable parallel SW sequence alignments on GPUs and multi-core systems. The strategy of integrating Python with high-performance parallel compute languages to create a developer- and user-friendly environment should be considered for other computationally intensive bioinformatics algorithms.

Galaxy Workflows for Web-based Bioinformatics Analysis of Aptamer High-throughput Sequencing Data

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William H Thiel

2016-01-01

Full Text Available Development of RNA and DNA aptamers for diagnostic and therapeutic applications is a rapidly growing field. Aptamers are identified through iterative rounds of selection in a process termed SELEX (Systematic Evolution of Ligands by EXponential enrichment. High-throughput sequencing (HTS revolutionized the modern SELEX process by identifying millions of aptamer sequences across multiple rounds of aptamer selection. However, these vast aptamer HTS datasets necessitated bioinformatics techniques. Herein, we describe a semiautomated approach to analyze aptamer HTS datasets using the Galaxy Project, a web-based open source collection of bioinformatics tools that were originally developed to analyze genome, exome, and transcriptome HTS data. Using a series of Workflows created in the Galaxy webserver, we demonstrate efficient processing of aptamer HTS data and compilation of a database of unique aptamer sequences. Additional Workflows were created to characterize the abundance and persistence of aptamer sequences within a selection and to filter sequences based on these parameters. A key advantage of this approach is that the online nature of the Galaxy webserver and its graphical interface allow for the analysis of HTS data without the need to compile code or install multiple programs.

Phylogeny of the Serrasalmidae (Characiformes based on mitochondrial DNA sequences

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Guillermo Ortí

2008-01-01

Full Text Available Previous studies based on DNA sequences of mitochondrial (mt rRNA genes showed three main groups within the subfamily Serrasalminae: (1 a "pacu" clade of herbivores (Colossoma, Mylossoma, Piaractus; (2 the "Myleus" clade (Myleus, Mylesinus, Tometes, Ossubtus; and (3 the "piranha" clade (Serrasalmus, Pygocentrus, Pygopristis, Pristobrycon, Catoprion, Metynnis. The genus Acnodon was placed as the sister taxon of clade (2+3. However, poor resolution within each clade was obtained due to low levels of variation among rRNA gene sequences. Complete sequences of the hypervariable mtDNA control region for a total of 45 taxa, and additional sequences of 12S and 16S rRNA from a total of 74 taxa representing all genera in the family are now presented to address intragroup relationships. Control region sequences of several serrasalmid species exhibit tandem repeats of short motifs (12 to 33 bp in the 3' end of this region, accounting for substantial length variation. Bayesian inference and maximum parsimony analyses of these sequences identify the same groupings as before and provide further evidence to support the following observations: (a Serrasalmus gouldingi and species of Pristobrycon (non-striolatus form a monophyletic group that is the sister group to other species of Serrasalmus and Pygocentrus; (b Catoprion, Pygopristis, and Pristobrycon striolatus form a well supported clade, sister to the group described above; (c some taxa assigned to the genus Myloplus (M. asterias, M tiete, M ternetzi, and M rubripinnis form a well supported group whereas other Myloplus species remain with uncertain affinities (d Mylesinus, Tometes and Myleus setiger form a monophyletic group.

3D stratigraphic modeling of the Congo turbidite system since 210 ka: an investigation of factors controlling sedimentation

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Laurent, Dimitri; Picot, Marie; Marsset, Tania; Droz, Laurence; Rabineau, Marina; Granjeon, Didier; Molliex, Stéphane

2017-04-01

The geometry and internal functioning of turbidite systems are relatively well-constrained today. However, the respective role of autogenic (topographic compensation, dynamics of turbidity currents…) and allogenic factors (tectonics, sea-level, climate) governing their architectural evolution is still under debate. The geometry of the Quaternary Congo Fan is characterized by successive sedimentary prograding/retrograding cycles bounded by upfan avulsions, reflecting a periodic control of sedimentation (Picot et al., 2016). Multi-proxy studies revealed a strong interplay between autogenic control and climate forcing as evidenced by changes in fluvial sediment supplies consistent with arid and humid periods in the Congo River Basin. In the light of these results, the aim of this study is to investigate the relative impact of internal and external forcing factors controlling, both in time and space, the formation and evolution of depocenters of the Congo Deep-Sea Fan since 210 ka. This work represents the first attempt to model in 3D the stratigraphic architecture of the Congo turbidite system using DionisosFlow (IFP-EN), a diffusion process-based software. It allows the simulation of sediment transport and the 3D geometry reproduction of sedimentary units based on physical processes such as sea level changes, tectonics, sediment supply and transport. According to the modeling results, the role of topographic compensation in the deep-sea fan geometry is secondary compared to climate changes in the drainage basin. It appears that a periodic variation of sediment discharge and water flow is necessary to simulate the timing and volume of prograding/retrograding sedimentary cycles and more particularly the upfan avulsion events. The best-fit simulations show that the overriding factor for such changes corresponds to the expansion of the vegetation cover in the catchment basin associated to the Milankovitch cycle of precession which controlled the West African Monsoon

Application of Sequence-based Methods in Human MicrobialEcology

Energy Technology Data Exchange (ETDEWEB)

Weng, Li; Rubin, Edward M.; Bristow, James

2005-08-29

Ecologists studying microbial life in the environment have recognized the enormous complexity of microbial diversity for many years, and the development of a variety of culture-independent methods, many of them coupled with high-throughput DNA sequencing, has allowed this diversity to be explored in ever greater detail. Despite the widespread application of these new techniques to the characterization of uncultivated microbes and microbial communities in the environment, their application to human health and disease has lagged behind. Because DNA based-techniques for defining uncultured microbes allow not only cataloging of microbial diversity, but also insight into microbial functions, investigators are beginning to apply these tools to the microbial communities that abound on and within us, in what has aptly been called the second Human Genome Project. In this review we discuss the sequence-based methods for microbial analysis that are currently available and their application to identify novel human pathogens, improve diagnosis of known infectious diseases, and to advance understanding of our relationship with microbial communities that normally reside in and on the human body.

Streaming support for data intensive cloud-based sequence analysis.

Science.gov (United States)

Issa, Shadi A; Kienzler, Romeo; El-Kalioby, Mohamed; Tonellato, Peter J; Wall, Dennis; Bruggmann, Rémy; Abouelhoda, Mohamed

2013-01-01

Cloud computing provides a promising solution to the genomics data deluge problem resulting from the advent of next-generation sequencing (NGS) technology. Based on the concepts of "resources-on-demand" and "pay-as-you-go", scientists with no or limited infrastructure can have access to scalable and cost-effective computational resources. However, the large size of NGS data causes a significant data transfer latency from the client's site to the cloud, which presents a bottleneck for using cloud computing services. In this paper, we provide a streaming-based scheme to overcome this problem, where the NGS data is processed while being transferred to the cloud. Our scheme targets the wide class of NGS data analysis tasks, where the NGS sequences can be processed independently from one another. We also provide the elastream package that supports the use of this scheme with individual analysis programs or with workflow systems. Experiments presented in this paper show that our solution mitigates the effect of data transfer latency and saves both time and cost of computation.

Streaming Support for Data Intensive Cloud-Based Sequence Analysis

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Shadi A. Issa

2013-01-01

Full Text Available Cloud computing provides a promising solution to the genomics data deluge problem resulting from the advent of next-generation sequencing (NGS technology. Based on the concepts of “resources-on-demand” and “pay-as-you-go”, scientists with no or limited infrastructure can have access to scalable and cost-effective computational resources. However, the large size of NGS data causes a significant data transfer latency from the client’s site to the cloud, which presents a bottleneck for using cloud computing services. In this paper, we provide a streaming-based scheme to overcome this problem, where the NGS data is processed while being transferred to the cloud. Our scheme targets the wide class of NGS data analysis tasks, where the NGS sequences can be processed independently from one another. We also provide the elastream package that supports the use of this scheme with individual analysis programs or with workflow systems. Experiments presented in this paper show that our solution mitigates the effect of data transfer latency and saves both time and cost of computation.

Streaming Support for Data Intensive Cloud-Based Sequence Analysis

Science.gov (United States)

Issa, Shadi A.; Kienzler, Romeo; El-Kalioby, Mohamed; Tonellato, Peter J.; Wall, Dennis; Bruggmann, Rémy; Abouelhoda, Mohamed

2013-01-01

Cloud computing provides a promising solution to the genomics data deluge problem resulting from the advent of next-generation sequencing (NGS) technology. Based on the concepts of “resources-on-demand” and “pay-as-you-go”, scientists with no or limited infrastructure can have access to scalable and cost-effective computational resources. However, the large size of NGS data causes a significant data transfer latency from the client's site to the cloud, which presents a bottleneck for using cloud computing services. In this paper, we provide a streaming-based scheme to overcome this problem, where the NGS data is processed while being transferred to the cloud. Our scheme targets the wide class of NGS data analysis tasks, where the NGS sequences can be processed independently from one another. We also provide the elastream package that supports the use of this scheme with individual analysis programs or with workflow systems. Experiments presented in this paper show that our solution mitigates the effect of data transfer latency and saves both time and cost of computation. PMID:23710461

PHYLOViZ: phylogenetic inference and data visualization for sequence based typing methods

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Francisco Alexandre P

2012-05-01

Full Text Available Abstract Background With the decrease of DNA sequencing costs, sequence-based typing methods are rapidly becoming the gold standard for epidemiological surveillance. These methods provide reproducible and comparable results needed for a global scale bacterial population analysis, while retaining their usefulness for local epidemiological surveys. Online databases that collect the generated allelic profiles and associated epidemiological data are available but this wealth of data remains underused and are frequently poorly annotated since no user-friendly tool exists to analyze and explore it. Results PHYLOViZ is platform independent Java software that allows the integrated analysis of sequence-based typing methods, including SNP data generated from whole genome sequence approaches, and associated epidemiological data. goeBURST and its Minimum Spanning Tree expansion are used for visualizing the possible evolutionary relationships between isolates. The results can be displayed as an annotated graph overlaying the query results of any other epidemiological data available. Conclusions PHYLOViZ is a user-friendly software that allows the combined analysis of multiple data sources for microbial epidemiological and population studies. It is freely available at http://www.phyloviz.net.

K2 and K2*: efficient alignment-free sequence similarity measurement based on Kendall statistics.

Science.gov (United States)

Lin, Jie; Adjeroh, Donald A; Jiang, Bing-Hua; Jiang, Yue

2018-05-15

Alignment-free sequence comparison methods can compute the pairwise similarity between a huge number of sequences much faster than sequence-alignment based methods. We propose a new non-parametric alignment-free sequence comparison method, called K2, based on the Kendall statistics. Comparing to the other state-of-the-art alignment-free comparison methods, K2 demonstrates competitive performance in generating the phylogenetic tree, in evaluating functionally related regulatory sequences, and in computing the edit distance (similarity/dissimilarity) between sequences. Furthermore, the K2 approach is much faster than the other methods. An improved method, K2*, is also proposed, which is able to determine the appropriate algorithmic parameter (length) automatically, without first considering different values. Comparative analysis with the state-of-the-art alignment-free sequence similarity methods demonstrates the superiority of the proposed approaches, especially with increasing sequence length, or increasing dataset sizes. The K2 and K2* approaches are implemented in the R language as a package and is freely available for open access (http://community.wvu.edu/daadjeroh/projects/K2/K2_1.0.tar.gz). yueljiang@163.com. Supplementary data are available at Bioinformatics online.

Stratigraphy and stable isotope geochemistry of the carbonate sequence from the Paraguay belt

International Nuclear Information System (INIS)

Santos, Roberto Ventura.; Alvarenga, Carlos Jose Souza de; Dantas, Elton Luiz

2001-01-01

isotope data across 1300 m of carbonates from the northern Paraguay Belt that are stratigraphically placed above glacial sediments. The whole sequence may be divided into three different horizons that shows a general increase in δ 13 C PDB values from the base to the top: 1) a lower horizon in which the δ 13 C PDB values are negative; 2) a intermediate horizon dominated by slightly positive carbon isotope values; and 3) an upper horizon in which the carbon isotope values vary from -1% o to +9.3% o Compared to the carbonate sequences from the Brasilia Belt (Bambui Group), the amount of high δ 13 C PDB values in the Paraguay belt is much less prominent. Rocks from the lower horizon lay directly above the glacial diamictites and present variable δ 18 O PDB values. Besides presenting negative δ 13 C PDB values, they also display a negative carbon isotope peak that may reach values as low as 10% o . The intermediate horizon is best represented in the Provincia Serrana area and is characterized by homogeneous δ 13 C PDB values through out the sequence. This horizon is dominated by dolostones and present δ 18 O PDB values ranging between + 1.9% o and +2.7% o . The upper horizon is dominated by dolostones and present variable δ 13 C PDB and δ 18 O PDB values. The highest δ 13 C PDB values were found on samples from a narrow layer from the Provincia Serrana area. Although the Guia area also has positive values (+3.8% o , they were not as high as those from the Provincia Serrana. At the end of the profile, and just bellow the contact with the upper siliciclastic unit, there is an abrupt decrease in the δ 13 C PDB values down to -2.0% o (au)

Structured prediction models for RNN based sequence labeling in clinical text.

Science.gov (United States)

Jagannatha, Abhyuday N; Yu, Hong

2016-11-01

Sequence labeling is a widely used method for named entity recognition and information extraction from unstructured natural language data. In clinical domain one major application of sequence labeling involves extraction of medical entities such as medication, indication, and side-effects from Electronic Health Record narratives. Sequence labeling in this domain, presents its own set of challenges and objectives. In this work we experimented with various CRF based structured learning models with Recurrent Neural Networks. We extend the previously studied LSTM-CRF models with explicit modeling of pairwise potentials. We also propose an approximate version of skip-chain CRF inference with RNN potentials. We use these methodologies for structured prediction in order to improve the exact phrase detection of various medical entities.

HomPPI: a class of sequence homology based protein-protein interface prediction methods

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Dobbs Drena

2011-06-01

Full Text Available Abstract Background Although homology-based methods are among the most widely used methods for predicting the structure and function of proteins, the question as to whether interface sequence conservation can be effectively exploited in predicting protein-protein interfaces has been a subject of debate. Results We studied more than 300,000 pair-wise alignments of protein sequences from structurally characterized protein complexes, including both obligate and transient complexes. We identified sequence similarity criteria required for accurate homology-based inference of interface residues in a query protein sequence. Based on these analyses, we developed HomPPI, a class of sequence homology-based methods for predicting protein-protein interface residues. We present two variants of HomPPI: (i NPS-HomPPI (Non partner-specific HomPPI, which can be used to predict interface residues of a query protein in the absence of knowledge of the interaction partner; and (ii PS-HomPPI (Partner-specific HomPPI, which can be used to predict the interface residues of a query protein with a specific target protein. Our experiments on a benchmark dataset of obligate homodimeric complexes show that NPS-HomPPI can reliably predict protein-protein interface residues in a given protein, with an average correlation coefficient (CC of 0.76, sensitivity of 0.83, and specificity of 0.78, when sequence homologs of the query protein can be reliably identified. NPS-HomPPI also reliably predicts the interface residues of intrinsically disordered proteins. Our experiments suggest that NPS-HomPPI is competitive with several state-of-the-art interface prediction servers including those that exploit the structure of the query proteins. The partner-specific classifier, PS-HomPPI can, on a large dataset of transient complexes, predict the interface residues of a query protein with a specific target, with a CC of 0.65, sensitivity of 0.69, and specificity of 0.70, when homologs of

High Interlaboratory Reprocucibility of DNA Sequence-based Typing of Bacteria in a Multicenter Study

DEFF Research Database (Denmark)

Sousa, MA de; Boye, Kit; Lencastre, H de

2006-01-01

Current DNA amplification-based typing methods for bacterial pathogens often lack interlaboratory reproducibility. In this international study, DNA sequence-based typing of the Staphylococcus aureus protein A gene (spa, 110 to 422 bp) showed 100% intra- and interlaboratory reproducibility without...... extensive harmonization of protocols for 30 blind-coded S. aureus DNA samples sent to 10 laboratories. Specialized software for automated sequence analysis ensured a common typing nomenclature....

Universal sequence map (USM of arbitrary discrete sequences

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Almeida Jonas S

2002-02-01

Full Text Available Abstract Background For over a decade the idea of representing biological sequences in a continuous coordinate space has maintained its appeal but not been fully realized. The basic idea is that any sequence of symbols may define trajectories in the continuous space conserving all its statistical properties. Ideally, such a representation would allow scale independent sequence analysis – without the context of fixed memory length. A simple example would consist on being able to infer the homology between two sequences solely by comparing the coordinates of any two homologous units. Results We have successfully identified such an iterative function for bijective mappingψ of discrete sequences into objects of continuous state space that enable scale-independent sequence analysis. The technique, named Universal Sequence Mapping (USM, is applicable to sequences with an arbitrary length and arbitrary number of unique units and generates a representation where map distance estimates sequence similarity. The novel USM procedure is based on earlier work by these and other authors on the properties of Chaos Game Representation (CGR. The latter enables the representation of 4 unit type sequences (like DNA as an order free Markov Chain transition table. The properties of USM are illustrated with test data and can be verified for other data by using the accompanying web-based tool:http://bioinformatics.musc.edu/~jonas/usm/. Conclusions USM is shown to enable a statistical mechanics approach to sequence analysis. The scale independent representation frees sequence analysis from the need to assume a memory length in the investigation of syntactic rules.

Base Sequence Context Effects on Nucleotide Excision Repair

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Yuqin Cai

2010-01-01

Full Text Available Nucleotide excision repair (NER plays a critical role in maintaining the integrity of the genome when damaged by bulky DNA lesions, since inefficient repair can cause mutations and human diseases notably cancer. The structural properties of DNA lesions that determine their relative susceptibilities to NER are therefore of great interest. As a model system, we have investigated the major mutagenic lesion derived from the environmental carcinogen benzo[a]pyrene (B[a]P, 10S (+-trans-anti-B[a]P-2-dG in six different sequence contexts that differ in how the lesion is positioned in relation to nearby guanine amino groups. We have obtained molecular structural data by NMR and MD simulations, bending properties from gel electrophoresis studies, and NER data obtained from human HeLa cell extracts for our six investigated sequence contexts. This model system suggests that disturbed Watson-Crick base pairing is a better recognition signal than a flexible bend, and that these can act in concert to provide an enhanced signal. Steric hinderance between the minor groove-aligned lesion and nearby guanine amino groups determines the exact nature of the disturbances. Both nearest neighbor and more distant neighbor sequence contexts have an impact. Regardless of the exact distortions, we hypothesize that they provide a local thermodynamic destabilization signal for repair.

Stratigraphical distribution of the Ordovician conodont Erraticodon Dzik in Argentina

Science.gov (United States)

Heredia, S.; Carlorosi, J.; Mestre, A.; Soria, T.

2013-08-01

Three different species of the Ordovician genus Erraticodon Dzik are described and illustrated. Erraticodon patu Cooper is reported from the Lower-Midde Ordovician strata of the Acoite and Alto del Cóndor formations. E. cf. Erraticodon balticus and Erraticodon hexianensis from Middle Ordovician carbonate deposits of the San Juan Formation are analyzed and compared to specimens of these species from Australia, China, Newfoundland, and Baltica. E. patu and E. hexianensis are recorded for first time in the San Juan Formation of Precordillera. The elements of E. cf. E. balticus resemble closely E. balticus Dzik but lack the important denticle on the posterior process of the S elements. An evaluation of the stratigraphic occurrences of these species relative to those of key Lower and Middle Ordovician conodont species such as Trapezognathus diprion Lindström, Oepikodus intermedius Serpagli, Baltoniodus triangularis (Lindström), Baltoniodus navis Lindström, Yangtzeplacognathus crassus (Chen and Zhang) and Eoplacognathus pseudoplanus (Viira) indicates they value for biostratigraphic correlation.

Glacial sequence stratigraphy reveal the Weichselian glacial history of the SE sector of the Eurasian Ice Sheet

Science.gov (United States)

Räsänen, Matti

2016-04-01

Reconstructions of the last Weichselian glacial cycle 117,000-11,700 years (kyr) ago propose that S Finland, adjacent Russia and the Baltic countries in the SE sector of the Eurasian Ice Sheet (EIS), were glaciated during the Middle Weichselian time [marine isotope stage (MIS) 4, 71-57 kyr ago] and that this glaciation was preceded in S Finland by an Early Weichselian interstadial (MIS 5c, 105-93 kyr ago) with pine forest. Here glacial sequence stratigraphy (Powell and Cooper 2002) is applied to isolated Late Pleistocene onshore outcrop sections in S Finland. The analysed sedimentary records have traditionally been investigated, interpreted and published separately by different authors without an attempt to a methodologically more systematic survey. By putting new field data and old observations into a regional sequence stratigraphic framework it is shown how previously unnoticed regularities can be found in the lithofacies and fossil successions. It is shown that the proposed Middle Weichselian glaciation or the pine dominated interstadial did not take place at all (Räsänen et al. 2015). The one Late Weichselian glaciation (MIS 2, 29-11 kyr ago) at the SE sector of EIS was preceded in S Finland by a nearly 90 kyr long still poorly known non-glacial period, featuring tundra with permafrost and probably birch forest. The new Middle Weichselian paleoenvironmental scenario revises the configuration and hydrology of the S part of EIS and gives new setting for the evolution of Scandinavian biota. References Powell, R. D., and Cooper, J. M., 2002, A glacial sequence stratigraphic model for temperate, glaciated continental shelves, in Dowdeswell, J. A., and Cofaig, C. Ó. eds., Glacier-Influenced Sedimentation on High-Latitude Continental Margins: The Geological Society of London, London, Geological Society London, Special Publication v. 203, p. 215-244. Räsänen, M.E., Huitti, J.V., Bhattarai, S. Harvey, J. and Huttunen, S. 2015, The SE sector of the Middle

Neoproterozoic stratigraphic framework of the Tarim Craton in NW China: Implications for rift evolution

Science.gov (United States)

Wu, Lin; Guan, Shuwei; Zhang, Shuichang; Yang, Haijun; Jin, Jiuqiang; Zhang, Xiaodan; Zhang, Chunyu

2018-06-01

The Tarim Craton is overlain by thick Neoproterozoic sedimentary successions in rift tectonic setting. This study examines the latest outcrop, seismic, and drilling core data with the objective of investigating the regional stratigraphy to deeply recognize the evolution of rifting in the craton. Cryogenian to Lower Ediacaran successions are mainly composed of clastic rocks with thicknesses of 2000-3000 m, and the Upper Ediacaran successions are composed of carbonate rocks with thicknesses of 500-800 m. The rift basins and stratigraphic zones are divided into northern and southern parts by a central paleo-uplift. The northern rift basin extends through the northern Tarim Craton in an E-W direction with two depocenters (Aksu and Kuruktag). The southern rift basin is oriented NE-SW. There are three or four phases of tillites in the northern zone, while there are two in the southern zone. Given the north-south difference of the stratigraphic framework, the northern rift basin initiated at ca. 740 Ma and the southern rift basin initiated at ca. 780 Ma. During the Cryogenian and Ediacaran, the northern and southern rift basins were separated by the central paleo-uplift, finally connecting with each other in the early Cambrian. Tectonic deformation in the Late Ediacaran led to the formation of a parallel unconformity in the rift basins and an angular unconformity in the central paleo-uplift. The Neoproterozoic rift basins continued to affect the distribution of Lower Cambrian hydrocarbon source rocks. The north-south distribution and evolution of the rift basins in the Tarim Craton have implications for reconstructions of the Rodinia supercontinent.

Autonomously Generating Operations Sequences for a Mars Rover Using Artificial Intelligence-Based Planning

Science.gov (United States)

Sherwood, R.; Mutz, D.; Estlin, T.; Chien, S.; Backes, P.; Norris, J.; Tran, D.; Cooper, B.; Rabideau, G.; Mishkin, A.; Maxwell, S.

2001-07-01

This article discusses a proof-of-concept prototype for ground-based automatic generation of validated rover command sequences from high-level science and engineering activities. This prototype is based on ASPEN, the Automated Scheduling and Planning Environment. This artificial intelligence (AI)-based planning and scheduling system will automatically generate a command sequence that will execute within resource constraints and satisfy flight rules. An automated planning and scheduling system encodes rover design knowledge and uses search and reasoning techniques to automatically generate low-level command sequences while respecting rover operability constraints, science and engineering preferences, environmental predictions, and also adhering to hard temporal constraints. This prototype planning system has been field-tested using the Rocky 7 rover at JPL and will be field-tested on more complex rovers to prove its effectiveness before transferring the technology to flight operations for an upcoming NASA mission. Enabling goal-driven commanding of planetary rovers greatly reduces the requirements for highly skilled rover engineering personnel. This in turn greatly reduces mission operations costs. In addition, goal-driven commanding permits a faster response to changes in rover state (e.g., faults) or science discoveries by removing the time-consuming manual sequence validation process, allowing rapid "what-if" analyses, and thus reducing overall cycle times.

Mesoarchean Banded Iron Formation sequences in Dixon Island-Cleaverville Formation, Pilbara Australia: Oxygenic signal from DXCL project

Science.gov (United States)

Kiyokawa, S.; Ito, T.; Ikehara, M.; Yamaguchi, K. E.; Naraoka, H.; Onoue, T.; Horie, K.; Sakamoto, R.; Aihara, Y.; Miki, T.

2013-12-01

The 3.2-3.1 Ga Dixon island-Cleaverville formations are well-preserved Banded Iron Formation (BIF) within hydrothermal oceanic sequence at oceanic island arc setting (Kiyokawa et al., 2002, 2006, 2012). The stratigraphy of the Dixon Island (3195+15Ma) -Cleaverville (3108+13Ma) formations shows the well preserved environmental condition at the Mesoarchean ocean floor. The stratigraphy of these formations are formed about volcano-sedimentary sequences with hydrothermal chert, black shale and banded iron formation to the top. Based on the scientific drilling of DXCL project at 2007 and 2011, detail lithology between BIF sequence was clearly understood. Four drilling holes had been done at coastal sites; the Dixon Island Formation is DX site (100m) and the Cleaverville Formation is CL2 (40m), CL1 (60m) and CL3 (200m) sites and from stratigraphic bottom to top. Coarsening and thickening upward black shale-BIF sequences are well preserved of the stratigraphy form the core samples. The Dixon Island Formation consists komatiite-rhyolite sequences with many hydrothermal veins and very fine laminated cherty rocks above them. The Cleaverville Formation contains black shale, fragments-bearing pyroclastic beds, white chert, greenish shale and BIF. The CL3 core, which drilled through BIF, shows siderite-chert beds above black shale identified before magnetite lamination bed. U-Pb SHRIMP data of the tuff in lower Dixon Island Formation is 3195+15 Ma and the pyroclastic sequence below the Cleaverville BIF is 3108+13 Ma. Sedimentation rate of these sequence is 2-8 cm/ 1000year. The hole section of the organic carbon rich black shales below BIF are similar amount of organic content and 13C isotope (around -30per mill). There are very weak sulfur MIF signal (less 0.2%) in these black shale sequence. Our result show that thick organic rich sediments may be triggered to form iron rich siderite and magnetite iron beds. The stratigraphy in this sequence quite resemble to other Iron

[Sequence-based typing of enviromental Legionella pneumophila isolates in Guangzhou].

Science.gov (United States)

Zhang, Ying; Qu, Pinghua; Zhang, Jian; Chen, Shouyi

2011-03-01

To characterize the genes of Legionella pneumophila isolated from different water source in Guangzhou from 2006 to 2009. To genotype the strains by using sequence-based typing (SBT) scheme. In total 44 L. pneumophila strains were identified by SBT with 7 diversifying genes of flaA, asd, mip, pilE, mompS, proA and neuA. Analysis of the amplicons sequence was taken in the European Working Group for Legionella Infections (EWGLI) international SBT database to obtain the allelic profiles and sequence types (STs). Serogroups were typed by latex agglutination test. Data from SBT revealed a high diversity among the strains and ST01 accounts for 30% (13/ 44). Fifteen new STs were discovered from 20 STs and 2 of them were newly assigned (ST887 and ST888) by EWGLI. SBT Phylogenetic tree was generated by SplitsTree and BURST programs. High diversity and specificity were observed of the L. pneumophila strains in Guangzhou. SBT is useful for L. pneumophila genomic study and epidemiological surveillance.

Stratigraphic architecture of a fluvial-lacustrine basin-fill succession at Desolation Canyon, Uinta Basin, Utah: Reference to Walthers’ Law and implications for the petroleum industry

Science.gov (United States)

Ford, Grace L.; David R. Pyles,; Dechesne, Marieke

2016-01-01

A continuous window into the fluvial-lacustrine basin-fill succession of the Uinta Basin is exposed along a 48-mile (77-kilometer) transect up the modern Green River from Three Fords to Sand Wash in Desolation Canyon, Utah. In ascending order the stratigraphic units are: 1) Flagstaff Limestone, 2) lower Wasatch member of the Wasatch Formation, 3) middle Wasatch member of the Wasatch Formation, 4) upper Wasatch member of the Wasatch Formation, 5) Uteland Butte member of the lower Green River Formation, 6) lower Green River Formation, 7) Renegade Tongue of the lower Green River Formation, 8) middle Green River Formation, and 9) the Mahogany oil shale zone marking the boundary between the middle and upper Green River Formations. This article uses regional field mapping, geologic maps, photographs, and descriptions of the stratigraphic unit including: 1) bounding surfaces, 2) key upward stratigraphic characteristics within the unit, and 3) longitudinal changes along the river transect. This information is used to create a north-south cross section through the basin-fill succession and a detailed geologic map of Desolation Canyon. The cross section documents stratigraphic relationships previously unreported and contrasts with earlier interpretations in two ways: 1) abrupt upward shifts in the stratigraphy documented herein, contrast with the gradual interfingering relationships proposed by Ryder et al., (1976) and Fouch et al., (1994), 2) we document fluvial deposits of the lower and middle Wasatch to be distinct and more widespread than previously recognized. In addition, we document that the Uteland Butte member of the lower Green River Formation was deposited in a lacustrine environment in Desolation Canyon.

Genomic prediction in families of perennial ryegrass based on genotyping-by-sequencing

DEFF Research Database (Denmark)

Ashraf, Bilal

In this thesis we investigate the potential for genomic prediction in perennial ryegrass using genotyping-by-sequencing (GBS) data. Association method based on family-based breeding systems was developed, genomic heritabilities, genomic prediction accurancies and effects of some key factors wer...... explored. Results show that low sequencing depth caused underestimation of allele substitution effects in GWAS and overestimation of genomic heritability in prediction studies. Other factors susch as SNP marker density, population structure and size of training population influenced accuracy of genomic...... prediction. Overall, GBS allows for genomic prediction in breeding families of perennial ryegrass and holds good potential to expedite genetic gain and encourage the application of genomic prediction...

3D knee segmentation based on three MRI sequences from different planes.

Science.gov (United States)

Zhou, L; Chav, R; Cresson, T; Chartrand, G; de Guise, J

2016-08-01

In clinical practice, knee MRI sequences with 3.5~5 mm slice distance in sagittal, coronal, and axial planes are often requested for the knee examination since its acquisition is faster than high-resolution MRI sequence in a single plane, thereby reducing the probability of motion artifact. In order to take advantage of the three sequences from different planes, a 3D segmentation method based on the combination of three knee models obtained from the three sequences is proposed in this paper. In the method, the sub-segmentation is respectively performed with sagittal, coronal, and axial MRI sequence in the image coordinate system. With each sequence, an initial knee model is hierarchically deformed, and then the three deformed models are mapped to reference coordinate system defined by the DICOM standard and combined to obtain a patient-specific model. The experimental results verified that the three sub-segmentation results can complement each other, and their integration can compensate for the insufficiency of boundary information caused by 3.5~5 mm gap between consecutive slices. Therefore, the obtained patient-specific model is substantially more accurate than each sub-segmentation results.

A DNA Structure-Based Bionic Wavelet Transform and Its Application to DNA Sequence Analysis

Directory of Open Access Journals (Sweden)

Fei Chen

2003-01-01

Full Text Available DNA sequence analysis is of great significance for increasing our understanding of genomic functions. An important task facing us is the exploration of hidden structural information stored in the DNA sequence. This paper introduces a DNA structure-based adaptive wavelet transform (WT – the bionic wavelet transform (BWT – for DNA sequence analysis. The symbolic DNA sequence can be separated into four channels of indicator sequences. An adaptive symbol-to-number mapping, determined from the structural feature of the DNA sequence, was introduced into WT. It can adjust the weight value of each channel to maximise the useful energy distribution of the whole BWT output. The performance of the proposed BWT was examined by analysing synthetic and real DNA sequences. Results show that BWT performs better than traditional WT in presenting greater energy distribution. This new BWT method should be useful for the detection of the latent structural features in future DNA sequence analysis.

A sedimentological approach to refining reservoir architecture in a mature hydrocarbon province: the Brent Province, UK North Sea

Energy Technology Data Exchange (ETDEWEB)

Hampson, G.J.; Sixsmith, P.J.; Johnson, H.D. [Imperial College, London (United Kingdom). Dept. of Earth Science and Engineering

2004-04-01

Improved reservoir characterisation in the mature Brent Province of the North Sea, aimed at maximising both in-field and near-field hydrocarbon potential, requires a clearer understanding of sub-seismic stratigraphy and facies distributions. In this context, we present a regional, high-resolution sequence stratigraphic framework for the Brent Group, UK North Sea based on extensive sedimentological re-interpretation of core and wireline-log data, combined with palynostratigraphy and published literature. This framework is used to place individual reservoirs in an appropriate regional context, thus resulting in the identification of subtle sedimentological and tectono-stratigraphic features of reservoir architecture that have been previously overlooked. We emphasise the following insights gained from our regional, high-resolution sequence stratigraphic synthesis: (1) improved definition of temporal and spatial trends in deposition both within and between individual reservoirs, (2) development of regionally consistent, predictive sedimentological models for two enigmatic reservoir intervals (the Broom and Tarbert Formations), and (3) recognition of subtle local tectono-stratigraphic controls on reservoir architecture, and their links to the regional, Middle Jurassic structural evolution of the northern North Sea. We discuss the potential applications of these insights to the identification of additional exploration potential and to improved ultimate recovery. (author)

Role of different types of solid models in hydrodynamic modeling and their effects on groundwater protection processes

Science.gov (United States)

Bódi, Erika; Buday, Tamás; McIntosh, Richard William

2013-04-01

Defining extraction-modified flow patterns with hydrodynamic models is a pivotal question in preserving groundwater resources regarding both quality and quantity. Modeling is the first step in groundwater protection the main result of which is the determination of the protective area depending on the amount of extracted water. Solid models have significant effects on hydrodynamic models as they are based on the solid models. Due to the legislative regulations, on protection areas certain restrictions must be applied which has firm consequences on economic activities. In Hungarian regulations there are no clear instructions for the establishment of either geological or hydrodynamic modeling, however, modeling itself is an obligation. Choosing the modeling method is a key consideration for further numerical calculations and it is decisive regarding the shape and size of the groundwater protection area. The geometry of hydrodynamic model layers is derived from the solid model. There are different geological approaches including lithological and sequence stratigraphic classifications furthermore in the case of regional models, formation-based hydrostratigraphic units are also applicable. Lithological classification is based on assigning and mapping of lithotypes. When the geometry (e.g. tectonic characteristics) of the research area is not known, horizontal bedding is assumed the probability of which can not be assessed based on only lithology. If the geological correlation is based on sequence stratigraphic studies, the cyclicity of sediment deposition is also considered. This method is more integrated thus numerous parameters (e.g. electrofacies) are taken into consideration studying the geological conditions ensuring more reliable modeling. Layers of sequence stratigraphic models can be either lithologically homogeneous or they may include greater cycles of sediments containing therefore several lithological units. The advantage of this is that the modeling can

Criteria for the recognition and correlation of sandstone units in the Precambrian and Paleozoic-Mesozoic clastic sequence in the near east

Science.gov (United States)

Weissbrod, T.; Perath, I.

A systematic study of the Precambrian and Paleozoic-Mesozoic clastic sequences (Nubian Sandstone) in Israel and Sinai, and a comparative analysis of its stratigraphy in neighbouring countries, has shown that besides the conventional criteria of subdivision (lithology, field appearance, photogeological features, fossil content), additional criteria can be applied, which singly or in mutual conjuction enable the recognition of widespread units and boundaries. These criteria show lateral constancy, and recurrence of a similar vertical sequence over great distances, and are therefore acceptable for the identification of synchronous, region-wide sedimentary units (and consequently, major unconformities). They also enable, once the units are established, to identify detached (not in situ) samples, samples from isolated or discontinous outcrops, borehole material or archive material. The following rock properties were tested and found to be usefuls in stratigraphic interpretation, throughout large distribution areas of the clastic sequence: Landscape, which is basically the response of a particular textural-chemic al aggregate to atmospheric weathering. Characteristic outcrop feature — styles of roundness or massivity, fissuring or fliatin, slope profile, bedding — express a basic uniformity of these platform-type clastics. Colors are often stratigraphically constant over hundreds of kilometers, through various climates and topographies, and express some intrinsic unity of the rock bodies. Grain size and sorting, when cross-plotted, enable to differentiate existing unit. The method requires the analysis of representative numbers of samples. Vertical trends of median grain size and sorting show reversals, typically across unconformities. Feldstar content diminishes from 15-50% in Precambrian-Paleozoic rocks to a mere 5% or less in Mesozoic sandstones — a distinctive regionwide time trend. Dominance of certain feldstar types characterizes Precambrian and Paleozoic

Adaptive Processing for Sequence Alignment

KAUST Repository

Zidan, Mohammed A.; Bonny, Talal; Salama, Khaled N.

2012-01-01

Disclosed are various embodiments for adaptive processing for sequence alignment. In one embodiment, among others, a method includes obtaining a query sequence and a plurality of database sequences. A first portion of the plurality of database sequences is distributed to a central processing unit (CPU) and a second portion of the plurality of database sequences is distributed to a graphical processing unit (GPU) based upon a predetermined splitting ratio associated with the plurality of database sequences, where the database sequences of the first portion are shorter than the database sequences of the second portion. A first alignment score for the query sequence is determined with the CPU based upon the first portion of the plurality of database sequences and a second alignment score for the query sequence is determined with the GPU based upon the second portion of the plurality of database sequences.

Adaptive Processing for Sequence Alignment

KAUST Repository

Zidan, Mohammed A.

2012-01-26

Disclosed are various embodiments for adaptive processing for sequence alignment. In one embodiment, among others, a method includes obtaining a query sequence and a plurality of database sequences. A first portion of the plurality of database sequences is distributed to a central processing unit (CPU) and a second portion of the plurality of database sequences is distributed to a graphical processing unit (GPU) based upon a predetermined splitting ratio associated with the plurality of database sequences, where the database sequences of the first portion are shorter than the database sequences of the second portion. A first alignment score for the query sequence is determined with the CPU based upon the first portion of the plurality of database sequences and a second alignment score for the query sequence is determined with the GPU based upon the second portion of the plurality of database sequences.

Roche genome sequencer FLX based high-throughput sequencing of ancient DNA

DEFF Research Database (Denmark)

Alquezar-Planas, David E; Fordyce, Sarah Louise

2012-01-01

Since the development of so-called "next generation" high-throughput sequencing in 2005, this technology has been applied to a variety of fields. Such applications include disease studies, evolutionary investigations, and ancient DNA. Each application requires a specialized protocol to ensure...... that the data produced is optimal. Although much of the procedure can be followed directly from the manufacturer's protocols, the key differences lie in the library preparation steps. This chapter presents an optimized protocol for the sequencing of fossil remains and museum specimens, commonly referred...

Adaptation of Shift Sequence Based Method for High Number in Shifts Rostering Problem for Health Care Workers

Directory of Open Access Journals (Sweden)

Mindaugas Liogys

2013-08-01

Full Text Available Purpose—is to investigate a shift sequence-based approach efficiency then problem consisting of a high number of shifts.Research objectives:• Solve health care workers rostering problem using a shift sequence based method.• Measure its efficiency then number of shifts increases.Design/methodology/approach—Usually rostering problems are highly constrained. Constraints are classified to soft and hard constraints. Soft and hard constraints of the problem are additionally classified to: sequence constraints, schedule constraints and roster constraints. Sequence constraints are considered when constructing shift sequences. Schedule constraints are considered when constructing a schedule. Roster constraints are applied, then constructing overall solution, i.e. combining all schedules.Shift sequence based approach consists of two stages:• Shift sequences construction,• The construction of schedules.In the shift sequences construction stage, the shift sequences are constructed for each set of health care workers of different skill, considering sequence constraints. Shifts sequences are ranked by their penalties for easier retrieval in later stage.In schedules construction stage, schedules for each health care worker are constructed iteratively, using the shift sequences produced in stage 1.Shift sequence based method is an adaptive iterative method where health care workers who received the highest schedule penalties in the last iteration are scheduled first at the current iteration.During the roster construction, and after a schedule has been generated for the current health care worker, an improvement method based on an efficient greedy local search is carried out on the partial roster. It simply swaps any pair of shifts between two health care workers in the (partial roster, as long as the swaps satisfy hard constraints and decrease the roster penalty.Findings—Using shift sequence method for solving health care workers rostering problem

Adaptation of Shift Sequence Based Method for High Number in Shifts Rostering Problem for Health Care Workers

Directory of Open Access Journals (Sweden)

Mindaugas Liogys

2011-08-01

Full Text Available Purpose—is to investigate a shift sequence-based approach efficiency then problem consisting of a high number of shifts. Research objectives:• Solve health care workers rostering problem using a shift sequence based method.• Measure its efficiency then number of shifts increases. Design/methodology/approach—Usually rostering problems are highly constrained.Constraints are classified to soft and hard constraints. Soft and hard constraints of the problem are additionally classified to: sequence constraints, schedule constraints and roster constraints. Sequence constraints are considered when constructing shift sequences. Schedule constraints are considered when constructing a schedule. Roster constraints are applied, then constructing overall solution, i.e. combining all schedules.Shift sequence based approach consists of two stages:• Shift sequences construction,• The construction of schedules.In the shift sequences construction stage, the shift sequences are constructed for each set of health care workers of different skill, considering sequence constraints. Shifts sequences are ranked by their penalties for easier retrieval in later stage.In schedules construction stage, schedules for each health care worker are constructed iteratively, using the shift sequences produced in stage 1. Shift sequence based method is an adaptive iterative method where health care workers who received the highest schedule penalties in the last iteration are scheduled first at the current iteration. During the roster construction, and after a schedule has been generated for the current health care worker, an improvement method based on an efficient greedy local search is carried out on the partial roster. It simply swaps any pair of shifts between two health care workers in the (partial roster, as long as the swaps satisfy hard constraints and decrease the roster penalty.Findings—Using shift sequence method for solving health care workers rostering

Geomorphologic, stratigraphic and sedimentologic evidences of tectonic activity in Sone-Ganga alluvial tract in Middle Ganga Plain, India

Science.gov (United States)

Sahu, Sudarsan; Saha, Dipankar

2014-08-01

The basement of the Ganga basin in the Himalayan foreland is criss-crossed by several faults, dividing the basin into several sub-blocks forming horsts, grabens, or half-grabens. Tectonic perturbations along basement faults have affected the fluvial regime and extent of sediment fill in different parts of the basin during Late Quaternary. The East Patna Fault (EPF) and the West Patna Fault (WPF), located in Sone-Ganga alluvial tract in the southern marginal parts of Middle Ganga Plain (MGP), have remained tectonically active. The EPF particularly has acted significantly and influenced in evolving the geomorphological landscape and the stratigraphic architecture of the area. The block bounded by the two faults has earlier been considered as a single entity, constituting a half-graben. The present investigation (by morpho-stratigraphic and sedimentologic means) has revealed the existence of yet another fault within the half-graben, referred to as Bishunpur-Khagaul Fault (BKF). Many of the long profile morphological characters (e.g., knick-zone, low width-depth ratio) of the Sone River at its lower reaches can be ascribed to local structural deformation along BKF. These basement faults in MGP lie parallel to each other in NE-SW direction.

Preliminary stratigraphic and hydrogeologic cross sections and seismic profile of the Floridan aquifer system of Broward County, Florida

Science.gov (United States)

Reese, Ronald S.; Cunningham, Kevin J.

2013-01-01

To help water-resource managers evaluate the Floridan aquifer system (FAS) as an alternative water supply, the U.S. Geological Survey initiated a study, in cooperation with the Broward County Environmental Protection and Growth Management Department, to refine the hydrogeologic framework of the FAS in the eastern part of Broward County. This report presents three preliminary cross sections illustrating stratigraphy and hydrogeology in eastern Broward County as well as an interpreted seismic profile along one of the cross sections. Marker horizons were identified using borehole geophysical data and were initially used to perform well-to-well correlation. Core sample data were integrated with the borehole geophysical data to support stratigraphic and hydrogeologic interpretations of marker horizons. Stratigraphic and hydrogeologic units were correlated across the county using borehole geophysical data from multiple wells. Seismic-reflection data were collected along the Hillsboro Canal. Borehole geophysical data were used to identify and correlate hydrogeologic units in the seismic-reflection profile. Faults and collapse structures that intersect hydrogeologic units were also identified in the seismic profile. The information provided in the cross sections and the seismic profile is preliminary and subject to revision.

COI (cytochrome oxidase-I) sequence based studies of Carangid fishes from Kakinada coast, India.

Science.gov (United States)

Persis, M; Chandra Sekhar Reddy, A; Rao, L M; Khedkar, G D; Ravinder, K; Nasruddin, K

2009-09-01

Mitochondrial DNA, cytochrome oxidase-1 gene sequences were analyzed for species identification and phylogenetic relationship among the very high food value and commercially important Indian carangid fish species. Sequence analysis of COI gene very clearly indicated that all the 28 fish species fell into five distinct groups, which are genetically distant from each other and exhibited identical phylogenetic reservation. All the COI gene sequences from 28 fishes provide sufficient phylogenetic information and evolutionary relationship to distinguish the carangid species unambiguously. This study proves the utility of mtDNA COI gene sequence based approach in identifying fish species at a faster pace.

Geology, lithogeochemistry and paleotectonic setting of the host sequence to the Kangasjärvi Zn-Cu deposit, central Finland: implications for volcanogenic massive sulphide exploration in the Vihanti-Pyhäsalmi district

Directory of Open Access Journals (Sweden)

Michael D. Roberts

2004-01-01

Full Text Available The Kangasjärvi Zn-Cu deposit is a highly deformed and metamorphosed Paleoproterozoic volcanogenic massive sulphide (VMS deposit located in the Vihanti-Pyhäsalmi base metal mining district of central Finland. The host sequence to the deposit, referred to as the Inner Volcanic Sequence (IVS, is comprised of a bimodal suite of metavolcanic rocks and a regionally extensive tonalite-trondhjemite gneiss (sub-volcanic intrusions?. A separate and perhaps younger sequence of mafic volcanic rocks, with irregular intervals of undifferentiated intermediate to felsic schists and metalimestones, referred to as the Outer Volcanic Sequence (OVS, are separated from the IVS sequence by intervals of metagreywacke and U-P-bearing graphitic schists. A stratigraphic scheme for rocks within the IVS is proposed based on outcrop observations, locally preserved volcanic textures, aspects of seafloor-related hydrothermal alteration and lithogeochemistry. In this scheme, rare andesites form the lowermostvolcanic stratigraphy and are overlain by typical island-arc basalts that were erupted in a subaqueous setting. Tonalite-trondhjemite subvolcanic intrusions were locally emplaced within andesites and coeval rhyolites were extruded on the basaltic substrate. The extrusion of rhyolites, including high-silica rhyolites, was coeval with regional-scale, pre-metamorphic seafloor hydrothermal alteration and local sulphide mineralization. Extensively altered rhyolites envelope massive sulphides and are underlain by altered basalts. The latter rocks are now characterized by a variety of low-variance metamorphic mineral assemblages (e.g. orthoamphibole-cordierite rocks and define a domain of intense pre-metamorphic chlorite ± sericite alteration in the stratigraphic footwall of the deposit. The altered nature of these rocks is attributed to reaction with seawater-related hydrothermal fluids within a zone of upflow at or near the seafloor. The fundamental controls on convective

Winnowing DNA for rare sequences: highly specific sequence and methylation based enrichment.

Directory of Open Access Journals (Sweden)

Jason D Thompson

Full Text Available Rare mutations in cell populations are known to be hallmarks of many diseases and cancers. Similarly, differential DNA methylation patterns arise in rare cell populations with diagnostic potential such as fetal cells circulating in maternal blood. Unfortunately, the frequency of alleles with diagnostic potential, relative to wild-type background sequence, is often well below the frequency of errors in currently available methods for sequence analysis, including very high throughput DNA sequencing. We demonstrate a DNA preparation and purification method that through non-linear electrophoretic separation in media containing oligonucleotide probes, achieves 10,000 fold enrichment of target DNA with single nucleotide specificity, and 100 fold enrichment of unmodified methylated DNA differing from the background by the methylation of a single cytosine residue.

Winnowing DNA for rare sequences: highly specific sequence and methylation based enrichment.

Science.gov (United States)

Thompson, Jason D; Shibahara, Gosuke; Rajan, Sweta; Pel, Joel; Marziali, Andre

2012-01-01

Rare mutations in cell populations are known to be hallmarks of many diseases and cancers. Similarly, differential DNA methylation patterns arise in rare cell populations with diagnostic potential such as fetal cells circulating in maternal blood. Unfortunately, the frequency of alleles with diagnostic potential, relative to wild-type background sequence, is often well below the frequency of errors in currently available methods for sequence analysis, including very high throughput DNA sequencing. We demonstrate a DNA preparation and purification method that through non-linear electrophoretic separation in media containing oligonucleotide probes, achieves 10,000 fold enrichment of target DNA with single nucleotide specificity, and 100 fold enrichment of unmodified methylated DNA differing from the background by the methylation of a single cytosine residue.

Stratigraphic and structural controls on groundwater flow in an outcropping fossil fan delta: the case of Sant Llorenç del Munt range (NE Spain)

Science.gov (United States)

Anglés, Marc; Folch, Albert; Oms, Oriol; Maestro, Eudald; Mas-Pla, Josep

2017-12-01

Hydrogeological models of mountain regions present the opportunity to understand the role of geological factors on groundwater resources. The effects of sedimentary facies and fracture distribution on groundwater flow and resource exploitation are studied in the ancient fan delta of Sant Llorenç de Munt (central Catalonia, Spain) by integrating geological field observations (using sequence stratigraphy methods) and hydrogeological data (pumping tests, hydrochemistry and environmental isotopes). A comprehensive analysis of data portrays the massif as a single unit, constituted by different compartments determined by specific layers and sets of fractures. Two distinct flow systems—local and regional—are identified based on pumping test analysis as well as hydrochemical and isotopic data. Drawdown curves derived from pumping tests indicate that the behavior of the saturated layers, whose main porosity is given by the fracture network, corresponds to a confined aquifer. Pumping tests also reflect a double porosity within the system and the occurrence of impervious boundaries that support a compartmentalized model for the whole aquifer system. Hydrochemical data and associated spatial evolution show the result of water-rock interaction along the flow lines. Concentration of magnesium, derived from dolomite dissolution, is a tracer of the flow-path along distinct stratigraphic units. Water stable isotopes indicate that evaporation (near a 5% loss) occurs in a thick unsaturated zone within the massif before infiltration reaches the water table. The hydrogeological analysis of this outcropping system provides a methodology for the conceptualization of groundwater flow in similar buried systems where logging and hydrogeological information are scarce.

DeepBase: annotation and discovery of microRNAs and other noncoding RNAs from deep-sequencing data.

Science.gov (United States)

Yang, Jian-Hua; Qu, Liang-Hu

2012-01-01

Recent advances in high-throughput deep-sequencing technology have produced large numbers of short and long RNA sequences and enabled the detection and profiling of known and novel microRNAs (miRNAs) and other noncoding RNAs (ncRNAs) at unprecedented sensitivity and depth. In this chapter, we describe the use of deepBase, a database that we have developed to integrate all public deep-sequencing data and to facilitate the comprehensive annotation and discovery of miRNAs and other ncRNAs from these data. deepBase provides an integrative, interactive, and versatile web graphical interface to evaluate miRBase-annotated miRNA genes and other known ncRNAs, explores the expression patterns of miRNAs and other ncRNAs, and discovers novel miRNAs and other ncRNAs from deep-sequencing data. deepBase also provides a deepView genome browser to comparatively analyze these data at multiple levels. deepBase is available at http://deepbase.sysu.edu.cn/.

Full 3-D stratigraphic inversion with a priori information: a powerful way to optimize data integration

Energy Technology Data Exchange (ETDEWEB)

Grizon, L.; Leger, M.; Dequirez, P.Y.; Dumont, F.; Richard, V.

1998-12-31

Integration between seismic and geological data is crucial to ensure that a reservoir study is accurate and reliable. To reach this goal, there is used a post-stack stratigraphic inversion with a priori information. The global cost-function combines two types of constraints. One is relevant to seismic amplitudes, and the other to an a priori impedance model. This paper presents this flexible and interpretative inversion to determine acoustic impedances constrained by seismic data, log data and geologic information. 5 refs., 8 figs.

Palynoflora from Deccan volcano-sedimentary sequence ...

Indian Academy of Sciences (India)

Prakash

2009-11-02

Nov 2, 2009 ... The eruption of Deccan volcanic flows severely affected the existing floral association and ... higher stratigraphic levels, abundance of fungi especially the .... dicot; Mohabey and Udhoji 1996), fruits of Capparidaceae.

Introduction of the hybcell-based compact sequencing technology and comparison to state-of-the-art methodologies for KRAS mutation detection.

Science.gov (United States)

Zopf, Agnes; Raim, Roman; Danzer, Martin; Niklas, Norbert; Spilka, Rita; Pröll, Johannes; Gabriel, Christian; Nechansky, Andreas; Roucka, Markus

2015-03-01

The detection of KRAS mutations in codons 12 and 13 is critical for anti-EGFR therapy strategies; however, only those methodologies with high sensitivity, specificity, and accuracy as well as the best cost and turnaround balance are suitable for routine daily testing. Here we compared the performance of compact sequencing using the novel hybcell technology with 454 next-generation sequencing (454-NGS), Sanger sequencing, and pyrosequencing, using an evaluation panel of 35 specimens. A total of 32 mutations and 10 wild-type cases were reported using 454-NGS as the reference method. Specificity ranged from 100% for Sanger sequencing to 80% for pyrosequencing. Sanger sequencing and hybcell-based compact sequencing achieved a sensitivity of 96%, whereas pyrosequencing had a sensitivity of 88%. Accuracy was 97% for Sanger sequencing, 85% for pyrosequencing, and 94% for hybcell-based compact sequencing. Quantitative results were obtained for 454-NGS and hybcell-based compact sequencing data, resulting in a significant correlation (r = 0.914). Whereas pyrosequencing and Sanger sequencing were not able to detect multiple mutated cell clones within one tumor specimen, 454-NGS and the hybcell-based compact sequencing detected multiple mutations in two specimens. Our comparison shows that the hybcell-based compact sequencing is a valuable alternative to state-of-the-art methodologies used for detection of clinically relevant point mutations.

Geochemistry of Precambrian sedimentary rocks used to solve stratigraphical problems: An example from the Neoproterozoic Volta basin, Ghana

DEFF Research Database (Denmark)

Kalsbeek, F.; Frei, Robert

2010-01-01

The Neoproterozoic Volta basin of Ghana (not, vert, similar115,000 km2; depth up to 5–7 km) consists of flat-lying sedimentary rocks, mainly sandstones that unconformably overlie the crystalline basement of the West-African craton. The stratigraphical column has been subdivided into three main...... and Obosum Groups is used to solve one of the outstanding controversies regarding the stratigraphy of the Volta basin....

Ordovician and Silurian Phi Kappa and Trail Creek formations, Pioneer Mountains, central Idaho; stratigraphic and structural revisions, and new data on graptolite faunas

Science.gov (United States)

Dover, James H.; Berry, William B.N.; Ross, Reuben James

1980-01-01

Recent geologic mapping in the northern Pioneer Mountains combined with the identification of graptolites from 116 new collections indicate that the Ordovician and Silurian Phi Kappa and Trail Creek Formations occur in a series of thrust-bounded slices within a broad zone of imbricate thrust faulting. Though confirming a deformational style first reported in a 1963 study by Michael Churkin, our data suggest that the complexity and regional extent of the thrust zone were not previously recognized. Most previously published sections of the Phi Kappa and Trail Creek Formations were measured across unrecognized thrust faults and therefore include not only structural repetitions of graptolitic Ordovician and Silurian rocks but also other tectonically juxtaposed lithostratigraphic units of diverse ages as well. Because of this discovery, the need to reconsider the stratigraphic validity of these formations and their lithology, nomenclature, structural distribution, facies relations, and graptolite faunas has arisen. The Phi Kappa Formation in most thrust slices has internal stratigraphic continuity despite the intensity of deformation to which it was subjected. As revised herein, the Phi Kappa Formation is restricted to a structurally repeated succession of predominantly black, carbonaceous, graptolitic argillite and shale. Some limy, light-gray-weathering shale occurs in the middle part of the section, and fine-grained locally pebbly quartzite is present at the base. The basal quartzite is here named the Basin Gulch Quartzite Member of the Phi Kappa. The Phi Kappa redefined on a lithologic basis represents the span of Ordovician time from W. B. N. Berry's graptolite zones 2-4 through 15 and also includes approximately 17 m of lithologically identical shale of Early and Middle Silurian age at the top. The lower contact of the formation as revised is tectonic. The Phi Kappa is gradationally overlain by the Trail Creek Formation as restricted herein. Most of the coarser

Implementation of an RFID-Based Sequencing-Error-Proofing System for Automotive Manufacturing Logistics

Directory of Open Access Journals (Sweden)

Yong-Shin Kang

2018-01-01

Full Text Available Serialized tracing provides the ability to track and trace the lifecycle of the products and parts. Unlike barcodes, Radio frequency identification (RFID, which is an important building block for internet of things (IoT, does not require a line of sight and has the advantages of recognizing many objects simultaneously and rapidly, and storing more information than barcodes. Therefore, RFID has been used in a variety of application domains such as logistics, distributions, and manufacturing, significantly improving traceability and process efficiency. In this study, we applied RFID to improve the just-in-sequence operation of an automotive inbound logistics process. First, we implemented an RFID-based visibility system for real-time traceability and control of part supply from the production lines of suppliers to the assembly line of a car manufacturer. Second, we developed an RFID-based sequence-error proofing system to avoid accidental line stops due to incorrect part sequencing. The whole system has been successfully installed in a rear-axle inbound logistics process of GM Korea. We achieved a significant amount of cost savings, especially due to the prevention of sequencing errors and part shortages, and the reduction of manual operations. Thorough cost-benefit analysis demonstrates the clear economic feasibility of using RFID technologies for the just-in-sequence inbound logistics in an automobile manufacturing environment.

Heart rate measurement based on face video sequence

Science.gov (United States)

Xu, Fang; Zhou, Qin-Wu; Wu, Peng; Chen, Xing; Yang, Xiaofeng; Yan, Hong-jian

2015-03-01

This paper proposes a new non-contact heart rate measurement method based on photoplethysmography (PPG) theory. With this method we can measure heart rate remotely with a camera and ambient light. We collected video sequences of subjects, and detected remote PPG signals through video sequences. Remote PPG signals were analyzed with two methods, Blind Source Separation Technology (BSST) and Cross Spectral Power Technology (CSPT). BSST is a commonly used method, and CSPT is used for the first time in the study of remote PPG signals in this paper. Both of the methods can acquire heart rate, but compared with BSST, CSPT has clearer physical meaning, and the computational complexity of CSPT is lower than that of BSST. Our work shows that heart rates detected by CSPT method have good consistency with the heart rates measured by a finger clip oximeter. With good accuracy and low computational complexity, the CSPT method has a good prospect for the application in the field of home medical devices and mobile health devices.

Efficient DNA fingerprinting based on the targeted sequencing of active retrotransposon insertion sites using a bench-top high-throughput sequencing platform.

Science.gov (United States)

Monden, Yuki; Yamamoto, Ayaka; Shindo, Akiko; Tahara, Makoto

2014-10-01

In many crop species, DNA fingerprinting is required for the precise identification of cultivars to protect the rights of breeders. Many families of retrotransposons have multiple copies throughout the eukaryotic genome and their integrated copies are inherited genetically. Thus, their insertion polymorphisms among cultivars are useful for DNA fingerprinting. In this study, we conducted a DNA fingerprinting based on the insertion polymorphisms of active retrotransposon families (Rtsp-1 and LIb) in sweet potato. Using 38 cultivars, we identified 2,024 insertion sites in the two families with an Illumina MiSeq sequencing platform. Of these insertion sites, 91.4% appeared to be polymorphic among the cultivars and 376 cultivar-specific insertion sites were identified, which were converted directly into cultivar-specific sequence-characterized amplified region (SCAR) markers. A phylogenetic tree was constructed using these insertion sites, which corresponded well with known pedigree information, thereby indicating their suitability for genetic diversity studies. Thus, the genome-wide comparative analysis of active retrotransposon insertion sites using the bench-top MiSeq sequencing platform is highly effective for DNA fingerprinting without any requirement for whole genome sequence information. This approach may facilitate the development of practical polymerase chain reaction-based cultivar diagnostic system and could also be applied to the determination of genetic relationships. © The Author 2014. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.

Construction of a phylogenetic tree of photosynthetic prokaryotes based on average similarities of whole genome sequences.

Directory of Open Access Journals (Sweden)

Soichirou Satoh

Full Text Available Phylogenetic trees have been constructed for a wide range of organisms using gene sequence information, especially through the identification of orthologous genes that have been vertically inherited. The number of available complete genome sequences is rapidly increasing, and many tools for construction of genome trees based on whole genome sequences have been proposed. However, development of a reasonable method of using complete genome sequences for construction of phylogenetic trees has not been established. We have developed a method for construction of phylogenetic trees based on the average sequence similarities of whole genome sequences. We used this method to examine the phylogeny of 115 photosynthetic prokaryotes, i.e., cyanobacteria, Chlorobi, proteobacteria, Chloroflexi, Firmicutes and nonphotosynthetic organisms including Archaea. Although the bootstrap values for the branching order of phyla were low, probably due to lateral gene transfer and saturated mutation, the obtained tree was largely consistent with the previously reported phylogenetic trees, indicating that this method is a robust alternative to traditional phylogenetic methods.

Spike-Based Bayesian-Hebbian Learning of Temporal Sequences

DEFF Research Database (Denmark)

Tully, Philip J; Lindén, Henrik; Hennig, Matthias H

2016-01-01

Many cognitive and motor functions are enabled by the temporal representation and processing of stimuli, but it remains an open issue how neocortical microcircuits can reliably encode and replay such sequences of information. To better understand this, a modular attractor memory network is proposed...... in which meta-stable sequential attractor transitions are learned through changes to synaptic weights and intrinsic excitabilities via the spike-based Bayesian Confidence Propagation Neural Network (BCPNN) learning rule. We find that the formation of distributed memories, embodied by increased periods...

Shotgun protein sequencing.

Energy Technology Data Exchange (ETDEWEB)

Faulon, Jean-Loup Michel; Heffelfinger, Grant S.

2009-06-01

A novel experimental and computational technique based on multiple enzymatic digestion of a protein or protein mixture that reconstructs protein sequences from sequences of overlapping peptides is described in this SAND report. This approach, analogous to shotgun sequencing of DNA, is to be used to sequence alternative spliced proteins, to identify post-translational modifications, and to sequence genetically engineered proteins.

Controlling factors of stratigraphic occurrences of fine-grained turbidites: Examples from the Japanese waters

Science.gov (United States)

Ikehara, K.

2017-12-01

Fine-grained turbidite has been used for subaqueous paleoseismology, and has been recognized from shallow- to deep-water environments around the Japanese islands. Stratigraphic occurrence of fine-grained turbidites in the deepest Beppu Bay, south Japan, with its water depth of 75 m suggest clear influence of sea-level changes. Turbidite frequency was high during the post glacial sea-level rising and last 2.7 ka, and was low during the Holocene maximum sea-level highstand (5.3-2.7 ka). Retreat and progress of coastal delta front of the nearby river might affect the sediment supply to the deepest basin. On the other hand, fine-grained turbidites found in the forearc basins ( 3500 and 4500 m in water depths) and trench floor ( 6000 m in water depth) along the southern Ryukyu arc have no clear relation with sea-level changes. Sediment and bathymetric characteristics suggest that origin of these fine-grained turbidites is Taiwan. Remarkable tectonic uplift of Taiwanese coast with small mountainous rivers and narrow shelf may produce the continuous supply of fine-grained turbidites in this area. The Japan Trench floor composes of a series of small basins reflecting subducting horst-graben structure of the Pacific Plate. Each small basin acts as a natural sediment trap receiving the earthquake-induced turbidity currents. Thick fine-grained turbidites are also occurred in the small basins in the Japan Trench floor ( 7500 m in water depth). These are most likely induced by huge earthquakes along the Japan Trench. Thus, their stratigraphic occurrences might have close relation with recurrence of huge earthquakes in the past.

Upper Ordovician-Lower Silurian shelf sequences of the Eastern Great Basin: Barn Hills and Lakeside Mountains, Utah

Energy Technology Data Exchange (ETDEWEB)

Harris, M.T. (Univ. of Wisconsin, Milwaukee, WI (United States). Dept. of Geosciences); Sheehan, P.M. (Milwaukee Public Museum, WI (United States). Dept of Geology)

1993-04-01

Detailed stratigraphic sections through Upper Ordovician-Lower Silurian shelf strata of the Eastern Great Basin were measured in two Utah localities, Barn Hills (Confusion Range) and Lakeside Mountains. Six major subfacies occur in these strata: mud-cracked and crinkly laminated subfacies, Laminated mudstone subfacies, cross-bedded grainstone subfacies, cross-laminated packstone subfacies, grainy bioturbated subfacies, muddy bioturbated subfacies, and thalassinoides burrowed subfacies. These occur in 1--10 m thick cycles in three facies: muddy cyclic laminite facies (tidal flats), cross-bedded facies (subtidal shoals), and bioturbated facies (moderate to low-energy shelf). The vertical facies succession, stacking patterns of meter-scale cycles, and exposure surfaces define correlatable sequences. The authors recognize four Upper Ordovician sequences (Mayvillian to Richmondian). An uppermost Ordovician (Hirnantian) sequence is missing in these sections but occurs basinward. Lower Silurian sequences are of early Llandoverian (A), middle Llandoverian (B), early late Llandoverian (C1--C3), late late Llandoverian (C4--C5), latest Llandoverian (C6) to early Wenlock age. In general, Upper Ordovician and latest Llandoverian-Wenlockian facies are muddier than intervening Llandoverian facies. The shift to muddier shelf facies in latest Llandoverian probably corresponds to the development of a rimmed shelf. The sequence framework improves correlation of these strata by combining sedimentologic patterns with the biostratigraphic data. For example, in the Lakesides, the Ordovician-Silurian boundary is shifted 37 m downward from recent suggestions. In addition, the sequence approach highlights intervals for which additional biostratigraphic information is needed.

Implementation of Cloud based next generation sequencing data analysis in a clinical laboratory.

Science.gov (United States)

Onsongo, Getiria; Erdmann, Jesse; Spears, Michael D; Chilton, John; Beckman, Kenneth B; Hauge, Adam; Yohe, Sophia; Schomaker, Matthew; Bower, Matthew; Silverstein, Kevin A T; Thyagarajan, Bharat

2014-05-23

The introduction of next generation sequencing (NGS) has revolutionized molecular diagnostics, though several challenges remain limiting the widespread adoption of NGS testing into clinical practice. One such difficulty includes the development of a robust bioinformatics pipeline that can handle the volume of data generated by high-throughput sequencing in a cost-effective manner. Analysis of sequencing data typically requires a substantial level of computing power that is often cost-prohibitive to most clinical diagnostics laboratories. To address this challenge, our institution has developed a Galaxy-based data analysis pipeline which relies on a web-based, cloud-computing infrastructure to process NGS data and identify genetic variants. It provides additional flexibility, needed to control storage costs, resulting in a pipeline that is cost-effective on a per-sample basis. It does not require the usage of EBS disk to run a sample. We demonstrate the validation and feasibility of implementing this bioinformatics pipeline in a molecular diagnostics laboratory. Four samples were analyzed in duplicate pairs and showed 100% concordance in mutations identified. This pipeline is currently being used in the clinic and all identified pathogenic variants confirmed using Sanger sequencing further validating the software.

Stratigraphy, climate and downhole logging data - an example from the ICDP Dead Sea deep drilling project

Science.gov (United States)

Coianiz, Lisa; Ben-Avraham, Zvi; Lazar, Michael

2017-04-01

During the late Quaternary a series of lakes occupied the Dead Sea tectonic basin. The sediments that accumulated within these lakes preserved the environmental history (tectonic and climatic) of the basin and its vicinity. Most of the information on these lakes was deduced from exposures along the marginal terraces of the modern Dead Sea, e.g. the exposures of the last glacial Lake Lisan and Holocene Dead Sea. The International Continental Drilling Program (ICDP) project conducted in the Dead Sea during 2010-2011 recovered several cores that were drilled in the deep depocenter of the lake (water depth of 300 m) and at the margin (depth of 3 m offshore Ein Gedi spa). New high resolution logging data combined with a detailed lithological description and published age models for the deep 5017-1-A borehole were used to establish a sequence stratigraphic framework for the Lakes Amora, Samra, Lisan and Zeelim strata. This study presents a stratigraphic timescale for reconstructing the last ca 225 ka. It provides a context within which the timing of key sequence surfaces identified in the distal part of the basin can be mapped on a regional and stratigraphic time frame. In addition, it permitted the examination of depositional system tracts and related driving mechanisms controlling their formation. The sequence stratigraphic model developed for the Northern Dead Sea Basin is based on the identification of sequence bounding surfaces including: sequence boundary (SB), transgressive surface (TS) and maximum flooding surface (MFS). They enabled the division of depositional sequences into a Lowstand systems tracts (LST), Transgressive systems tracts (TST) and Highstand systems tracts (HST), which can be interpreted in terms of relative lake level changes. The analysis presented here show that system tract stacking patterns defined for the distal 5017-1-A borehole can be correlated to the proximal part of the basin, and widely support the claim that changes in relative lake

Sequence stratigraphy of the Upper Cambrian (Furongian; Jiangshanian and Sunwaptan) Tunnel City Group, Upper Mississippi Valley: Transgressing assumptions of cratonic flooding

Science.gov (United States)

Eoff, Jennifer D.

2014-01-01

New data from detailed measured sections permit comprehensive analysis of the sequence framework of the Furongian (Upper Cambrian; Jiangshanian and Sunwaptan stages) Tunnel City Group (Lone Rock Formation and Mazomanie Formation) of Wisconsin and Minnesota. The sequence-stratigraphic architecture of the lower part of the Sunwaptan Stage at the base of the Tunnel City Group, at the contact between the Wonewoc Formation and Lone Rock Formation, records the first part of complex polyphase flooding (Sauk III) of the Laurentian craton, at a scale smaller than most events recorded by global sea-level curves. Flat-pebble conglomerate and glauconite document transgressive ravinement and development of a condensed section when creation of accommodation exceeded its consumption by sedimentation. Thinly-bedded, fossiliferous sandstone represents the most distal setting during earliest highstand. Subsequent deposition of sandstone characterized by hummocky or trough cross-stratification records progradational pulses of shallower, storm- and wave-dominated environments across the craton before final flooding of Sauk III commenced with carbonate deposition during the middle part of the Sunwaptan Stage. Comparison of early Sunwaptan flooding of the inner Laurentian craton to published interpretations from other parts of North America suggests that Sauk III was not a single, long-term accommodation event as previously proposed.

Stratigraphic framework of Cambrian and Ordovician rocks in the central Appalachian Basin from Medina County, Ohio, through southwestern and south-central Pennsylvania to Hampshire County, West Virginia

Science.gov (United States)

Ryder, Robert T.; Harris, Anita G.; Repetski, John E.; revised and digitized by Crangle, Robert D.

2003-01-01

A 275-mi-long restored stratigraphic cross section from Medina County, Ohio, through southwestern and south-central Pennsylvania to Hampshire County, W. Va., provides new details on Cambrian and Ordovician stratigraphy in the central Appalachian basin and the structure of underlying Precambrian basement rocks. From west to east, the major structural elements of the block-faulted basement in this section are (1) the relatively stable, slightly extended craton, which includes the Wooster arch, (2) the fault-controlled Ohio-West Virginia hinge zone, which separates the craton from the adjoining Rome trough, (3) the Rome trough, which consists of an east-facing asymmetric graben and an overlying sag basin, and (4) a positive fault block, named here the South-central Pennsylvania arch, which borders the eastern margin of the graben part of the Rome trough. Pre-Middle Ordovician structural relief on Precambrian basement rocks across the down-to-the-west normal fault that separates the Rome trough and the adjoining South-central Pennsylvania arch amounted to between 6,000 and 7,000 ft. The restored cross section shows eastward thickening of the Cambrian and Ordovician sequence from about 3,000 ft near the crest of the Wooster arch at the western end of the section to about 5,150 ft at the Ohio-West Virginia hinge zone adjoining the western margin of the Rome trough to about 19,800 ft near the depositional axis of the Rome trough. East of the Rome trough, at the adjoining western edge of the South-central Pennsylvania arch, the Cambrian and Ordovician sequence thins abruptly to about 13,500 ft and then thins gradually eastward across the arch to about 12,700 ft near the Allegheny structural front and to about 10,150 ft at the eastern end of the restored section. In general, the Cambrian and Ordovician sequence along this section consists of four major lithofacies that are predominantly shallow marine to peritidal in origin. In ascending stratigraphic order, the lithofacies

When did the Penglai orogeny begin on Taiwan?: Geochronological and petrographic constraints on the exhumed mountain belts and foreland-basin sequences

Science.gov (United States)

Chen, W. S.; Syu, S. J.; Yeh, J. J.

2017-12-01

Foreland basin receives large amounts of synorogenic infill that is eroded from the adjacent exhumed mountain belt, and therefore provides the important information on exhumation evolution. Furthermore, a complete stratigraphic sequence of Taiwan mountain belt consists of five units of Miocene sedimentary rocks (the Western Foothills and the uppermost sequence on the proto-Taiwan mountain belt), Oligocene argillite (the Hsuehshan Range), Eocene quartzite (the Hsuehshan Range), Eocene-Miocene slate and schist (Backbone Range), and Cretaceous schist (Backbone Range) from top to bottom. Based on the progressive unroofing history, the initiation of foreland basin received sedimentary lithic sediments from the uppermost sequence of proto-Taiwan mountain belt, afterwards, and receiving low- to medium-grade metamorphic lithic sediments in ascending order of argillite, quartzite, slate, and schist clasts. Therefore, the sedimentary lithics from mountain belt were deposited which represents the onset of the mountain uplift. In this study, the first appearance of sedimentary lithic sediments occurs in the Hengchun Peninsula at the middle Miocene (ca. 12-10 Ma). Thus, sandstone petrography of the late Miocene formation (10-5.3 Ma) shows a predominantly recycled sedimentary and low-grade metamorphic sources, including sandstone, argillite and quartzite lithic sediments of 10-25% which records erosion to slightly deeper metamorphic terrane on the mountain belt. Based on the results of previous thermogeochronological studies of the Yuli belt, it suggests that the middle Miocene occurred mountain uplift. The occurrence of low-grade metamorphic lithic sediments in the Hengchun Peninsula during late Miocene is coincident with the cooling ages of uplift and denuded Yuli schist belt at the eastern limb of Backbone Range.

High-throughput Sequencing Based Immune Repertoire Study during Infectious Disease

Directory of Open Access Journals (Sweden)

Dongni Hou

2016-08-01

Full Text Available The selectivity of the adaptive immune response is based on the enormous diversity of T and B cell antigen-specific receptors. The immune repertoire, the collection of T and B cells with functional diversity in the circulatory system at any given time, is dynamic and reflects the essence of immune selectivity. In this article, we review the recent advances in immune repertoire study of infectious diseases that achieved by traditional techniques and high-throughput sequencing techniques. High-throughput sequencing techniques enable the determination of complementary regions of lymphocyte receptors with unprecedented efficiency and scale. This progress in methodology enhances the understanding of immunologic changes during pathogen challenge, and also provides a basis for further development of novel diagnostic markers, immunotherapies and vaccines.

CT Image Sequence Restoration Based on Sparse and Low-Rank Decomposition

Science.gov (United States)

Gou, Shuiping; Wang, Yueyue; Wang, Zhilong; Peng, Yong; Zhang, Xiaopeng; Jiao, Licheng; Wu, Jianshe

2013-01-01

Blurry organ boundaries and soft tissue structures present a major challenge in biomedical image restoration. In this paper, we propose a low-rank decomposition-based method for computed tomography (CT) image sequence restoration, where the CT image sequence is decomposed into a sparse component and a low-rank component. A new point spread function of Weiner filter is employed to efficiently remove blur in the sparse component; a wiener filtering with the Gaussian PSF is used to recover the average image of the low-rank component. And then we get the recovered CT image sequence by combining the recovery low-rank image with all recovery sparse image sequence. Our method achieves restoration results with higher contrast, sharper organ boundaries and richer soft tissue structure information, compared with existing CT image restoration methods. The robustness of our method was assessed with numerical experiments using three different low-rank models: Robust Principle Component Analysis (RPCA), Linearized Alternating Direction Method with Adaptive Penalty (LADMAP) and Go Decomposition (GoDec). Experimental results demonstrated that the RPCA model was the most suitable for the small noise CT images whereas the GoDec model was the best for the large noisy CT images. PMID:24023764

C, Sr and Pb isotopic chemostratigraphy in precambrian carbonate sequences in the eastern transversal domain of the Borborema Province, northastern Brazil

International Nuclear Information System (INIS)

Santos, V. H.; Ferreira, V.P.; Sial, A.N; Babinski, M; Pimentel, M.M

2001-01-01

The Transversal Domain, in the Borborema Structural Province, northeastern Brazil, is characterized by a system of NE-trending, left-lateral, transcurrent mega-structure and dextral E-W trending fault zones (Jardim de Sa, 1994). This domain is formed by supracrustal metasedimentary and metavolcansedimentary sequences overlying a gneissic-migmatitic basement. Geological sequences of this domain exhibit distinct lithotectono-stratigraphy that characterize different terranes, separated by shear zones developed during the Cariris Velhos cycle (1.1-0.95 Ga), and that have been reworked during the Brasiliano orogen at the end of the Neoproterozoic (Brito Neves et al., 1995). The objective of this work is to show the results of C, Sr and Pb isotope studies performed in marble lens located near (and in both sides) the proposed boundary between two tectono-stratigraphic terranes (Alto Moxoto and Rio Capibaribe) in the Transversal Domain (au)

Stratigraphic controls on fluid and solute fluxes across the sediment-water interface of an estuary

Science.gov (United States)

Sawyer, Audrey H.; Lazareva, Olesya; Kroeger, Kevin D.; Crespo, Kyle; Chan, Clara S.; Stieglitz, Thomas; Michael, Holly A.

2014-01-01

Shallow stratigraphic features, such as infilled paleovalleys, modify fresh groundwater discharge to coastal waters and fluxes of saltwater and nutrients across the sediment–water interface. We quantify the spatial distribution of shallow surface water–groundwater exchange and nitrogen fluxes near a paleovalley in Indian River Bay, Delaware, using a hand resistivity probe, conventional seepage meters, and pore-water samples. In the interfluve (region outside the paleovalley) most nitrate-rich fresh groundwater discharges rapidly near the coast with little mixing of saline pore water, and nitrogen transport is largely conservative. In the peat-filled paleovalley, fresh groundwater discharge is negligible, and saltwater exchange is deep (∼1 m). Long pore-water residence times and abundant sulfate and organic matter promote sulfate reduction and ammonium production in shallow sediment. Reducing, iron-rich fresh groundwater beneath paleovalley peat discharges diffusely around paleovalley margins offshore. In this zone of diffuse fresh groundwater discharge, saltwater exchange and dispersion are enhanced, ammonium is produced in shallow sediments, and fluxes of ammonium to surface water are large. By modifying patterns of groundwater discharge and the nature of saltwater exchange in shallow sediments, paleovalleys and other stratigraphic features influence the geochemistry of discharging groundwater. Redox reactions near the sediment–water interface affect rates and patterns of geochemical fluxes to coastal surface waters. For example, at this site, more than 99% of the groundwater-borne nitrate flux to the Delaware Inland Bays occurs within the interfluve portion of the coastline, and more than 50% of the ammonium flux occurs at the paleovalley margin.

PRIMAL: Page Rank-Based Indoor Mapping and Localization Using Gene-Sequenced Unlabeled WLAN Received Signal Strength

Directory of Open Access Journals (Sweden)

Mu Zhou

2015-09-01

Full Text Available Due to the wide deployment of wireless local area networks (WLAN, received signal strength (RSS-based indoor WLAN localization has attracted considerable attention in both academia and industry. In this paper, we propose a novel page rank-based indoor mapping and localization (PRIMAL by using the gene-sequenced unlabeled WLAN RSS for simultaneous localization and mapping (SLAM. Specifically, first of all, based on the observation of the motion patterns of the people in the target environment, we use the Allen logic to construct the mobility graph to characterize the connectivity among different areas of interest. Second, the concept of gene sequencing is utilized to assemble the sporadically-collected RSS sequences into a signal graph based on the transition relations among different RSS sequences. Third, we apply the graph drawing approach to exhibit both the mobility graph and signal graph in a more readable manner. Finally, the page rank (PR algorithm is proposed to construct the mapping from the signal graph into the mobility graph. The experimental results show that the proposed approach achieves satisfactory localization accuracy and meanwhile avoids the intensive time and labor cost involved in the conventional location fingerprinting-based indoor WLAN localization.

PRIMAL: Page Rank-Based Indoor Mapping and Localization Using Gene-Sequenced Unlabeled WLAN Received Signal Strength.

Science.gov (United States)

Zhou, Mu; Zhang, Qiao; Xu, Kunjie; Tian, Zengshan; Wang, Yanmeng; He, Wei

2015-09-25

Due to the wide deployment of wireless local area networks (WLAN), received signal strength (RSS)-based indoor WLAN localization has attracted considerable attention in both academia and industry. In this paper, we propose a novel page rank-based indoor mapping and localization (PRIMAL) by using the gene-sequenced unlabeled WLAN RSS for simultaneous localization and mapping (SLAM). Specifically, first of all, based on the observation of the motion patterns of the people in the target environment, we use the Allen logic to construct the mobility graph to characterize the connectivity among different areas of interest. Second, the concept of gene sequencing is utilized to assemble the sporadically-collected RSS sequences into a signal graph based on the transition relations among different RSS sequences. Third, we apply the graph drawing approach to exhibit both the mobility graph and signal graph in a more readable manner. Finally, the page rank (PR) algorithm is proposed to construct the mapping from the signal graph into the mobility graph. The experimental results show that the proposed approach achieves satisfactory localization accuracy and meanwhile avoids the intensive time and labor cost involved in the conventional location fingerprinting-based indoor WLAN localization.

Research on Image Encryption Based on DNA Sequence and Chaos Theory

Science.gov (United States)

Tian Zhang, Tian; Yan, Shan Jun; Gu, Cheng Yan; Ren, Ran; Liao, Kai Xin

2018-04-01

Nowadays encryption is a common technique to protect image data from unauthorized access. In recent years, many scientists have proposed various encryption algorithms based on DNA sequence to provide a new idea for the design of image encryption algorithm. Therefore, a new method of image encryption based on DNA computing technology is proposed in this paper, whose original image is encrypted by DNA coding and 1-D logistic chaotic mapping. First, the algorithm uses two modules as the encryption key. The first module uses the real DNA sequence, and the second module is made by one-dimensional logistic chaos mapping. Secondly, the algorithm uses DNA complementary rules to encode original image, and uses the key and DNA computing technology to compute each pixel value of the original image, so as to realize the encryption of the whole image. Simulation results show that the algorithm has good encryption effect and security.

A stratigraphic model to support remediation of groundwater contamination in the southern San Francisco Bay area

International Nuclear Information System (INIS)

Steinpress, M.G.

1993-01-01

Some early regional studies in the southern San Francisco Bay Area applied the term 'older bay mud' to Wisconsin and older deposits thought to be estuarine in origin. This outdated interpretation has apparently contributed to an expectation of laterally-continuous aquifers and aquitards. In fact, heterogeneous alluvial deposits often create complex hydrogeologic settings that defy simple remedial approaches. A more useful stratigraphic model provides a foundation for conducting site investigations and assessing the feasibility of remediation. A synthesis of recent regional studies and drilling results at one site on the southwest margin of the Bay indicate that the upper quaternary stratigraphy consists of four primary units in the upper 200 feet of sediments (oldest to youngest): (1) Illinoian glacial-age alluvium (an important groundwater source); (2) Sangamon interglacial-age deposits, which include fine-grained alluvial deposits and estuarine deposits equivalent to the Yerba Buena Mud (a regional confining layer); (3) Wisconsin glacial-age alluvial fan and floodplain deposits; and (4) Holocene interglacial-age sediments, which include fine-grained alluvial and estuarine deposits equivalent to the 'younger bay mud'. Remedial investigations generally focus on groundwater contamination in the Wisconsin and Holocene alluvial deposits. Detailed drilling results indicate that narrow sand and gravel channels occur in anastomosing patterns within a Wisconsin to Holocene floodplain sequence dominated by interchannel silts and clays. The identification of these small-scale high-permeability conduits is critical to understanding and predicting contaminant transport on a local scale. Discontinuous site-specific aquitards do not provide competent separation where stacked channels occur and the correlation of aquitards over even small distance is often tenuous at best

Status of image analysis methods to delineate stratigraphic position in the Topopah Spring Member of the Paintbrush Tuff, Yucca Mountain, Nye County, Nevada

International Nuclear Information System (INIS)

Campbell, K.; Broxton, D.E.; Spaw, J.

1989-10-01

The Topopah Spring Member of the Paintbrush Tuff is an ash-flow cooling unit that is the candidate host rock for a potential high-level nuclear waste repository at Yucca Mountain, Nevada. The repository workings will be mostly confined to the member's rhyolitic portion, which is chemically homogenous but texturally variable. This report describes the status of work to develop a useful internal stratigraphy for the rhyolitic portion of the member; our approach is to use an image analysis technique to map textural variations within the member as a function of stratigraphic height. Fifteen petrographic thin sections of Topopah Spring rhyolitic tuff were studied in each of two drill holes (USW GU-3 and USW G-4). Digital color images were collected in transmitted light for two scenes 1 cm on a side for each thin section. Objects within a scene were classified by color, and measurements of area, elongation, and roughness were determined for each object. Summary statistics were compiled for all measurements for each color component within a scene, and each variable was statistically examined for correlations with stratigraphic position. Our initial studies using image analysis have not yet produced a useful method for determining stratigraphic position within the Topopah Spring Member. Simplifications made in this preliminary application of image analysis may be largely responsible for these negative results. The technique deserves further investigation, and more detailed analysis of existing data is recommended. 9 refs., 11 figs., 4 tabs

Stratigraphic evidence of desertification in the west-central Great Plains within the past 1000 yr

Science.gov (United States)

Madole, R.F.

1994-01-01

Stratigraphic and geomorphic relations, archaeological data, and eight radiocarbon ages at five widely scattered localities in northeastern Colorado indicate that eolian sand was mobilized over broad areas within the past 1000 yr. The mobilization began after 1 ka, was episodic, and ended at some as yet undetermined time prior to the latter part of the 19th century. Given that climate-model simulations suggest only slight variation in average surface temperature and annual precipitation in this region during the past 1000 yr, this part of the Great Plains evidently is near the threshold of widespread eolian sand transport under the present climate. -Author

The geostatistical approach for structural and stratigraphic framework analysis of offshore NW Bonaparte Basin, Australia

International Nuclear Information System (INIS)

Wahid, Ali; Salim, Ahmed Mohamed Ahmed; Yusoff, Wan Ismail Wan; Gaafar, Gamal Ragab

2016-01-01

Geostatistics or statistical approach is based on the studies of temporal and spatial trend, which depend upon spatial relationships to model known information of variable(s) at unsampled locations. The statistical technique known as kriging was used for petrophycial and facies analysis, which help to assume spatial relationship to model the geological continuity between the known data and the unknown to produce a single best guess of the unknown. Kriging is also known as optimal interpolation technique, which facilitate to generate best linear unbiased estimation of each horizon. The idea is to construct a numerical model of the lithofacies and rock properties that honor available data and further integrate with interpreting seismic sections, techtonostratigraphy chart with sea level curve (short term) and regional tectonics of the study area to find the structural and stratigraphic growth history of the NW Bonaparte Basin. By using kriging technique the models were built which help to estimate different parameters like horizons, facies, and porosities in the study area. The variograms were used to determine for identification of spatial relationship between data which help to find the depositional history of the North West (NW) Bonaparte Basin

The geostatistical approach for structural and stratigraphic framework analysis of offshore NW Bonaparte Basin, Australia

Energy Technology Data Exchange (ETDEWEB)

Wahid, Ali, E-mail: ali.wahid@live.com; Salim, Ahmed Mohamed Ahmed, E-mail: mohamed.salim@petronas.com.my; Yusoff, Wan Ismail Wan, E-mail: wanismail-wanyusoff@petronas.com.my [Universiti Teknologi PETRONAS, Bandar Seri Iskandar, 32610 Tronoh, Perak (Malaysia); Gaafar, Gamal Ragab, E-mail: gaafargr@gmail.com [Petroleum Engineering Division, PETRONAS Carigali Sdn Bhd, Kuala Lumpur (Malaysia)

2016-02-01

Geostatistics or statistical approach is based on the studies of temporal and spatial trend, which depend upon spatial relationships to model known information of variable(s) at unsampled locations. The statistical technique known as kriging was used for petrophycial and facies analysis, which help to assume spatial relationship to model the geological continuity between the known data and the unknown to produce a single best guess of the unknown. Kriging is also known as optimal interpolation technique, which facilitate to generate best linear unbiased estimation of each horizon. The idea is to construct a numerical model of the lithofacies and rock properties that honor available data and further integrate with interpreting seismic sections, techtonostratigraphy chart with sea level curve (short term) and regional tectonics of the study area to find the structural and stratigraphic growth history of the NW Bonaparte Basin. By using kriging technique the models were built which help to estimate different parameters like horizons, facies, and porosities in the study area. The variograms were used to determine for identification of spatial relationship between data which help to find the depositional history of the North West (NW) Bonaparte Basin.

Correlation chart of Pennsylvanian rocks in Alabama, Tennessee, Kentucky, Virginia, West Virginia, Ohio, Maryland, and Pennsylvania showing approximate position of coal beds, coal zones, and key stratigraphic units: Chapter D.2 in Coal and petroleum resources in the Appalachian basin: distribution, geologic framework, and geochemical character

Science.gov (United States)

Ruppert, Leslie F.; Trippi, Michael H.; Slucher, Ernie R.; Ruppert, Leslie F.; Ryder, Robert T.

2014-01-01

The Appalachian basin, one of the largest Pennsylvanian bituminous coal-producing regions in the world, currently contains nearly one-half of the top 15 coal-producing States in the United States (Energy Information Agency, 2006). Anthracite of Pennsylvanian age occurs in synclinal basins in eastern Pennsylvania, but production is minimal. A simplified correlation chart was compiled from published and unpublished sources as a means of visualizing currently accepted stratigraphic relations between the rock formations, coal beds, coal zones, and key stratigraphic units in Alabama, Tennessee, Kentucky, Virginia, West Virginia, Ohio, Maryland, and Pennsylvania. The thickness of each column is based on chronostratigraphic divisions (Lower, Middle, and Upper Pennsylvanian), not the thickness of strata. Researchers of Pennsylvanian strata in the Appalachian basin also use biostratigraphic markers and other relative and absolute geologic age associations between the rocks to better understand the spatial relations of the strata. Thus, the stratigraphic correlation data in this chart should be considered provisional and will be updated as coal-bearing rocks within the Appalachian coal regions continue to be evaluated.

Sequence comparison alignment-free approach based on suffix tree and L-words frequency.

Science.gov (United States)

Soares, Inês; Goios, Ana; Amorim, António

2012-01-01

The vast majority of methods available for sequence comparison rely on a first sequence alignment step, which requires a number of assumptions on evolutionary history and is sometimes very difficult or impossible to perform due to the abundance of gaps (insertions/deletions). In such cases, an alternative alignment-free method would prove valuable. Our method starts by a computation of a generalized suffix tree of all sequences, which is completed in linear time. Using this tree, the frequency of all possible words with a preset length L-L-words--in each sequence is rapidly calculated. Based on the L-words frequency profile of each sequence, a pairwise standard Euclidean distance is then computed producing a symmetric genetic distance matrix, which can be used to generate a neighbor joining dendrogram or a multidimensional scaling graph. We present an improvement to word counting alignment-free approaches for sequence comparison, by determining a single optimal word length and combining suffix tree structures to the word counting tasks. Our approach is, thus, a fast and simple application that proved to be efficient and powerful when applied to mitochondrial genomes. The algorithm was implemented in Python language and is freely available on the web.

CGKB: an annotation knowledge base for cowpea (Vigna unguiculata L. methylation filtered genomic genespace sequences

Directory of Open Access Journals (Sweden)

Spraggins Thomas A

2007-04-01

Full Text Available Abstract Background Cowpea [Vigna unguiculata (L. Walp.] is one of the most important food and forage legumes in the semi-arid tropics because of its ability to tolerate drought and grow on poor soils. It is cultivated mostly by poor farmers in developing countries, with 80% of production taking place in the dry savannah of tropical West and Central Africa. Cowpea is largely an underexploited crop with relatively little genomic information available for use in applied plant breeding. The goal of the Cowpea Genomics Initiative (CGI, funded by the Kirkhouse Trust, a UK-based charitable organization, is to leverage modern molecular genetic tools for gene discovery and cowpea improvement. One aspect of the initiative is the sequencing of the gene-rich region of the cowpea genome (termed the genespace recovered using methylation filtration technology and providing annotation and analysis of the sequence data. Description CGKB, Cowpea Genespace/Genomics Knowledge Base, is an annotation knowledge base developed under the CGI. The database is based on information derived from 298,848 cowpea genespace sequences (GSS isolated by methylation filtering of genomic DNA. The CGKB consists of three knowledge bases: GSS annotation and comparative genomics knowledge base, GSS enzyme and metabolic pathway knowledge base, and GSS simple sequence repeats (SSRs knowledge base for molecular marker discovery. A homology-based approach was applied for annotations of the GSS, mainly using BLASTX against four public FASTA formatted protein databases (NCBI GenBank Proteins, UniProtKB-Swiss-Prot, UniprotKB-PIR (Protein Information Resource, and UniProtKB-TrEMBL. Comparative genome analysis was done by BLASTX searches of the cowpea GSS against four plant proteomes from Arabidopsis thaliana, Oryza sativa, Medicago truncatula, and Populus trichocarpa. The possible exons and introns on each cowpea GSS were predicted using the HMM-based Genscan gene predication program and the

A unique fossil record from neptunian sills: the world's most extreme example of stratigraphic condensation (Jurassic, western Sicily)

Science.gov (United States)

Wendt, Jobst

2017-06-01

Neptunian sills at Rocca Busambra, a fragment of the Trapanese/Saccense Domain in western Sicily, host the most abundant ammonite and gastropod fauna which has ever been recorded from the Jurassic of the western Tethys. The fauna is dominated by parautochthonous organisms which were swept into the sills by gentle transport. Ammonites are characterized by perfect preservation and small size, a feature which is due to the predominance of microconchs but also of stunting. The most complete sill is 0.7 m thick and could be separated into 17 levels which range in age from the early Toarcian into the late Kimmeridgian, thus representing the most extreme case of palaeontologically and depositionally documented stratigraphic condensation in Earth history. The unique feature of the Rocca Busambra sills is due to the interaction of three processes: extreme stratigraphic condensation on the sea floor, weak tectonic fracturing of the host rock and repeated reopening on top of already existing sills. Contrasting percentages of gastropods in individual levels reflect sea-level oscillations which correspond to long known low- and highstands during the Jurassic of the western Tethys. Comparisons with other ammonite-bearing sill faunas reveal several similarities, but represent only short-timed phases of tectonic pulses and deposition.

incaRNAfbinv: a web server for the fragment-based design of RNA sequences

Science.gov (United States)

Drory Retwitzer, Matan; Reinharz, Vladimir; Ponty, Yann; Waldispühl, Jérôme; Barash, Danny

2016-01-01

Abstract In recent years, new methods for computational RNA design have been developed and applied to various problems in synthetic biology and nanotechnology. Lately, there is considerable interest in incorporating essential biological information when solving the inverse RNA folding problem. Correspondingly, RNAfbinv aims at including biologically meaningful constraints and is the only program to-date that performs a fragment-based design of RNA sequences. In doing so it allows the design of sequences that do not necessarily exactly fold into the target, as long as the overall coarse-grained tree graph shape is preserved. Augmented by the weighted sampling algorithm of incaRNAtion, our web server called incaRNAfbinv implements the method devised in RNAfbinv and offers an interactive environment for the inverse folding of RNA using a fragment-based design approach. It takes as input: a target RNA secondary structure; optional sequence and motif constraints; optional target minimum free energy, neutrality and GC content. In addition to the design of synthetic regulatory sequences, it can be used as a pre-processing step for the detection of novel natural occurring RNAs. The two complementary methodologies RNAfbinv and incaRNAtion are merged together and fully implemented in our web server incaRNAfbinv, available at http://www.cs.bgu.ac.il/incaRNAfbinv. PMID:27185893

Integrated Sedimentological Approach to Assess Reservoir Quality and Architecture of Khuff Carbonates: Outcrop Analog, Central Saudi Arabia

Science.gov (United States)

Osman, Mutsim; Abdullatif, Osman

2017-04-01

The Permian to Triassic Khuff carbonate reservoirs (and equivalents) in the Middle East are estimated to contain about 38.4% of the world's natural gas reserves. Excellent exposed outcrops in central Saudi Arabia provide good outcrop equivalents to subsurface Khuff reservoirs. This study conduct high resolution outcrop scale investigations on an analog reservoir for upper Khartam of Khuff Formation. The main objective is to reconstruct litho- and chemo- stratigraphic outcrop analog model that may serve to characterize reservoir high resolution (interwell) heterogeneity, continuity and architecture. Given the fact of the limitation of subsurface data and toolsin capturing interwell reservoir heterogeneity, which in turn increases the value of this study.The methods applied integrate sedimentological, stratigraphic petrographic, petrophysical data and chemical analyses for major, trace and rare earth elements. In addition, laser scanning survey (LIDAR) was also utilized in this study. The results of the stratigraphic investigations revealed that the lithofacies range from mudstone, wackestone, packestone and grainstone. These lithofacies represent environments ranging from supratidal, intertidal, subtidal and shoal complex. Several meter-scale and less high resolution sequences and composite sequences within 4th and 5th order cycles were also recognized in the outcrop analog. The lithofacies and architectural analysis revealed several vertically and laterally stacked sequences at the outcrop as revealed from the stratigraphic sections and the lidar scan. Chemostratigraphy is effective in identifying lithofacies and sequences within the outcrop analog. Moreover, different chemical signatures were also recognized and allowed establishing and correlating high resolution lithofacies, reservoir zones, layers and surfaces bounding reservoirs and non-reservoir zones at scale of meters or less. The results of this high resolution outcrop analog study might help to understand

Late Pleistocene sequence architecture on the geostrophic current-dominated southwest margin of the Ulleung Basin, East Sea

Science.gov (United States)

Choi, Dong-Lim; Shin, Dong-Hyeok; Kum, Byung-Cheol; Jang, Seok; Cho, Jin-Hyung; Jou, Hyeong-Tae; Jang, Nam-Do

2018-06-01

High-resolution multichannel seismic data were collected to identify depositional sequences on the southwestern shelf of the Ulleung Basin, where a unidirectional ocean current is dominant at water depths exceeding 130 m. Four aggradational stratigraphic sequences with a 100,000-year cycle were recognized since marine isotope stage (MIS) 10. These sequences consist only of lowstand systems tracts (LSTs) and falling-stage systems tracts (FSSTs). Prograding wedge-shaped deposits are present in the LSTs near the shelf break. Oblique progradational clinoforms of forced regressive deposits are present in the FSSTs on the outer continental shelf. Each FSST has non-uniform forced regressional stratal geometries, reflecting that the origins of sediments in each depositional sequence changed when sea level was falling. Slump deposits are characteristically developed in the upper layer of the FSSTs, and this was used as evidence to distinguish the sequence boundaries. The subsidence rates around the shelf break reached as much as 0.6 mm/year since MIS 10, which contributed to the well-preserved depositional sequence. During the Quaternary sea-level change, the water depth in the Korea Strait declined and the intensity of the Tsushima Current flowing near the bottom of the inner continental shelf increased. This resulted in greater erosion of sediments that were delivered to the outer continental shelf, which was the main cause of sediment deposition on the deep, low-angled outer shelf. Therefore, a depositional sequence formation model that consists of only FSSTs and LSTs, excluding highstand systems tracts (HSTs) and transgressive systems tracts (TSTs), best explains the depositional sequence beneath this shelf margin dominated by a geostrophic current.

A Shellcode Detection Method Based on Full Native API Sequence and Support Vector Machine

Science.gov (United States)

Cheng, Yixuan; Fan, Wenqing; Huang, Wei; An, Jing

2017-09-01

Dynamic monitoring the behavior of a program is widely used to discriminate between benign program and malware. It is usually based on the dynamic characteristics of a program, such as API call sequence or API call frequency to judge. The key innovation of this paper is to consider the full Native API sequence and use the support vector machine to detect the shellcode. We also use the Markov chain to extract and digitize Native API sequence features. Our experimental results show that the method proposed in this paper has high accuracy and low detection rate.

Nuevos datos sobre estratigrafía del Ordovícico y estructura varisca en el Macizo de Santa María la Real de Nieva

OpenAIRE

Alonso, F.; Rubio, F. J.; Martín Parra, L. M.; Rodríguez Fernández, L. R.

2004-01-01

We present a new geological map of the lower Ordovician materials cropping out in the Santa Maria la Real de Nieva Massif. The Ordovician sequence, Fm. Capas de Domingo García, comprises two separate stratigraphic units. The lower unit contains conglomerate with clasts of felsic volcanic rocks at its base, slates, and quartzite with cruziana. The upper unit is composed by the quartzite and slate, which is considered a regional equivalent of the sequence at the base of the Armorica...

Final Technical Report on the Genome Sequence DataBase (GSDB): DE-FG03 95 ER 62062 September 1997-September 1999

Energy Technology Data Exchange (ETDEWEB)

Harger, Carol A.

1999-10-28

Since September 1997 NCGR has produced two web-based tools for researchers to use to access and analyze data in the Genome Sequence DataBase (GSDB). These tools are: Sequence Viewer, a nucleotide sequence and annotation visualization tool, and MAR-Finder, a tool that predicts, base upon statistical inferences, the location of matrix attachment regions (MARS) within a nucleotide sequence. [The annual report for June 1996 to August 1997 is included as an attachment to this final report.

Sedimentological and Stratigraphic Controls on Natural Fracture Distribution in Wajid Group, SW Saudi Arabia

Science.gov (United States)

Benaafi, Mohammed; Hariri, Mustafa; Abdullatif, Osman; Makkawi, Mohammed; Korvin, Gabor

2016-04-01

The Cambro-Permian Wajid Group, SW Saudi Arabia, is the main groundwater aquifer in Wadi Al-Dawasir and Najran areas. In addition, it has a reservoir potentiality for oil and natural gas in Rub' Al-Khali Basin. Wajid Group divided into four formations, ascending Dibsiyah, Sanamah, Khussyayan and Juwayl. They are mainly sandstone and exposed in an area extend from Wadi Al-Dawasir southward to Najran city and deposited within fluvial, shallow marine and glacial environments. This study aims to investigate the sedimentological and stratigraphic controls on the distribution of natural fractures within Wajid Group outcrops. A scanline sampling method was used to study the natural fracture network within Wajid Group outcrops, where the natural fractures were measured and characterized in 12 locations. Four regional natural fracture sets were observed with mean strikes of 050o, 075o, 345o, and 320o. Seven lithofacies characterized the Wajid Group at these locations and include fine-grained sandstone, coarse to pebbly sandstone, cross-bedded sandstone, massive sandstone, bioturbated sandstone, conglomerate sandstone, and conglomerate lithofacies. We found that the fine-grained and small scale cross-bedded sandstones lithofacies are characterized by high fracture intensity. In contrast, the coarse-grained sandstone and conglomerate lithofacies have low fracture intensity. Therefore, the relative fracture intensity and spacing of natural fractures within Wajid Group in the subsurface can be predicted by using the lithofacies and their depositional environments. In terms of stratigraphy, we found that the bed thickness and the stratigraphic architecture are the main controls on fractures intensity. The outcomes of this study can help to understand and predict the natural fracture distribution within the subsurface fractured sandstone hosting groundwater and hydrocarbon in Wajid and Rub' Al-Khali Basins. Hence, the finding of this study might help to explore and develop the

Geophysical mapping of the occurrence of shallow oil sands in ...

African Journals Online (AJOL)

ISHIOMA

studied the tectonic evolution and stratigraphy of the. Dahomey basin in which they subdivided the sequence into stratigraphic units namely Ise formation, Afowo formation and Araromi formation based on the lithos- tratigraphic study of some boreholes from the area. The. Ise formation lying uncomfortably on the basement.

BioPig: a Hadoop-based analytic toolkit for large-scale sequence data.

Science.gov (United States)

Nordberg, Henrik; Bhatia, Karan; Wang, Kai; Wang, Zhong

2013-12-01

The recent revolution in sequencing technologies has led to an exponential growth of sequence data. As a result, most of the current bioinformatics tools become obsolete as they fail to scale with data. To tackle this 'data deluge', here we introduce the BioPig sequence analysis toolkit as one of the solutions that scale to data and computation. We built BioPig on the Apache's Hadoop MapReduce system and the Pig data flow language. Compared with traditional serial and MPI-based algorithms, BioPig has three major advantages: first, BioPig's programmability greatly reduces development time for parallel bioinformatics applications; second, testing BioPig with up to 500 Gb sequences demonstrates that it scales automatically with size of data; and finally, BioPig can be ported without modification on many Hadoop infrastructures, as tested with Magellan system at National Energy Research Scientific Computing Center and the Amazon Elastic Compute Cloud. In summary, BioPig represents a novel program framework with the potential to greatly accelerate data-intensive bioinformatics analysis.

DNA sequence of 15 base pairs is sufficient to mediate both glucocorticoid and progesterone induction of gene expression

International Nuclear Information System (INIS)

Straehle, U.; Klock, G.; Schuetz, G.

1987-01-01

To define the recognition sequence of the glucocorticoid receptor and its relationship with that of the progesterone receptor, oligonucleotides derived from the glucocorticoid response element of the tyrosine aminotransferase gene were tested upstream of a heterologous promoter for their capacity to mediate effects of these two steroids. The authors show that a 15-base-pair sequence with partial symmetry is sufficient to confer glucocorticoid inducibility on the promoter of the herpes simplex virus thymidine kinase gene. The same 15-base-pair sequence mediates induction by progesterone. Point mutations in the recognition sequence affect inducibility by glucocorticoids and progesterone similarly. Together with the strong conservation of the sequence of the DNA-binding domain of the two receptors, these data suggest that both proteins recognize a sequence that is similar, if not the same

Pseudoclypeina? crnogorica Radoičić, 1972: Stratigraphic revision and taxonomic note on a little known dasycladalean alga from Montenegro

Directory of Open Access Journals (Sweden)

Radoičić Rajka

2013-01-01

Full Text Available Pseudoclypeina? crnogorica was first described in 1972 from the Lower, Cretaceous limestone of the Njegoš Mt. area, Montenegro, Dinaric Carbonate Platform. It differs from other species of the genus Pseudoclypeina by its calcification pattern, the shape and relative length of the first and second order laterals, and by the presence in the type-material (a thin section containing the holotype of sections standing for the sterile portion of the thallus. This is why in this paper, the generic name is left in open nomenclature. On this occasion the species, whose presence is also reported from southern Iran, is re-described and better illustrated, based on material originating from other outcrops in Montenegro. The stratigraphic position is reviewed as well. Pseudoclypeina? crnogorica occurs in shallow water inner platform facies of early Neocomian age, along with Selliporella neocomiensis.

Variations in petrophysical properties of shales along a stratigraphic section in the Whitby mudstone (UK)

Science.gov (United States)

Barnhoorn, Auke; Houben, Maartje; Lie-A-Fat, Joella; Ravestein, Thomas; Drury, Martyn

2015-04-01

In unconventional tough gas reservoirs (e.g. tight sandstones or shales) the presence of fractures, either naturally formed or hydraulically induced, is almost always a prerequisite for hydrocarbon productivity to be economically viable. One of the formations classified so far as a potential interesting formation for shale gas exploration in the Netherlands is the Lower Jurassic Posidonia Shale Formation (PSF). However data of the Posidonia Shale Formation is scarce so far and samples are hard to come by, especially on the variability and heterogeneity of the petrophysical parameters of this shale little is known. Therefore research and sample collection is conducted on a time and depositional analogue of the PSF: the Whitby Mudstone Formation (WMF) in the United Kingdom. A large number of samples along a ~7m stratigraphic section of the Whitby Mudstone Formation have been collected and analysed. Standard petrophysical properties such as porosity and matrix densities are quantified for a number of samples throughout the section, as well as mineral composition analysis based on XRD/XRF and SEM analyses. Seismic velocity measurements are also conducted at multiple heights in the section and in multiple directions to elaborate on anisotropy of the material. Attenuation anisotropy is incorporated as well as Thomsen's parameters combined with elastic parameters, e.g. Young's modulus and Poisson's ratio, to quantify the elastic anisotropy. Furthermore rock mechanical experiments are conducted to determine the elastic constants, rock strength, fracture characteristics, brittleness index, fraccability and rock mechanical anisotropy across the stratigraphic section of the Whitby mudstone formation. Results show that the WMF is highly anisotropic and it exhibits an anisotropy on the large limit of anisotropy reported for US gas shales. The high anisotropy of the Whitby shales has an even larger control on the formation of the fracture network. Furthermore, most petrophysical

Proterozoic rifting and major unconformities in Rajasthan, and their implications for uranium mineralisation

International Nuclear Information System (INIS)

Sinha-Roy, S.

2004-01-01

Evolution of the Precambrian terrain in Rajasthan has taken place via crustal consolidation of the basement at ca. 2.9 Ga, its cratonisation at ca. 2.5 Ga, through protracted tectonostratigraphic evolution of the Proterozoic cover sequences, following repeated rifting and Wilson cycles in the Aravalli and Delhi foldbelts. Consequently, the Proterozoic rift basins are characterised by growth faults and pull-aparts, and multitier volcanose dimentary sequences that contain a number of unconformities and stratigraphic breaks. The Archaean basement of the Mewar terrain that witnessed end-Archaean K-magmatism and ductile shearing, led to the creation of a possible uranium province, namely uranium enriched basement. This province acted as the source of remobilised uranium and its concentration at suitable multilevel structural and stratigraphic traps within the Proterozoic rift basins to give rise to unconformity-related syngenetic uranium mineralisation. Late Neoproterozoic to Pan-African tectonothermal reworking of the basement rocks produced fracture zones and caused Na-metasomatism giving rise to albitite-related uranium mineralisation. Based on an analysis of Proterozoic rift kinematics and lithofacies characteristics, five possible uranium-enriched stratigraphic horizons have been identified in the Aravalli and its equivalent sequences as well as in the North Delhi foldbelt sequences. From a regional synthesis, ten possible uranium metallogenic events, spanning ca. 2.5-0.5 Ga, are recognised in Rajasthan. These uranium events have predictive value for delineation of target areas for exploration. (author)

Discrimination of the Lactobacillus acidophilus group using sequencing, species-specific PCR and SNaPshot mini-sequencing technology based on the recA gene.

Science.gov (United States)

Huang, Chien-Hsun; Chang, Mu-Tzu; Huang, Mu-Chiou; Wang, Li-Tin; Huang, Lina; Lee, Fwu-Ling

2012-10-01

To clearly identify specific species and subspecies of the Lactobacillus acidophilus group using phenotypic and genotypic (16S rDNA sequence analysis) techniques alone is difficult. The aim of this study was to use the recA gene for species discrimination in the L. acidophilus group, as well as to develop a species-specific primer and single nucleotide polymorphism primer based on the recA gene sequence for species and subspecies identification. The average sequence similarity for the recA gene among type strains was 80.0%, and most members of the L. acidophilus group could be clearly distinguished. The species-specific primer was designed according to the recA gene sequencing, which was employed for polymerase chain reaction with the template DNA of Lactobacillus strains. A single 231-bp species-specific band was found only in L. delbrueckii. A SNaPshot mini-sequencing assay using recA as a target gene was also developed. The specificity of the mini-sequencing assay was evaluated using 31 strains of L. delbrueckii species and was able to unambiguously discriminate strains belonging to the subspecies L. delbrueckii subsp. bulgaricus. The phylogenetic relationships of most strains in the L. acidophilus group can be resolved using recA gene sequencing, and a novel method to identify the species and subspecies of the L. delbrueckii and L. delbrueckii subsp. bulgaricus was developed by species-specific polymerase chain reaction combined with SNaPshot mini-sequencing. Copyright © 2012 Society of Chemical Industry.

MISTICA: Minimum Spanning Tree-Based Coarse Image Alignment for Microscopy Image Sequences.

Science.gov (United States)

Ray, Nilanjan; McArdle, Sara; Ley, Klaus; Acton, Scott T

2016-11-01

Registration of an in vivo microscopy image sequence is necessary in many significant studies, including studies of atherosclerosis in large arteries and the heart. Significant cardiac and respiratory motion of the living subject, occasional spells of focal plane changes, drift in the field of view, and long image sequences are the principal roadblocks. The first step in such a registration process is the removal of translational and rotational motion. Next, a deformable registration can be performed. The focus of our study here is to remove the translation and/or rigid body motion that we refer to here as coarse alignment. The existing techniques for coarse alignment are unable to accommodate long sequences often consisting of periods of poor quality images (as quantified by a suitable perceptual measure). Many existing methods require the user to select an anchor image to which other images are registered. We propose a novel method for coarse image sequence alignment based on minimum weighted spanning trees (MISTICA) that overcomes these difficulties. The principal idea behind MISTICA is to reorder the images in shorter sequences, to demote nonconforming or poor quality images in the registration process, and to mitigate the error propagation. The anchor image is selected automatically making MISTICA completely automated. MISTICA is computationally efficient. It has a single tuning parameter that determines graph width, which can also be eliminated by the way of additional computation. MISTICA outperforms existing alignment methods when applied to microscopy image sequences of mouse arteries.

ITS-2 sequences-based identification of Trichogramma species in South America

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R. P. Almeida

Full Text Available Abstract ITS2 (Internal transcribed spacer 2 sequences have been used in systematic studies and proved to be useful in providing a reliable identification of Trichogramma species. DNAr sequences ranged in size from 379 to 632 bp. In eleven T. pretiosum lines Wolbachia-induced parthenogenesis was found for the first time. These thelytokous lines were collected in Peru (9, Colombia (1 and USA (1. A dichotomous key for species identification was built based on the size of the ITS2 PCR product and restriction analysis using three endonucleases (EcoRI, MseI and MaeI. This molecular technique was successfully used to distinguish among seventeen native/introduced Trichogramma species collected in South America.

Sequence Comparison Alignment-Free Approach Based on Suffix Tree and L-Words Frequency

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Inês Soares

2012-01-01

Full Text Available The vast majority of methods available for sequence comparison rely on a first sequence alignment step, which requires a number of assumptions on evolutionary history and is sometimes very difficult or impossible to perform due to the abundance of gaps (insertions/deletions. In such cases, an alternative alignment-free method would prove valuable. Our method starts by a computation of a generalized suffix tree of all sequences, which is completed in linear time. Using this tree, the frequency of all possible words with a preset length L—L-words—in each sequence is rapidly calculated. Based on the L-words frequency profile of each sequence, a pairwise standard Euclidean distance is then computed producing a symmetric genetic distance matrix, which can be used to generate a neighbor joining dendrogram or a multidimensional scaling graph. We present an improvement to word counting alignment-free approaches for sequence comparison, by determining a single optimal word length and combining suffix tree structures to the word counting tasks. Our approach is, thus, a fast and simple application that proved to be efficient and powerful when applied to mitochondrial genomes. The algorithm was implemented in Python language and is freely available on the web.

Storm-related sedimentation influenced by coastal configuration in the stratigraphic record of a tectonically active shelf (Upper Pleistocene Le Castella terrace, Italy)

Science.gov (United States)

Nalin, Ronald; Massari, Francesco

2018-03-01

Analysis of patterns of coastal circulation and sediment dispersal is an essential step for the study of controlling factors influencing the long-term dynamics of coastal systems. Modern settings offer the possibility to monitor relevant parameters over relatively short time spans. However, geological examples complement this perspective by providing a time-averaged record where longer trends and stratigraphically significant processes can be evaluated. This study investigates the shallow marine deposits of Le Castella terrace (Upper Pleistocene, southern Italy) to document how patterns of circulation influenced by coastline configuration can affect the preserved millennial-scale depositional record of a progradational shoreline system. The regressive portion of the Le Castella terrace deposits, developed during a relative sea-level highstand and falling stage, consists of a progradational wedge mainly composed of redistributed skeletal particles of a coeval shallow water carbonate factory. Preservation of the morphology of the paleocoastline and abundant current-related sedimentary structures allow reconstruction of the predominant sediment dispersal dynamics responsible for the formation of this sedimentary wedge. Facies and paleocurrent analysis indicate offshore and alongshore sediment transport modes, consistent with coastal circulation driven by storms normally incident to the shoreline and a sharp change in coastline orientation. This coastal inflection influenced circulation patterns causing flow separation and eddy formation in the lee of the curved coastline. Syndepositional tectonic deformation also affected the architecture of the preserved deposits, controlling the nucleation and development of a clinostratified body and determining localized lateral stratigraphic variability. This study illustrates how transient but recurrent circulation patterns associated with changes in coastal orientation and related to high-energy storm events can leave a

Negative Sequence Droop Method based Hierarchical Control for Low Voltage Ride-Through in Grid-Interactive Microgrids

DEFF Research Database (Denmark)

Zhao, Xin; Firoozabadi, Mehdi Savaghebi; Quintero, Juan Carlos Vasquez

2015-01-01

. In this paper, a voltage support strategy based on negative sequence droop control, which regulate the positive/negative sequence active and reactive power flow by means of sending proper voltage reference to the inner control loop, is proposed for the grid connected MGs to ride through voltage sags under...... complex line impedance conditions. In this case, the MGs should inject a certain amount of positive and negative sequence power to the grid so that the voltage quality at load side can be maintained at a satisfied level. A two layer hierarchical control strategy is proposed in this paper. The primary...... control loop consists of voltage and current inner loops, conventional droop control and virtual impedance loop while the secondary control loop is based on positive/negative sequence droop control which can achieve power injection under voltage sags. Experimental results with asymmetrical voltage sags...

Optimal pseudorandom sequence selection for online c-VEP based BCI control applications

DEFF Research Database (Denmark)

Isaksen, Jonas L.; Mohebbi, Ali; Puthusserypady, Sadasivan

2017-01-01

to predict the chance of completion and accuracy score. Results: No specific pseudorandom sequence showed superior accuracy on the group basis. When isolating the individual performances with the highest accuracy, time consumption per identification was not significantly increased. The Accuracy Score aids...... is a laborious process. Aims: This study aimed to suggest an efficient method for choosing the optimal stimulus sequence based on a fast test and simple measures to increase the performance and minimize the time consumption for research trials. Methods: A total of 21 healthy subjects were included in an online...... wheelchair control task and completed the same task using stimuli based on the m-code, the gold-code, and the Barker-code. Correct/incorrect identification and time consumption were obtained for each identification. Subject-specific templates were characterized and used in a forward-step first-order model...

Review and protection possibilities of some trans-border (East Serbia-West Bulgaria stratigraphic/palaeontological geosites

Directory of Open Access Journals (Sweden)

Jovanović Velimir

2012-01-01

Full Text Available Stratigraphic/palaeontological geosites of Stara Planina Mountain in east Serbia are well developed in the area of Serbian/Bulgarian state border, where with this occassion, three sections of exeptional geological and scientific interest are selected: Jelovica, Rosomač and Senokos. These geosites represent the important localities for study of Triassic and Jurassic terrigene-carbonate deposits, for which the scientific value from the domains of palaeontology, stratigraphy and sedimentology is widely known. The aim of this work is to represent the main scientific arguments for inventory and protection of detached transborder geological sites that are unique according to their composition and content.[Projekat Ministarstva nauke Republike Srbije, br. 176008

The discussion on the relationship between high-resolution sequence stratigraphy and uranium mineralization of Zhiluo formation in Dongsheng area, ordos basin

International Nuclear Information System (INIS)

Chen Xiaolin; Xiang Weidong; Li Tiangang; Fang Xiheng; Pang Yaqing

2007-01-01

According to the data of drill cores, outcrops and well logging, two orders base-level cycles are recognized from Zhiluo Formation in Dongsheng area, which consist of 8-14 short-term base-level cycles and 3 mid-term base-level cycles, and their structural types and stacking patterns are discussed by using principles and methods of high-resolution sequence stratigraphic theory. Based on the correlation of mid-term base-level cycles, the control of the A/S (Accommodation/Sediment supply) ratio in mid-term base-level cycles on the scale of sand bodies and physical properties of reservoir is analysed. Studies show that the sand bodies of braided stream in MSC1 of Zhiluo Formation are favourable to uranium mineralization, however, the sand bodies of meandering river in MSC2 and MSC3 are not favourable to uranium mineralization. The change of the A/S results in the difference in characters of sand body, such as physical properties, continuity and so on, which control the fluid flowing path. After discussing the immigration of uranium-bearing oxidizing ground water in the braided channel sand bodies, the paper tries to present the answers to the question of why the host orebody occurs mainly in the middle and upper sand body which the lower limb is thicker than the upper limb in the limb orebodies. (authors)

Anatomy of extremely thin marine sequences landward of a passive-margin hinge zone: Neogene Calvert Cliffs succession, Maryland, U.S.A.

Energy Technology Data Exchange (ETDEWEB)

Kidwell, S.M. [Univ. of Chicago, IL (United States). Dept. of Geophysical Sciences

1997-03-01

Detailed examination of Neogene strata in cliffs 25--35 m high along the western shore of Chesapeake Bay, Maryland, reveals the complexity of the surviving record of siliciclastic sequences {approximately}150 km inland of the structural hinge zone of the Atlantic passive margin. Previous study of the lower to middle Miocene Calvert (Plum Point Member) and Choptank Formations documented a series of third-order sequences 7--10 m thick in which lowstand deposits are entirely lacking, transgressive tracts comprise a mosaic of condensed bioclastic facies, and regressive (highstand) tracts are present but partially truncated by the next sequence boundary; smaller-scale (fourth-order) cyclic units could not be resolved. Together, these sequences constitute the transgressive and early highstand tracts of a larger (second-order Miocene) composite sequence. The present paper documents stratigraphic relations higher in the Calvert Cliffs succession, including the upper Miocene St. Marys Formation, which represents late highstand marine deposits of the Miocene second-order sequence, and younger Neogene fluvial and tidal-inlet deposits representing incised-valley deposits of the succeeding second-order cycle. The St. Marys Formation consists of a series of tabular units 2--5 m thick, each with an exclusively transgressive array of facies and bounded by stranding surfaces of abrupt shallowing. These units, which are opposite to the flooding-surface-bounded regressive facies arrays of model parasequences, are best characterized as shaved sequences in which only the transgressive tract survives, and are stacked into larger transgressive, highstand, and forced-regression sets.

Seismic sequence stratigraphy and platform to basin reservoir structuring of Lower Cretaceous deposits in the Sidi Aïch-Majoura region (Central Tunisia)

Science.gov (United States)

Azaïez, Hajer; Bédir, Mourad; Tanfous, Dorra; Soussi, Mohamed

2007-05-01

In central Tunisia, Lower Cretaceous deposits represent carbonate and sandstone reservoir series that correspond to proven oil fields. The main problems for hydrocarbon exploration of these levels are their basin tectonic configuration and their sequence distribution in addition to the source rock availability. The Central Atlas of Tunisia is characterized by deep seated faults directed northeast-southwest, northwest-southeast and north-south. These faults limit inherited tectonic blocks and show intruded Triassic salt domes. Lower Cretaceous series outcropping in the region along the anticline flanks present platform deposits. The seismic interpretation has followed the Exxon methodologies in the 26th A.A.P.G. Memoir. The defined Lower Cretaceous seismic units were calibrated with petroleum well data and tied to stratigraphic sequences established by outcrop studies. This allows the subsurface identification of subsiding zones and thus sequence deposit distribution. Seismic mapping of these units boundary shows a structuring from a platform to basin blocks zones and helps to understand the hydrocarbon reservoir systems-tract and horizon distribution around these domains.

Cluster based on sequence comparison of homologous proteins of 95 organism species - Gclust Server | LSDB Archive [Life Science Database Archive metadata

Lifescience Database Archive (English)

Full Text Available List Contact us Gclust Server Cluster based on sequence comparison of homologous proteins of 95 organism spe...cies Data detail Data name Cluster based on sequence comparison of homologous proteins of 95 organism specie...istory of This Database Site Policy | Contact Us Cluster based on sequence compariso

Sequence-based classification using discriminatory motif feature selection.

Directory of Open Access Journals (Sweden)

Hao Xiong

Full Text Available Most existing methods for sequence-based classification use exhaustive feature generation, employing, for example, all k-mer patterns. The motivation behind such (enumerative approaches is to minimize the potential for overlooking important features. However, there are shortcomings to this strategy. First, practical constraints limit the scope of exhaustive feature generation to patterns of length ≤ k, such that potentially important, longer (> k predictors are not considered. Second, features so generated exhibit strong dependencies, which can complicate understanding of derived classification rules. Third, and most importantly, numerous irrelevant features are created. These concerns can compromise prediction and interpretation. While remedies have been proposed, they tend to be problem-specific and not broadly applicable. Here, we develop a generally applicable methodology, and an attendant software pipeline, that is predicated on discriminatory motif finding. In addition to the traditional training and validation partitions, our framework entails a third level of data partitioning, a discovery partition. A discriminatory motif finder is used on sequences and associated class labels in the discovery partition to yield a (small set of features. These features are then used as inputs to a classifier in the training partition. Finally, performance assessment occurs on the validation partition. Important attributes of our approach are its modularity (any discriminatory motif finder and any classifier can be deployed and its universality (all data, including sequences that are unaligned and/or of unequal length, can be accommodated. We illustrate our approach on two nucleosome occupancy datasets and a protein solubility dataset, previously analyzed using enumerative feature generation. Our method achieves excellent performance results, with and without optimization of classifier tuning parameters. A Python pipeline implementing the approach is

MendeLIMS: a web-based laboratory information management system for clinical genome sequencing.

Science.gov (United States)

Grimes, Susan M; Ji, Hanlee P

2014-08-27

Large clinical genomics studies using next generation DNA sequencing require the ability to select and track samples from a large population of patients through many experimental steps. With the number of clinical genome sequencing studies increasing, it is critical to maintain adequate laboratory information management systems to manage the thousands of patient samples that are subject to this type of genetic analysis. To meet the needs of clinical population studies using genome sequencing, we developed a web-based laboratory information management system (LIMS) with a flexible configuration that is adaptable to continuously evolving experimental protocols of next generation DNA sequencing technologies. Our system is referred to as MendeLIMS, is easily implemented with open source tools and is also highly configurable and extensible. MendeLIMS has been invaluable in the management of our clinical genome sequencing studies. We maintain a publicly available demonstration version of the application for evaluation purposes at http://mendelims.stanford.edu. MendeLIMS is programmed in Ruby on Rails (RoR) and accesses data stored in SQL-compliant relational databases. Software is freely available for non-commercial use at http://dna-discovery.stanford.edu/software/mendelims/.

Dog Y chromosomal DNA sequence: identification, sequencing and SNP discovery

Directory of Open Access Journals (Sweden)

Kirkness Ewen

2006-10-01

Full Text Available Abstract Background Population genetic studies of dogs have so far mainly been based on analysis of mitochondrial DNA, describing only the history of female dogs. To get a picture of the male history, as well as a second independent marker, there is a need for studies of biallelic Y-chromosome polymorphisms. However, there are no biallelic polymorphisms reported, and only 3200 bp of non-repetitive dog Y-chromosome sequence deposited in GenBank, necessitating the identification of dog Y chromosome sequence and the search for polymorphisms therein. The genome has been only partially sequenced for one male dog, disallowing mapping of the sequence into specific chromosomes. However, by comparing the male genome sequence to the complete female dog genome sequence, candidate Y-chromosome sequence may be identified by exclusion. Results The male dog genome sequence was analysed by Blast search against the human genome to identify sequences with a best match to the human Y chromosome and to the female dog genome to identify those absent in the female genome. Candidate sequences were then tested for male specificity by PCR of five male and five female dogs. 32 sequences from the male genome, with a total length of 24 kbp, were identified as male specific, based on a match to the human Y chromosome, absence in the female dog genome and male specific PCR results. 14437 bp were then sequenced for 10 male dogs originating from Europe, Southwest Asia, Siberia, East Asia, Africa and America. Nine haplotypes were found, which were defined by 14 substitutions. The genetic distance between the haplotypes indicates that they originate from at least five wolf haplotypes. There was no obvious trend in the geographic distribution of the haplotypes. Conclusion We have identified 24159 bp of dog Y-chromosome sequence to be used for population genetic studies. We sequenced 14437 bp in a worldwide collection of dogs, identifying 14 SNPs for future SNP analyses, and

The predictable nature of the Paleozoic sedimentary sequence beneath the Bruce nuclear site in Southern Ontario, Canada

International Nuclear Information System (INIS)

Parmenter, Andrew; Jensen, Mark; Crowe, Richard

2012-01-01

hydrocarbon occurrences within the sedimentary sequence underlying the Bruce nuclear site. This information, coupled with in-situ geophysical and hydraulic borehole testing, characterization of groundwater and matrix pore fluids and laboratory based petrophysical analyses, provides a unique opportunity to describe the sub-surface geologic conditions relevant to DGR implementation and safety. Core logging revealed that the stratigraphic sequence comprises 34 distinct bedrock formations/members/units, consistent with the known regional stratigraphic framework. These sedimentary formations dip 0.6 deg. (∼10 m/km) to the southwest with highly uniform thicknesses both at the site- and regional-scale, particularly the Ordovician formations, which vary on the order of metres. The occurrence of steeply-dipping faults originating within the underlying crystalline basement is not evident through surface outcrop fracture mapping, micro-seismic (M ≥ 1) monitoring, or intersection of hydrothermally dolomitized hydrocarbon reservoir systems. Potential fault structures, interpreted from the 2-D seismic survey, were drilled and cored by angled boreholes, which found no evidence for their existence. Formation-specific continuity is evidenced by the lateral traceability of chronostratigraphic marker beds, as well as, litho-facies and their vertical transitions, at decimetre scale through the sedimentary sequence. The correlation of hydraulic conductivities, porosities and diffusion coefficients within these near-horizontal lithostratigraphic units, regardless of which individual borehole dataset is examined, is a significant factor influencing confidence in sub-surface exploration. Effective horizontal hydraulic conductivities estimated by in-situ hydraulic testing yields uniformly low values (≤10 -13 m/s) for the host Cobourg Formation and enclosing rock mass. In addition, there are evident trends, for example, between formation sheet silicate content (shale 50%; carbonate -13 and 10

Stratigraphic units overlying the Zambales Ophiolite Complex (ZOC) in Luzon, (Philippines): Tectonostratigraphic significance and regional implications

Science.gov (United States)

Queaño, Karlo L.; Dimalanta, Carla B.; Yumul, Graciano P.; Marquez, Edanjarlo J.; Faustino-Eslava, Decibel V.; Suzuki, Shigeyuki; Ishida, Keisuke

2017-07-01

The Zambales Ophiolite Complex (ZOC) on the island of Luzon, Philippines is one of the most well-studied crust-mantle sequences in the region. Several massifs comprise the ZOC, one of which is the Coto Block overlain by clastic sedimentary units previously dated as Eocene. Geochronologic studies from diabase, granodiorites and other late-stage magmatic products similarly yielded the same age. Succeeding tectonic models have therefore all been grounded on the assumption that the entire ZOC is Eocene. Recent investigations, however, revealed the presence of chert blocks within the Early to Middle Miocene clastic formation overlying the Acoje Block in the northern part of the ophiolite complex. Radiolarians extracted from the cherts yielded a stratigraphic range that suggests a Late Jurassic to Early Cretaceous age. The recognition of a much older age than previously reported of the ZOC warrants a re-examination of its actual distribution and genesis. Correlating with other similarly-aged ophiolites, we suggest defining a western Mesozoic ophiolite belt, largely extending from the west-central portion of the archipelago to the northeastern tip of Luzon island. Tentatively, we attribute the Mesozoic ophiolitic and associated rocks in western Luzon to an arc-continent collision involving the Philippine Mobile Belt and the Palawan Microcontinental Block. In addition, differences in the clastic compositions of the Cenozoic sedimentary formations provide material not only for deciphering the ZOC's unroofing history but also for constraining the timing of province linkage. The intermittent appearance of lithic fragments and detrital minerals from the ophiolite in the units of the Middle Miocene Candelaria Limestone and the Late Miocene to Early Pliocene Sta. Cruz Formation indicates significant but geographically variable contributions from the ophiolite complex. In the northern Zambales Range, the Sta. Cruz Formation caps the Coto Block and the Acoje Block of the ZOC

Quartz Ti-center in ESR dating of Xigeda formation in Sichuanand contrast with magnetic stratigraphic profiles

International Nuclear Information System (INIS)

Wang Ping; Li Jianping; Liu Chunru; Han Fei; Gao Lu; Wang Jiancun

2011-01-01

Xigeda formation is a famous fluvial-lacustrine sedimentation formed in late cenozoic in southwest China, distributed in the valley of Dadu River, Anning River, Chin-sha River etc. The age of Xigeda formation,ranges between 4.18 and 1.78 Ma BP, depending on the magnetic stratigraphy research of the stratigraphic section. Quartz Ti-center in ESR dating of sand samples from several typical sections of Xigeda formation in Sichuan shows that they are sediments in mid-pleistocene. Comparing the ESR ages and mainly normal polarity, Xigeda formation can be confirmed in Brunhes epoch according to magnetic stratigraphy. (authors)

Final Technical Report on the Genome Sequence DataBase (GSDB): DE-FG03 95 ER 62062 September 1997-September 1999; FINAL

International Nuclear Information System (INIS)

Harger, Carol A.

1999-01-01

Since September 1997 NCGR has produced two web-based tools for researchers to use to access and analyze data in the Genome Sequence DataBase (GSDB). These tools are: Sequence Viewer, a nucleotide sequence and annotation visualization tool, and MAR-Finder, a tool that predicts, base upon statistical inferences, the location of matrix attachment regions (MARS) within a nucleotide sequence.[The annual report for June 1996 to August 1997 is included as an attachment to this final report.

The paleozoic of Amazonas basin south edge: Tapajos river, Para state; O paleozoico da borda sul da bacia do Amazonas: rio Tapajos, estado do Para

Energy Technology Data Exchange (ETDEWEB)

Matsuda, Nilo Siguehiko [Petrobras E e P, Rio de Janeiro, RJ (Brazil). Exploracao. Estratigrafia e Sedimentologia Geologia Aplicada a Exploracao], E-mail: nilo@petrobras.com.br; Winter, Wilson Rubem [Petrobras, Campoas dos Goytacases, RJ (Brazil). Exploracao. Sedimentologia e Estratigrafia], E-mail: winter@petrobras.com.br; Wanderley Filho, Joaquim Ribeiro; Cacela, Alessandra Suzely Moda [Petrobras, Manaus, AM (Brazil). Exploracao. Unidade de Operacoes de Exploracao e Producao da Amazonia], Emails: jwand@petrobras.com.br, alessandra.suzely@petrobras.com.br

2009-11-15

The intracratonic Amazonas Basin covers an area close to 500.000km{sup 2} shared between the Amazonas and Para states. The phanerozoic stratigraphic framework is up to 6.000m thick and may be subdivided into two, first order depositional sequences: the Paleozoic sequence, intruded by diabase dikes and sills and the Mesozoic-Cenozoic sequence. Analyzing the stratigraphic framework, the great tectonic influence on the basin development can be appreciated. The mainly NW-SE structural directions of the basement, which mark the boundaries of the geochronological provinces of the Amazonas, are clearly identified along the Tapajos River. The Paleozoic sequence outcrops on the southern border of the Amazonas Basin embraces potential source rocks, reservoirs and seal rocks. They can be subdivided in three, second order sequences, limited by regional unconformities, as: the Ordovician/Devonian, which corresponds to the Pitinga lithostratigraphic formation; the Devonian-Tournaisian, which corresponds to the Maecuru, Erere, Barreirinha and Curiri formations and, the Pensylvanian-Permian that are represented by the Monte Alegre and Itaituba formations. This field trip guide presents these classic lithostratigraphic outcrop units, together with a brief sedimentological description and an analysis of their positioning related to sequence stratigraphical concepts. (author)

CloudAligner: A fast and full-featured MapReduce based tool for sequence mapping

Directory of Open Access Journals (Sweden)

Shi Weisong

2011-06-01

Full Text Available Abstract Background Research in genetics has developed rapidly recently due to the aid of next generation sequencing (NGS. However, massively-parallel NGS produces enormous amounts of data, which leads to storage, compatibility, scalability, and performance issues. The Cloud Computing and MapReduce framework, which utilizes hundreds or thousands of shared computers to map sequencing reads quickly and efficiently to reference genome sequences, appears to be a very promising solution for these issues. Consequently, it has been adopted by many organizations recently, and the initial results are very promising. However, since these are only initial steps toward this trend, the developed software does not provide adequate primary functions like bisulfite, pair-end mapping, etc., in on-site software such as RMAP or BS Seeker. In addition, existing MapReduce-based applications were not designed to process the long reads produced by the most recent second-generation and third-generation NGS instruments and, therefore, are inefficient. Last, it is difficult for a majority of biologists untrained in programming skills to use these tools because most were developed on Linux with a command line interface. Results To urge the trend of using Cloud technologies in genomics and prepare for advances in second- and third-generation DNA sequencing, we have built a Hadoop MapReduce-based application, CloudAligner, which achieves higher performance, covers most primary features, is more accurate, and has a user-friendly interface. It was also designed to be able to deal with long sequences. The performance gain of CloudAligner over Cloud-based counterparts (35 to 80% mainly comes from the omission of the reduce phase. In comparison to local-based approaches, the performance gain of CloudAligner is from the partition and parallel processing of the huge reference genome as well as the reads. The source code of CloudAligner is available at http

CloudAligner: A fast and full-featured MapReduce based tool for sequence mapping.

Science.gov (United States)

Nguyen, Tung; Shi, Weisong; Ruden, Douglas

2011-06-06

Research in genetics has developed rapidly recently due to the aid of next generation sequencing (NGS). However, massively-parallel NGS produces enormous amounts of data, which leads to storage, compatibility, scalability, and performance issues. The Cloud Computing and MapReduce framework, which utilizes hundreds or thousands of shared computers to map sequencing reads quickly and efficiently to reference genome sequences, appears to be a very promising solution for these issues. Consequently, it has been adopted by many organizations recently, and the initial results are very promising. However, since these are only initial steps toward this trend, the developed software does not provide adequate primary functions like bisulfite, pair-end mapping, etc., in on-site software such as RMAP or BS Seeker. In addition, existing MapReduce-based applications were not designed to process the long reads produced by the most recent second-generation and third-generation NGS instruments and, therefore, are inefficient. Last, it is difficult for a majority of biologists untrained in programming skills to use these tools because most were developed on Linux with a command line interface. To urge the trend of using Cloud technologies in genomics and prepare for advances in second- and third-generation DNA sequencing, we have built a Hadoop MapReduce-based application, CloudAligner, which achieves higher performance, covers most primary features, is more accurate, and has a user-friendly interface. It was also designed to be able to deal with long sequences. The performance gain of CloudAligner over Cloud-based counterparts (35 to 80%) mainly comes from the omission of the reduce phase. In comparison to local-based approaches, the performance gain of CloudAligner is from the partition and parallel processing of the huge reference genome as well as the reads. The source code of CloudAligner is available at http://cloudaligner.sourceforge.net/ and its web version is at http

(Cretaceous-Palaeogene transition) of central India: implications for ...

Indian Academy of Sciences (India)

2009-11-02

Nov 2, 2009 ... Higher up in the stratigraphic sequence, similar forms continued with simultaneous appearance of new taxa including Scabrastephanocolpites spp. At still higher stratigraphic levels, abundance of fungi especially the mycorrhizal fungi, concurrent with sharp decline in pollen/spore recovery was observed.

Noncoding sequence classification based on wavelet transform analysis: part I

Science.gov (United States)

Paredes, O.; Strojnik, M.; Romo-Vázquez, R.; Vélez Pérez, H.; Ranta, R.; Garcia-Torales, G.; Scholl, M. K.; Morales, J. A.

2017-09-01

DNA sequences in human genome can be divided into the coding and noncoding ones. Coding sequences are those that are read during the transcription. The identification of coding sequences has been widely reported in literature due to its much-studied periodicity. Noncoding sequences represent the majority of the human genome. They play an important role in gene regulation and differentiation among the cells. However, noncoding sequences do not exhibit periodicities that correlate to their functions. The ENCODE (Encyclopedia of DNA elements) and Epigenomic Roadmap Project projects have cataloged the human noncoding sequences into specific functions. We study characteristics of noncoding sequences with wavelet analysis of genomic signals.

The high-resolution stratigraphic architecture and evolution of the Burdigalian carbonate-silici-clastic sedimentary systems on the Mut Basin, Turkey

Energy Technology Data Exchange (ETDEWEB)

Bassant, Ph

1999-06-01

The subject of this doctorate study are the Lower Miocene (Burdigalian) carbonate systems in the Mut basin, in south central Turkey. This area is chosen because it presents extraordinary large (seismic) scale 3D outcrops showing depositional geometries. In addition, these carbonates are considered as good outcrop analogues for time equivalent carbonate buildups in the Far East, that are oil and gas bearing. The carbonates were deposited in a complex relict topography, following a tectonically active phase in the Oligocene. During the Burdigalian transgression shallow platform carbonates were deposited in a variety of settings, locally accompanied by some silici-clastic input. Observations on the strata geometries and the facies were combined into a high resolution sequence stratigraphic framework controlled by bio-stratigraphy. With the help of relative sea level curves constructed for the three studied sites, a basin-wide correlation scheme is proposed. This chronostratigraphic framework permits the recognition of condensation and omission surfaces in the basinal and platform settings, to identify basin-wide variations in sedimentation pattern, and to evaluate the relative influence of tectonism, eustatism and the environment. The exceptional quality of the outcrops with its variety of environments, and its location at the Tethys margin, make this a good candidate for a reference model for Burdigalian reef and platform architectures. Examples of a quantitative approach of the geometries of potential carbonate reservoir bodies are given in the annex. The data-files are incorporated in the carbonate reservoir body database CARABAS. (author)

Next-generation Sequencing-based genomic profiling: Fostering innovation in cancer care?

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Gustavo S. Fernandes

Full Text Available OBJECTIVES: With the development of next-generation sequencing (NGS technologies, DNA sequencing has been increasingly utilized in clinical practice. Our goal was to investigate the impact of genomic evaluation on treatment decisions for heavily pretreated patients with metastatic cancer. METHODS: We analyzed metastatic cancer patients from a single institution whose cancers had progressed after all available standard-of-care therapies and whose tumors underwent next-generation sequencing analysis. We determined the percentage of patients who received any therapy directed by the test, and its efficacy. RESULTS: From July 2013 to December 2015, 185 consecutive patients were tested using a commercially available next-generation sequencing-based test, and 157 patients were eligible. Sixty-six patients (42.0% were female, and 91 (58.0% were male. The mean age at diagnosis was 52.2 years, and the mean number of pre-test lines of systemic treatment was 2.7. One hundred and seventy-seven patients (95.6% had at least one identified gene alteration. Twenty-four patients (15.2% underwent systemic treatment directed by the test result. Of these, one patient had a complete response, four (16.7% had partial responses, two (8.3% had stable disease, and 17 (70.8% had disease progression as the best result. The median progression-free survival time with matched therapy was 1.6 months, and the median overall survival was 10 months. CONCLUSION: We identified a high prevalence of gene alterations using an next-generation sequencing test. Although some benefit was associated with the matched therapy, most of the patients had disease progression as the best response, indicating the limited biological potential and unclear clinical relevance of this practice.

Combining sequence-based prediction methods and circular dichroism and infrared spectroscopic data to improve protein secondary structure determinations

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Lees Jonathan G

2008-01-01

Full Text Available Abstract Background A number of sequence-based methods exist for protein secondary structure prediction. Protein secondary structures can also be determined experimentally from circular dichroism, and infrared spectroscopic data using empirical analysis methods. It has been proposed that comparable accuracy can be obtained from sequence-based predictions as from these biophysical measurements. Here we have examined the secondary structure determination accuracies of sequence prediction methods with the empirically determined values from the spectroscopic data on datasets of proteins for which both crystal structures and spectroscopic data are available. Results In this study we show that the sequence prediction methods have accuracies nearly comparable to those of spectroscopic methods. However, we also demonstrate that combining the spectroscopic and sequences techniques produces significant overall improvements in secondary structure determinations. In addition, combining the extra information content available from synchrotron radiation circular dichroism data with sequence methods also shows improvements. Conclusion Combining sequence prediction with experimentally determined spectroscopic methods for protein secondary structure content significantly enhances the accuracy of the overall results obtained.

Context based computational analysis and characterization of ARS consensus sequences (ACS of Saccharomyces cerevisiae genome

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Vinod Kumar Singh

2016-09-01

Full Text Available Genome-wide experimental studies in Saccharomyces cerevisiae reveal that autonomous replicating sequence (ARS requires an essential consensus sequence (ACS for replication activity. Computational studies identified thousands of ACS like patterns in the genome. However, only a few hundreds of these sites act as replicating sites and the rest are considered as dormant or evolving sites. In a bid to understand the sequence makeup of replication sites, a content and context-based analysis was performed on a set of replicating ACS sequences that binds to origin-recognition complex (ORC denoted as ORC-ACS and non-replicating ACS sequences (nrACS, that are not bound by ORC. In this study, DNA properties such as base composition, correlation, sequence dependent thermodynamic and DNA structural profiles, and their positions have been considered for characterizing ORC-ACS and nrACS. Analysis reveals that ORC-ACS depict marked differences in nucleotide composition and context features in its vicinity compared to nrACS. Interestingly, an A-rich motif was also discovered in ORC-ACS sequences within its nucleosome-free region. Profound changes in the conformational features, such as DNA helical twist, inclination angle and stacking energy between ORC-ACS and nrACS were observed. Distribution of ACS motifs in the non-coding segments points to the locations of ORC-ACS which are found far away from the adjacent gene start position compared to nrACS thereby enabling an accessible environment for ORC-proteins. Our attempt is novel in considering the contextual view of ACS and its flanking region along with nucleosome positioning in the S. cerevisiae genome and may be useful for any computational prediction scheme.

A next generation semiconductor based sequencing approach for the identification of meat species in DNA mixtures.

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Francesca Bertolini

Full Text Available The identification of the species of origin of meat and meat products is an important issue to prevent and detect frauds that might have economic, ethical and health implications. In this paper we evaluated the potential of the next generation semiconductor based sequencing technology (Ion Torrent Personal Genome Machine for the identification of DNA from meat species (pig, horse, cattle, sheep, rabbit, chicken, turkey, pheasant, duck, goose and pigeon as well as from human and rat in DNA mixtures through the sequencing of PCR products obtained from different couples of universal primers that amplify 12S and 16S rRNA mitochondrial DNA genes. Six libraries were produced including PCR products obtained separately from 13 species or from DNA mixtures containing DNA from all species or only avian or only mammalian species at equimolar concentration or at 1:10 or 1:50 ratios for pig and horse DNA. Sequencing obtained a total of 33,294,511 called nucleotides of which 29,109,688 with Q20 (87.43% in a total of 215,944 reads. Different alignment algorithms were used to assign the species based on sequence data. Error rate calculated after confirmation of the obtained sequences by Sanger sequencing ranged from 0.0003 to 0.02 for the different species. Correlation about the number of reads per species between different libraries was high for mammalian species (0.97 and lower for avian species (0.70. PCR competition limited the efficiency of amplification and sequencing for avian species for some primer pairs. Detection of low level of pig and horse DNA was possible with reads obtained from different primer pairs. The sequencing of the products obtained from different universal PCR primers could be a useful strategy to overcome potential problems of amplification. Based on these results, the Ion Torrent technology can be applied for the identification of meat species in DNA mixtures.

Sequence-Based Introgression Mapping Identifies Candidate White Mold Tolerance Genes in Common Bean

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Sujan Mamidi

2016-07-01

Full Text Available White mold, caused by the necrotrophic fungus (Lib. de Bary, is a major disease of common bean ( L.. WM7.1 and WM8.3 are two quantitative trait loci (QTL with major effects on tolerance to the pathogen. Advanced backcross populations segregating individually for either of the two QTL, and a recombinant inbred (RI population segregating for both QTL were used to fine map and confirm the genetic location of the QTL. The QTL intervals were physically mapped using the reference common bean genome sequence, and the physical intervals for each QTL were further confirmed by sequence-based introgression mapping. Using whole-genome sequence data from susceptible and tolerant DNA pools, introgressed regions were identified as those with significantly higher numbers of single-nucleotide polymorphisms (SNPs relative to the whole genome. By combining the QTL and SNP data, WM7.1 was located to a 660-kb region that contained 41 gene models on the proximal end of chromosome Pv07, while the WM8.3 introgression was narrowed to a 1.36-Mb region containing 70 gene models. The most polymorphic candidate gene in the WM7.1 region encodes a BEACH-domain protein associated with apoptosis. Within the WM8.3 interval, a receptor-like protein with the potential to recognize pathogen effectors was the most polymorphic gene. The use of gene and sequence-based mapping identified two candidate genes whose putative functions are consistent with the current model of pathogenicity.

Carnian bauxite horizon on the Kopitov grič near Borovnica (Slovenia – is there a »forgotten« stratigraphic gap in its footwall?

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Bogomir Celarc

2008-12-01

Full Text Available Beds underlying the Carnian bauxite on the Kopitov gri~ (Slovenia are by the author’s opinion not Carnian (Cordevolian, but Ladinian age. The considerable stratigraphical gap is presented between Carnian clastic rocks and underlying limestones and dolomites. Bauxite is result of the weathering during the emersion.

Quality Control of the Traditional Patent Medicine Yimu Wan Based on SMRT Sequencing and DNA Barcoding

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Jia, Jing; Xu, Zhichao; Xin, Tianyi; Shi, Linchun; Song, Jingyuan

2017-01-01

Substandard traditional patent medicines may lead to global safety-related issues. Protecting consumers from the health risks associated with the integrity and authenticity of herbal preparations is of great concern. Of particular concern is quality control for traditional patent medicines. Here, we establish an effective approach for verifying the biological composition of traditional patent medicines based on single-molecule real-time (SMRT) sequencing and DNA barcoding. Yimu Wan (YMW), a classical herbal prescription recorded in the Chinese Pharmacopoeia, was chosen to test the method. Two reference YMW samples were used to establish a standard method for analysis, which was then applied to three different batches of commercial YMW samples. A total of 3703 and 4810 circular-consensus sequencing (CCS) reads from two reference and three commercial YMW samples were mapped to the ITS2 and psbA-trnH regions, respectively. Moreover, comparison of intraspecific genetic distances based on SMRT sequencing data with reference data from Sanger sequencing revealed an ITS2 and psbA-trnH intergenic spacer that exhibited high intraspecific divergence, with the sites of variation showing significant differences within species. Using the CCS strategy for SMRT sequencing analysis was adequate to guarantee the accuracy of identification. This study demonstrates the application of SMRT sequencing to detect the biological ingredients of herbal preparations. SMRT sequencing provides an affordable way to monitor the legality and safety of traditional patent medicines. PMID:28620408

Detection and quantification of Plasmodium falciparum in blood samples using quantitative nucleic acid sequence-based amplification

NARCIS (Netherlands)

Schoone, G. J.; Oskam, L.; Kroon, N. C.; Schallig, H. D.; Omar, S. A.

2000-01-01

A quantitative nucleic acid sequence-based amplification (QT-NASBA) assay for the detection of Plasmodium parasites has been developed. Primers and probes were selected on the basis of the sequence of the small-subunit rRNA gene. Quantification was achieved by coamplification of the RNA in the

New SHRIMP zircon results from Broken Hill: towards robust stratigraphic and event timing

International Nuclear Information System (INIS)

Page, R.W.; Stevens, B.P.J.

1999-01-01

Full text: Zircon U-Pb SHRIMP geochronology is a powerful means of elucidating geological ages, providing that it is integrated with unequivocal field constraints, and providing that the fundamental assumptions which are behind any isotopic dating methods are geologically validated. In an attempt to better quantify the timing of Broken Hill's complex history and to reduce some current uncertainties, we report initial results from a new U-Pb SHRIMP investigation. This program was planned within the background of our own disparate stratigraphic and structural approaches to Broken Hill geology, and with objectives to (a) benchmark our new age results with those of previous workers as well as our own previous work in the Broken Hill Group, (b) evaluate and test the evidence for reported Archaean basement terrain, (c) date stratigraphic units in the upper parts of the Willyama Supergroup, (d) better constrain the timing of deformational events. Our U-Pb SHRIMP work on zircons from layered paragneisses in the Redan Geophysical Zone near Farmcote was catalysed by Nutman and Ehlers' (1998a) preferred interpretation that these 'strondhjemitic' gneisses represent an original ∼2650 Ma protolith. Our work finds zircon provenance age signatures typical of almost all ca. 1700 Ma metasediments, whether in the Broken Hill Block or other Australian Palaeoproterozoic settings. This therefore suggests that the rocks are not Archaean basement, but are part of a Thackaringa Group package possibly deposited about 1705-1710 Ma ago. New SHRIMP work on the Alma Gneiss provides a magmatic age of 1704±3 Ma, and a minimum stratigraphic age for host Thackaringa Group. This result is within error of our ages for other granitoids (1703±3 Ma, 1704±3 Ma) in the same stratigraphic position near Farmcote. As the Thackaringa Group is no more than 1000-1500 metres thick and includes 1710-1700 Ma detrital zircons, pan of the Alma Gneiss intrusion may well have been shallowly intruded, and akin to

Security problems for a pseudorandom sequence generator based on the Chen chaotic system

Science.gov (United States)

Özkaynak, Fatih; Yavuz, Sırma

2013-09-01

Recently, a novel pseudorandom number generator scheme based on the Chen chaotic system was proposed. In this study, we analyze the security weaknesses of the proposed generator. By applying a brute force attack on a reduced key space, we show that 66% of the generated pseudorandom number sequences can be revealed. Executable C# code is given for the proposed attack. The computational complexity of this attack is O(n), where n is the sequence length. Both mathematical proofs and experimental results are presented to support the proposed attack.

Is sequence awareness mandatory for perceptual sequence learning: An assessment using a pure perceptual sequence learning design.

Science.gov (United States)

Deroost, Natacha; Coomans, Daphné

2018-02-01

We examined the role of sequence awareness in a pure perceptual sequence learning design. Participants had to react to the target's colour that changed according to a perceptual sequence. By varying the mapping of the target's colour onto the response keys, motor responses changed randomly. The effect of sequence awareness on perceptual sequence learning was determined by manipulating the learning instructions (explicit versus implicit) and assessing the amount of sequence awareness after the experiment. In the explicit instruction condition (n = 15), participants were instructed to intentionally search for the colour sequence, whereas in the implicit instruction condition (n = 15), they were left uninformed about the sequenced nature of the task. Sequence awareness after the sequence learning task was tested by means of a questionnaire and the process-dissociation-procedure. The results showed that the instruction manipulation had no effect on the amount of perceptual sequence learning. Based on their report to have actively applied their sequence knowledge during the experiment, participants were subsequently regrouped in a sequence strategy group (n = 14, of which 4 participants from the implicit instruction condition and 10 participants from the explicit instruction condition) and a no-sequence strategy group (n = 16, of which 11 participants from the implicit instruction condition and 5 participants from the explicit instruction condition). Only participants of the sequence strategy group showed reliable perceptual sequence learning and sequence awareness. These results indicate that perceptual sequence learning depends upon the continuous employment of strategic cognitive control processes on sequence knowledge. Sequence awareness is suggested to be a necessary but not sufficient condition for perceptual learning to take place. Copyright © 2018 Elsevier B.V. All rights reserved.

Rapid Multiplex Small DNA Sequencing on the MinION Nanopore Sequencing Platform

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Shan Wei

2018-05-01

Full Text Available Real-time sequencing of short DNA reads has a wide variety of clinical and research applications including screening for mutations, target sequences and aneuploidy. We recently demonstrated that MinION, a nanopore-based DNA sequencing device the size of a USB drive, could be used for short-read DNA sequencing. In this study, an ultra-rapid multiplex library preparation and sequencing method for the MinION is presented and applied to accurately test normal diploid and aneuploidy samples’ genomic DNA in under three hours, including library preparation and sequencing. This novel method shows great promise as a clinical diagnostic test for applications requiring rapid short-read DNA sequencing.

Experimental design-based functional mining and characterization of high-throughput sequencing data in the sequence read archive.

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Takeru Nakazato

Full Text Available High-throughput sequencing technology, also called next-generation sequencing (NGS, has the potential to revolutionize the whole process of genome sequencing, transcriptomics, and epigenetics. Sequencing data is captured in a public primary data archive, the Sequence Read Archive (SRA. As of January 2013, data from more than 14,000 projects have been submitted to SRA, which is double that of the previous year. Researchers can download raw sequence data from SRA website to perform further analyses and to compare with their own data. However, it is extremely difficult to search entries and download raw sequences of interests with SRA because the data structure is complicated, and experimental conditions along with raw sequences are partly described in natural language. Additionally, some sequences are of inconsistent quality because anyone can submit sequencing data to SRA with no quality check. Therefore, as a criterion of data quality, we focused on SRA entries that were cited in journal articles. We extracted SRA IDs and PubMed IDs (PMIDs from SRA and full-text versions of journal articles and retrieved 2748 SRA ID-PMID pairs. We constructed a publication list referring to SRA entries. Since, one of the main themes of -omics analyses is clarification of disease mechanisms, we also characterized SRA entries by disease keywords, according to the Medical Subject Headings (MeSH extracted from articles assigned to each SRA entry. We obtained 989 SRA ID-MeSH disease term pairs, and constructed a disease list referring to SRA data. We previously developed feature profiles of diseases in a system called "Gendoo". We generated hyperlinks between diseases extracted from SRA and the feature profiles of it. The developed project, publication and disease lists resulting from this study are available at our web service, called "DBCLS SRA" (http://sra.dbcls.jp/. This service will improve accessibility to high-quality data from SRA.

Sequence-based prediction of protein protein interaction using a deep-learning algorithm.

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Sun, Tanlin; Zhou, Bo; Lai, Luhua; Pei, Jianfeng

2017-05-25

Protein-protein interactions (PPIs) are critical for many biological processes. It is therefore important to develop accurate high-throughput methods for identifying PPI to better understand protein function, disease occurrence, and therapy design. Though various computational methods for predicting PPI have been developed, their robustness for prediction with external datasets is unknown. Deep-learning algorithms have achieved successful results in diverse areas, but their effectiveness for PPI prediction has not been tested. We used a stacked autoencoder, a type of deep-learning algorithm, to study the sequence-based PPI prediction. The best model achieved an average accuracy of 97.19% with 10-fold cross-validation. The prediction accuracies for various external datasets ranged from 87.99% to 99.21%, which are superior to those achieved with previous methods. To our knowledge, this research is the first to apply a deep-learning algorithm to sequence-based PPI prediction, and the results demonstrate its potential in this field.

Comparison of base composition analysis and Sanger sequencing of mitochondrial DNA for four U.S. population groups.

Science.gov (United States)

Kiesler, Kevin M; Coble, Michael D; Hall, Thomas A; Vallone, Peter M

2014-01-01

A set of 711 samples from four U.S. population groups was analyzed using a novel mass spectrometry based method for mitochondrial DNA (mtDNA) base composition profiling. Comparison of the mass spectrometry results with Sanger sequencing derived data yielded a concordance rate of 99.97%. Length heteroplasmy was identified in 46% of samples and point heteroplasmy was observed in 6.6% of samples in the combined mass spectral and Sanger data set. Using discrimination capacity as a metric, Sanger sequencing of the full control region had the highest discriminatory power, followed by the mass spectrometry base composition method, which was more discriminating than Sanger sequencing of just the hypervariable regions. This trend is in agreement with the number of nucleotides covered by each of the three assays. Published by Elsevier Ireland Ltd.

MetaSeq: privacy preserving meta-analysis of sequencing-based association studies.

Science.gov (United States)

Singh, Angad Pal; Zafer, Samreen; Pe'er, Itsik

2013-01-01

Human genetics recently transitioned from GWAS to studies based on NGS data. For GWAS, small effects dictated large sample sizes, typically made possible through meta-analysis by exchanging summary statistics across consortia. NGS studies groupwise-test for association of multiple potentially-causal alleles along each gene. They are subject to similar power constraints and therefore likely to resort to meta-analysis as well. The problem arises when considering privacy of the genetic information during the data-exchange process. Many scoring schemes for NGS association rely on the frequency of each variant thus requiring the exchange of identity of the sequenced variant. As such variants are often rare, potentially revealing the identity of their carriers and jeopardizing privacy. We have thus developed MetaSeq, a protocol for meta-analysis of genome-wide sequencing data by multiple collaborating parties, scoring association for rare variants pooled per gene across all parties. We tackle the challenge of tallying frequency counts of rare, sequenced alleles, for metaanalysis of sequencing data without disclosing the allele identity and counts, thereby protecting sample identity. This apparent paradoxical exchange of information is achieved through cryptographic means. The key idea is that parties encrypt identity of genes and variants. When they transfer information about frequency counts in cases and controls, the exchanged data does not convey the identity of a mutation and therefore does not expose carrier identity. The exchange relies on a 3rd party, trusted to follow the protocol although not trusted to learn about the raw data. We show applicability of this method to publicly available exome-sequencing data from multiple studies, simulating phenotypic information for powerful meta-analysis. The MetaSeq software is publicly available as open source.

Simultaneous genomic identification and profiling of a single cell using semiconductor-based next generation sequencing

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Manabu Watanabe

2014-09-01

Full Text Available Combining single-cell methods and next-generation sequencing should provide a powerful means to understand single-cell biology and obviate the effects of sample heterogeneity. Here we report a single-cell identification method and seamless cancer gene profiling using semiconductor-based massively parallel sequencing. A549 cells (adenocarcinomic human alveolar basal epithelial cell line were used as a model. Single-cell capture was performed using laser capture microdissection (LCM with an Arcturus® XT system, and a captured single cell and a bulk population of A549 cells (≈106 cells were subjected to whole genome amplification (WGA. For cell identification, a multiplex PCR method (AmpliSeq™ SNP HID panel was used to enrich 136 highly discriminatory SNPs with a genotype concordance probability of 1031–35. For cancer gene profiling, we used mutation profiling that was performed in parallel using a hotspot panel for 50 cancer-related genes. Sequencing was performed using a semiconductor-based bench top sequencer. The distribution of sequence reads for both HID and Cancer panel amplicons was consistent across these samples. For the bulk population of cells, the percentages of sequence covered at coverage of more than 100× were 99.04% for the HID panel and 98.83% for the Cancer panel, while for the single cell percentages of sequence covered at coverage of more than 100× were 55.93% for the HID panel and 65.96% for the Cancer panel. Partial amplification failure or randomly distributed non-amplified regions across samples from single cells during the WGA procedures or random allele drop out probably caused these differences. However, comparative analyses showed that this method successfully discriminated a single A549 cancer cell from a bulk population of A549 cells. Thus, our approach provides a powerful means to overcome tumor sample heterogeneity when searching for somatic mutations.

Histoimmunogenetics Markup Language 1.0: Reporting next generation sequencing-based HLA and KIR genotyping.

Science.gov (United States)

Milius, Robert P; Heuer, Michael; Valiga, Daniel; Doroschak, Kathryn J; Kennedy, Caleb J; Bolon, Yung-Tsi; Schneider, Joel; Pollack, Jane; Kim, Hwa Ran; Cereb, Nezih; Hollenbach, Jill A; Mack, Steven J; Maiers, Martin

2015-12-01

We present an electronic format for exchanging data for HLA and KIR genotyping with extensions for next-generation sequencing (NGS). This format addresses NGS data exchange by refining the Histoimmunogenetics Markup Language (HML) to conform to the proposed Minimum Information for Reporting Immunogenomic NGS Genotyping (MIRING) reporting guidelines (miring.immunogenomics.org). Our refinements of HML include two major additions. First, NGS is supported by new XML structures to capture additional NGS data and metadata required to produce a genotyping result, including analysis-dependent (dynamic) and method-dependent (static) components. A full genotype, consensus sequence, and the surrounding metadata are included directly, while the raw sequence reads and platform documentation are externally referenced. Second, genotype ambiguity is fully represented by integrating Genotype List Strings, which use a hierarchical set of delimiters to represent allele and genotype ambiguity in a complete and accurate fashion. HML also continues to enable the transmission of legacy methods (e.g. site-specific oligonucleotide, sequence-specific priming, and Sequence Based Typing (SBT)), adding features such as allowing multiple group-specific sequencing primers, and fully leveraging techniques that combine multiple methods to obtain a single result, such as SBT integrated with NGS. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

Generalized min-max bound-based MRI pulse sequence design framework for wide-range T1 relaxometry: A case study on the tissue specific imaging sequence.

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Yang Liu

Full Text Available This paper proposes a new design strategy for optimizing MRI pulse sequences for T1 relaxometry. The design strategy optimizes the pulse sequence parameters to minimize the maximum variance of unbiased T1 estimates over a range of T1 values using the Cramér-Rao bound. In contrast to prior sequences optimized for a single nominal T1 value, the optimized sequence using our bound-based strategy achieves improved precision and accuracy for a broad range of T1 estimates within a clinically feasible scan time. The optimization combines the downhill simplex method with a simulated annealing process. To show the effectiveness of the proposed strategy, we optimize the tissue specific imaging (TSI sequence. Preliminary Monte Carlo simulations demonstrate that the optimized TSI sequence yields improved precision and accuracy over the popular driven-equilibrium single-pulse observation of T1 (DESPOT1 approach for normal brain tissues (estimated T1 700-2000 ms at 3.0T. The relative mean estimation error (MSE for T1 estimation is less than 1.7% using the optimized TSI sequence, as opposed to less than 7.0% using DESPOT1 for normal brain tissues. The optimized TSI sequence achieves good stability by keeping the MSE under 7.0% over larger T1 values corresponding to different lesion tissues and the cerebrospinal fluid (up to 5000 ms. The T1 estimation accuracy using the new pulse sequence also shows improvement, which is more pronounced in low SNR scenarios.

Expectation violations in sensorimotor sequences: shifting from LTM-based attentional selection to visual search.

Science.gov (United States)

Foerster, Rebecca M; Schneider, Werner X

2015-03-01

Long-term memory (LTM) delivers important control signals for attentional selection. LTM expectations have an important role in guiding the task-driven sequence of covert attention and gaze shifts, especially in well-practiced multistep sensorimotor actions. What happens when LTM expectations are disconfirmed? Does a sensory-based visual-search mode of attentional selection replace the LTM-based mode? What happens when prior LTM expectations become valid again? We investigated these questions in a computerized version of the number-connection test. Participants clicked on spatially distributed numbered shapes in ascending order while gaze was recorded. Sixty trials were performed with a constant spatial arrangement. In 20 consecutive trials, either numbers, shapes, both, or no features switched position. In 20 reversion trials, participants worked on the original arrangement. Only the sequence-affecting number switches elicited slower clicking, visual search-like scanning, and lower eye-hand synchrony. The effects were neither limited to the exchanged numbers nor to the corresponding actions. Thus, expectation violations in a well-learned sensorimotor sequence cause a regression from LTM-based attentional selection to visual search beyond deviant-related actions and locations. Effects lasted for several trials and reappeared during reversion. © 2015 New York Academy of Sciences.

Radioactive waste isolation in salt: peer review of the Texas Bureau of Economic Geology's report on the Petrographic, Stratigraphic, and Structural Evidence for Dissolution of Upper Permian Bedded Salt, Texas Panhandle

International Nuclear Information System (INIS)

Fenster, D.F.; Anderson, R.Y.; Gonzales, S.; Baker, V.R.; Edgar, D.E.; Harrison, W.

1984-08-01

The following recommendations for improving the Texas Bureau of Economic Geology (TBEG) report entitled Petrographic, Stratigraphic, and Structural Evidence for Dissolution of Upper Permian Bedded Salt, Texas Panhandle have been abstracted from the body of this review report. The TBEG report should be resided to conform to one of the following alternatives: (1) If the report is intended to be a review or summary of previous work, it should contain more raw data, be edited to give equal treatment to all types of data, and include summary tables and additional figures. (2) If the report is intended to be a description and interpretation of petrographic evidence for salt dissolution, supported by collateral stratigraphic and structural evidence, the relevant indirect and direct data should become the focal point of the report. The following recommendations apply to one or both of the options listed above. (1) The text should differentiate more carefully between the data and inferences based on those data. (2) The authors should retain the qualifiers present in cited works. Statements in the report that are based on earlier papers are sometimes stronger than those in the papers themselves. (3) The next revision should present more complete data. (4) The authors should achieve a more balanced presentation of alternative hypotheses and interpretations. They could then discuss the relative merits of the alternative interpretations. (5) More attention should be given to clear exposition

Phylogenetic analysis of Demodex caprae based on mitochondrial 16S rDNA sequence.

Science.gov (United States)

Zhao, Ya-E; Hu, Li; Ma, Jun-Xian

2013-11-01

Demodex caprae infests the hair follicles and sebaceous glands of goats worldwide, which not only seriously impairs goat farming, but also causes a big economic loss. However, there are few reports on the DNA level of D. caprae. To reveal the taxonomic position of D. caprae within the genus Demodex, the present study conducted phylogenetic analysis of D. caprae based on mt16S rDNA sequence data. D. caprae adults and eggs were obtained from a skin nodule of the goat suffering demodicidosis. The mt16S rDNA sequences of individual mite were amplified using specific primers, and then cloned, sequenced, and aligned. The sequence divergence, genetic distance, and transition/transversion rate were computed, and the phylogenetic trees in Demodex were reconstructed. Results revealed the 339-bp partial sequences of six D. caprae isolates were obtained, and the sequence identity was 100% among isolates. The pairwise divergences between D. caprae and Demodex canis or Demodex folliculorum or Demodex brevis were 22.2-24.0%, 24.0-24.9%, and 22.9-23.2%, respectively. The corresponding average genetic distances were 2.840, 2.926, and 2.665, and the average transition/transversion rates were 0.70, 0.55, and 0.54, respectively. The divergences, genetic distances, and transition/transversion rates of D. caprae versus the other three species all reached interspecies level. The five phylogenetic trees all presented that D. caprae clustered with D. brevis first, and then with D. canis, D. folliculorum, and Demodex injai in sequence. In conclusion, D. caprae is an independent species, and it is closer to D. brevis than to D. canis, D. folliculorum, or D. injai.

Improved protection system for phase faults on marine vessels based on ratio between negative sequence and positive sequence of the fault current

DEFF Research Database (Denmark)

Ciontea, Catalin-Iosif; Hong, Qiteng; Booth, Campbell

2018-01-01

algorithm is implemented in a programmable digital relay embedded in a hardware-in-the-loop (HIL) test set-up that emulates a typical maritime feeder using a real-time digital simulator. The HIL set-up allows testing of the new protection method under a wide range of faults and network conditions......This study presents a new method to protect the radial feeders on marine vessels. The proposed protection method is effective against phase–phase (PP) faults and is based on evaluation of the ratio between the negative sequence and positive sequence of the fault currents. It is shown...... that the magnitude of the introduced ratio increases significantly during the PP fault, hence indicating the fault presence in an electric network. Here, the theoretical background of the new method of protection is firstly discussed, based on which the new protection algorithm is described afterwards. The proposed...

Phylogenetic analysis of Fusobacterium prausnitzii based upon the 16S rRNA gene sequence and PCR confirmation.

Science.gov (United States)

Wang, R F; Cao, W W; Cerniglia, C E

1996-01-01

In order to develop a PCR method to detect Fusobacterium prausnitzii in human feces and to clarify the phylogenetic position of this species, its 16S rRNA gene sequence was determined. The sequence described in this paper is different from the 16S rRNA gene sequence is specific for F. prausnitzii, and the results of this assay confirmed that F. prausnitzii is the most common species in human feces. However, a PCR assay based on the original GenBank sequence was negative when it was performed with two strains of F. prausnitzii obtained from the American Type Culture Collection. A phylogenetic tree based on the new 16S rRNA gene sequence was constructed. On this tree F. prausnitzii was not a member of the Fusobacterium group but was closer to some Eubacterium spp. and located between Clostridium "clusters III and IV" (M.D. Collins, P.A. Lawson, A. Willems, J.J. Cordoba, J. Fernandez-Garayzabal, P. Garcia, J. Cai, H. Hippe, and J.A.E. Farrow, Int. J. Syst. Bacteriol. 44:812-826, 1994).

Sedimentary dynamics and high-frequency sequence stratigraphy of the southwestern slope of Great Bahama Bank

Science.gov (United States)

Wunsch, Marco; Betzler, Christian; Eberli, Gregor P.; Lindhorst, Sebastian; Lüdmann, Thomas; Reijmer, John J. G.

2018-01-01

New geophysical data from the leeward slope of Great Bahama Bank show how contour currents shape the slope and induce re-sedimentation processes. Along slope segments with high current control, drift migration and current winnowing at the toe of slope form a deep moat. Here, the slope progradation is inhibited by large channel incisions and the accumulation of large mass transport complexes, triggered by current winnowing. In areas where the slope is bathed by weaker currents, the accumulation of mass transport complexes and channel incision is rather controlled by the position of the sea level. Large slope failures were triggered during the Mid-Pleistocene transition and Mid-Brunhes event, both periods characterized by changes in the cyclicity or the amplitude of sea-level fluctuations. Within the seismic stratigraphic framework of third order sequences, four sequences of higher order were identified in the succession of the upper Pleistocene. These higher order sequences also show clear differences in function of the slope exposure to contour currents. Two stochastic models emphasize the role of the contour currents and slope morphology in the facies distribution in the upper Pleistocene sequences. In areas of high current influence the interplay of erosional and depositional processes form a complex facies pattern with downslope and along strike facies alterations. In zones with lower current influence, major facies alternations occur predominately in downslope direction, and a layer-cake pattern characterizes the along strike direction. Therefore, this study highlights that contour currents are an underestimated driver for the sediment distribution and architecture of carbonate slopes.

Sequence based polymorphic (SBP marker technology for targeted genomic regions: its application in generating a molecular map of the Arabidopsis thaliana genome

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Sahu Binod B

2012-01-01

Full Text Available Abstract Background Molecular markers facilitate both genotype identification, essential for modern animal and plant breeding, and the isolation of genes based on their map positions. Advancements in sequencing technology have made possible the identification of single nucleotide polymorphisms (SNPs for any genomic regions. Here a sequence based polymorphic (SBP marker technology for generating molecular markers for targeted genomic regions in Arabidopsis is described. Results A ~3X genome coverage sequence of the Arabidopsis thaliana ecotype, Niederzenz (Nd-0 was obtained by applying Illumina's sequencing by synthesis (Solexa technology. Comparison of the Nd-0 genome sequence with the assembled Columbia-0 (Col-0 genome sequence identified putative single nucleotide polymorphisms (SNPs throughout the entire genome. Multiple 75 base pair Nd-0 sequence reads containing SNPs and originating from individual genomic DNA molecules were the basis for developing co-dominant SBP markers. SNPs containing Col-0 sequences, supported by transcript sequences or sequences from multiple BAC clones, were compared to the respective Nd-0 sequences to identify possible restriction endonuclease enzyme site variations. Small amplicons, PCR amplified from both ecotypes, were digested with suitable restriction enzymes and resolved on a gel to reveal the sequence based polymorphisms. By applying this technology, 21 SBP markers for the marker poor regions of the Arabidopsis map representing polymorphisms between Col-0 and Nd-0 ecotypes were generated. Conclusions The SBP marker technology described here allowed the development of molecular markers for targeted genomic regions of Arabidopsis. It should facilitate isolation of co-dominant molecular markers for targeted genomic regions of any animal or plant species, whose genomic sequences have been assembled. This technology will particularly facilitate the development of high density molecular marker maps, essential for

Sequence-to-Sequence Prediction of Vehicle Trajectory via LSTM Encoder-Decoder Architecture

OpenAIRE

Park, Seong Hyeon; Kim, ByeongDo; Kang, Chang Mook; Chung, Chung Choo; Choi, Jun Won

2018-01-01

In this paper, we propose a deep learning based vehicle trajectory prediction technique which can generate the future trajectory sequence of surrounding vehicles in real time. We employ the encoder-decoder architecture which analyzes the pattern underlying in the past trajectory using the long short-term memory (LSTM) based encoder and generates the future trajectory sequence using the LSTM based decoder. This structure produces the $K$ most likely trajectory candidates over occupancy grid ma...

A DNA sequence obtained by replacement of the dopamine RNA aptamer bases is not an aptamer.

Science.gov (United States)

Álvarez-Martos, Isabel; Ferapontova, Elena E

2017-08-05

A unique specificity of the aptamer-ligand biorecognition and binding facilitates bioanalysis and biosensor development, contributing to discrimination of structurally related molecules, such as dopamine and other catecholamine neurotransmitters. The aptamer sequence capable of specific binding of dopamine is a 57 nucleotides long RNA sequence reported in 1997 (Biochemistry, 1997, 36, 9726). Later, it was suggested that the DNA homologue of the RNA aptamer retains the specificity of dopamine binding (Biochem. Biophys. Res. Commun., 2009, 388, 732). Here, we show that the DNA sequence obtained by the replacement of the RNA aptamer bases for their DNA analogues is not able of specific biorecognition of dopamine, in contrast to the original RNA aptamer sequence. This DNA sequence binds dopamine and structurally related catecholamine neurotransmitters non-specifically, as any DNA sequence, and, thus, is not an aptamer and cannot be used neither for in vivo nor in situ analysis of dopamine in the presence of structurally related neurotransmitters. Copyright © 2017 Elsevier Inc. All rights reserved.

AlignMiner: a Web-based tool for detection of divergent regions in multiple sequence alignments of conserved sequences

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Claros M Gonzalo

2010-06-01

Full Text Available Abstract Background Multiple sequence alignments are used to study gene or protein function, phylogenetic relations, genome evolution hypotheses and even gene polymorphisms. Virtually without exception, all available tools focus on conserved segments or residues. Small divergent regions, however, are biologically important for specific quantitative polymerase chain reaction, genotyping, molecular markers and preparation of specific antibodies, and yet have received little attention. As a consequence, they must be selected empirically by the researcher. AlignMiner has been developed to fill this gap in bioinformatic analyses. Results AlignMiner is a Web-based application for detection of conserved and divergent regions in alignments of conserved sequences, focusing particularly on divergence. It accepts alignments (protein or nucleic acid obtained using any of a variety of algorithms, which does not appear to have a significant impact on the final results. AlignMiner uses different scoring methods for assessing conserved/divergent regions, Entropy being the method that provides the highest number of regions with the greatest length, and Weighted being the most restrictive. Conserved/divergent regions can be generated either with respect to the consensus sequence or to one master sequence. The resulting data are presented in a graphical interface developed in AJAX, which provides remarkable user interaction capabilities. Users do not need to wait until execution is complete and can.even inspect their results on a different computer. Data can be downloaded onto a user disk, in standard formats. In silico and experimental proof-of-concept cases have shown that AlignMiner can be successfully used to designing specific polymerase chain reaction primers as well as potential epitopes for antibodies. Primer design is assisted by a module that deploys several oligonucleotide parameters for designing primers "on the fly". Conclusions AlignMiner can be used